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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Plant Sci.</journal-id>
<journal-title>Frontiers in Plant Science</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Plant Sci.</abbrev-journal-title>
<issn pub-type="epub">1664-462X</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
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<article-meta>
<article-id pub-id-type="doi">10.3389/fpls.2023.1271368</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Plant Science</subject>
<subj-group>
<subject>Review</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>CRISPR-Cas-mediated unfolded protein response control for enhancing plant stress resistance</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Vu</surname>
<given-names>Bich Ngoc</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<xref ref-type="author-notes" rid="fn003">
<sup>&#x2020;</sup>
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<contrib contrib-type="author">
<name>
<surname>Vu</surname>
<given-names>Tien Van</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn003">
<sup>&#x2020;</sup>
</xref>
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<contrib contrib-type="author">
<name>
<surname>Yoo</surname>
<given-names>Jae Yong</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
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<contrib contrib-type="author">
<name>
<surname>Nguyen</surname>
<given-names>Ngan Thi</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
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<contrib contrib-type="author">
<name>
<surname>Ko</surname>
<given-names>Ki Seong</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
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</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Kim</surname>
<given-names>Jae-Yean</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<xref ref-type="aff" rid="aff3">
<sup>3</sup>
</xref>
<xref ref-type="author-notes" rid="fn001">
<sup>*</sup>
</xref>
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</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Lee</surname>
<given-names>Kyun Oh</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<xref ref-type="author-notes" rid="fn001">
<sup>*</sup>
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<aff id="aff1">
<sup>1</sup>
<institution>Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University</institution>, <addr-line>Jinju</addr-line>, <country>Republic of Korea</country>
</aff>
<aff id="aff2">
<sup>2</sup>
<institution>Division of Applied Life Science (BK21 Four), Gyeongsang National University</institution>, <addr-line>Jinju</addr-line>, <country>Republic of Korea</country>
</aff>
<aff id="aff3">
<sup>3</sup>
<institution>Nulla Bio Inc.</institution>, <addr-line>Jinju</addr-line>, <country>Republic of Korea</country>
</aff>
<author-notes>
<fn fn-type="edited-by">
<p>Edited by: Tong Zhang, South China Agricultural University, China</p>
</fn>
<fn fn-type="edited-by">
<p>Reviewed by: Changjun Huang, Yunnan Academy of Tobacco Agricultural Sciences, China; U. M. Aruna Kumara, University of Colombo, Sri Lanka</p>
</fn>
<fn fn-type="corresp" id="fn001">
<p>*Correspondence: Kyun Oh Lee, <email xlink:href="mailto:leeko@gnu.ac.kr">leeko@gnu.ac.kr</email>; Jae-Yean Kim, <email xlink:href="mailto:kimjy@gnu.ac.kr">kimjy@gnu.ac.kr</email>
</p>
</fn>
<fn fn-type="equal" id="fn003">
<p>&#x2020;These authors have contributed equally to this work</p>
</fn>
</author-notes>
<pub-date pub-type="epub">
<day>16</day>
<month>10</month>
<year>2023</year>
</pub-date>
<pub-date pub-type="collection">
<year>2023</year>
</pub-date>
<volume>14</volume>
<elocation-id>1271368</elocation-id>
<history>
<date date-type="received">
<day>02</day>
<month>08</month>
<year>2023</year>
</date>
<date date-type="accepted">
<day>02</day>
<month>10</month>
<year>2023</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#xa9; 2023 Vu, Vu, Yoo, Nguyen, Ko, Kim and Lee</copyright-statement>
<copyright-year>2023</copyright-year>
<copyright-holder>Vu, Vu, Yoo, Nguyen, Ko, Kim and Lee</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/">
<p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</p>
</license>
</permissions>
<abstract>
<p>Plants consistently encounter environmental stresses that negatively affect their growth and development. To mitigate these challenges, plants have developed a range of adaptive strategies, including the unfolded protein response (UPR), which enables them to manage endoplasmic reticulum (ER) stress resulting from various adverse conditions. The CRISPR-Cas system has emerged as a powerful tool for plant biotechnology, with the potential to improve plant tolerance and resistance to biotic and abiotic stresses, as well as enhance crop productivity and quality by targeting specific genes, including those related to the UPR. This review highlights recent advancements in UPR signaling pathways and CRISPR-Cas technology, with a particular focus on the use of CRISPR-Cas in studying plant UPR. We also explore prospective applications of CRISPR-Cas in engineering UPR-related genes for crop improvement. The integration of CRISPR-Cas technology into plant biotechnology holds the promise to revolutionize agriculture by producing crops with enhanced resistance to environmental stresses, increased productivity, and improved quality traits.</p>
</abstract>
<kwd-group>
<kwd>endoplasmic reticulum (ER) stress</kwd>
<kwd>unfolded protein response (UPR)</kwd>
<kwd>genome editing</kwd>
<kwd>CRISPR-Cas</kwd>
<kwd>crop improvement</kwd>
</kwd-group>
<contract-num rid="cn001">2020R1I1A1A01072130, 2020M3A9I4038352, 2020R1A6A1A03044344, 2021R1A5A8029490, 2022R1A2C3010331, 2021R1A2C1013516, 2022R1I1A1A01071947</contract-num>
<contract-num rid="cn002">PJ016236, PJ016867022022</contract-num>
<contract-sponsor id="cn001">National Research Foundation of Korea<named-content content-type="fundref-id">10.13039/501100003725</named-content>
</contract-sponsor>
<contract-sponsor id="cn002">Rural Development Administration<named-content content-type="fundref-id">10.13039/501100003627</named-content>
</contract-sponsor>
<counts>
<fig-count count="3"/>
<table-count count="3"/>
<equation-count count="0"/>
<ref-count count="166"/>
<page-count count="17"/>
<word-count count="8973"/>
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<custom-meta-wrap>
<custom-meta>
<meta-name>section-in-acceptance</meta-name>
<meta-value>Plant Biotechnology</meta-value>
</custom-meta>
</custom-meta-wrap>
</article-meta>
</front>
<body>
<sec id="s1" sec-type="intro">
<title>Introduction</title>
<p>The endoplasmic reticulum (ER) is a crucial organelle responsible for protein folding and modifications in eukaryotic cells (<xref ref-type="bibr" rid="B119">Schuldiner and Schwappach, 2013</xref>). Proper protein folding is essential for the proper function of secretory and membrane proteins, which account for approximately 30% of the total proteome (<xref ref-type="bibr" rid="B145">Wallin and Von Heijne, 1998</xref>; <xref ref-type="bibr" rid="B118">Schubert et&#xa0;al., 2000</xref>). Various post-translational modifications, such as N-linked glycosylation, disulfide bond formation, and chaperone-assisted folding, occur in the ER lumen to ensure proper protein folding (<xref ref-type="bibr" rid="B31">Duwi Fanata et&#xa0;al., 2013</xref>). However, protein folding, occurring within the ER, can be disrupted not only by internal factors, such as genetic mutations and hereditary metabolic defects, but also by external factors, such as biotic and abiotic stresses (<xref ref-type="bibr" rid="B105">Park and Park, 2019</xref>). When proteins fail to fold properly or become misfolded due to these intrinsic or extrinsic factors, their accumulation within the ER leads to an aberrant cellular condition known as ER stress (<xref ref-type="bibr" rid="B47">Howell, 2013</xref>). To address ER stress, eukaryotic cells activate a series of compensatory adaptive mechanisms, collectively called the unfolded protein response (UPR) (<xref ref-type="bibr" rid="B62">Kozutsumi et&#xa0;al., 1988</xref>; <xref ref-type="bibr" rid="B39">Harding et&#xa0;al., 2002</xref>). The UPR activates a process that increases the expression of ER chaperone genes, enhancing the protein folding capacity of the ER, while also inhibiting protein synthesis and promoting ER-associated protein degradation (ERAD) to alleviate the burden of misfolded proteins (<xref ref-type="bibr" rid="B31">Duwi Fanata et&#xa0;al., 2013</xref>). When the UPR is not able to mitigate ER stress, it can lead to apoptosis or cell death, which may contribute to the development of prominent stress-related phenotypes, such as inhibited growth or developmental abnormalities (<xref ref-type="bibr" rid="B46">Hetz, 2012</xref>; <xref ref-type="bibr" rid="B7">Angelos et&#xa0;al., 2017</xref>).</p>
<p>Numerous studies have reported on the evolutionarily conserved UPR mechanism in eukaryotes, from yeast to animals and plants (<xref ref-type="bibr" rid="B14">Chakraborty et&#xa0;al., 2016</xref>; <xref ref-type="bibr" rid="B48">Howell, 2021</xref>). The UPR has been extensively characterized in mammals, where it consists of three ER signaling pathways: activating transcription factor 6 (ATF6), inositol requiring enzyme 1 (IRE1)-mediated splicing activation of X-box binding protein 1 (XBP1) mRNA, and double-stranded RNA-activated protein kinase (PKR)-like endoplasmic reticulum kinase (PERK) (<xref ref-type="bibr" rid="B13">Chakrabarti et&#xa0;al., 2011</xref>). Aberrant UPR has been implicated in a wide range of disease states, including diabetes, immune and inflammatory disorders, and cancers (<xref ref-type="bibr" rid="B89">Marciniak, 2019</xref>). Thus, signaling pathways of the UPR have emerged as a potential therapeutic axis for treating various diseases (<xref ref-type="bibr" rid="B89">Marciniak, 2019</xref>). While UPR mechanisms in mammals have been a subject of extensive research, exploration into the molecular mechanisms of ER stress responses in plants began more recently. Early investigations into plant UPR primarily started in the early 2000s, with a surge of substantial research outputs emerging a decade later (<xref ref-type="bibr" rid="B59">Koizumi et&#xa0;al., 2001</xref>; <xref ref-type="bibr" rid="B100">Noh et&#xa0;al., 2002</xref>; <xref ref-type="bibr" rid="B28">Deng et&#xa0;al., 2011</xref>; <xref ref-type="bibr" rid="B96">Nagashima et&#xa0;al., 2011</xref>; <xref ref-type="bibr" rid="B95">Moreno et&#xa0;al., 2012</xref>). With the advent of omics technologies, the field of plant UPR research is now transitioning into a new era characterized by big data. Two ER stress-transducing pathways have been identified in plants: IRE1a and b, which are functional homologs of IRE1 in mammals, and basic leucine zipper protein 17 and 28 (bZIP17 and bZIP28), which are functional homologs of ATF6 in mammals (<xref ref-type="bibr" rid="B55">Kim et&#xa0;al., 2022a</xref>). These pathways are involved in the UPR and perform similar functions to their counterparts in mammals. However, the existence of the PERK branch in plants, which is present in mammalian cells, is still unknown (<xref ref-type="bibr" rid="B11">Bao and Howell, 2017</xref>).</p>
<p>In sessile plants, the inherent inability to evade unfavorable environmental conditions results in frequent exposure to various abiotic and biotic stresses, such as drought, temperature fluctuations, salinity, herbicidal exposure, and pathogen infection (<xref ref-type="bibr" rid="B105">Park and Park, 2019</xref>). These stresses detrimentally impact crop yields, posing significant challenges to global food security. Furthermore, climate change-induced alterations in pathogen and insect behavior contribute to substantial reductions in crop productivity worldwide (<xref ref-type="bibr" rid="B4">Anderegg et&#xa0;al., 2020</xref>; <xref ref-type="bibr" rid="B40">Hassani et&#xa0;al., 2020</xref>; <xref ref-type="bibr" rid="B137">Van Houtan et&#xa0;al., 2021</xref>; <xref ref-type="bibr" rid="B140">Von Der Gathen et&#xa0;al., 2021</xref>; <xref ref-type="bibr" rid="B160">Zandalinas et&#xa0;al., 2021</xref>). Therefore, it is important to better understand the mechanisms underlying the impacts of these stresses on various crops. This knowledge will facilitate the optimization of tolerance and resistance to both biotic and abiotic stresses, and will ultimately contribute to the optimization of plant growth, development, yield, and quality (<xref ref-type="bibr" rid="B112">Rivero et&#xa0;al., 2022</xref>).</p>
<p>In recent years, CRISPR-Cas-based precise genome editing has emerged as a powerful tool, enabling the study of molecular mechanisms associated with ER stress and crop improvements (<xref ref-type="bibr" rid="B124">Singh et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B136">Um et&#xa0;al., 2021</xref>). CRISPR-Cas9, initially discovered in bacteria, has been engineered for use in various plant species to improve yield, quality, and stress tolerance (<xref ref-type="bibr" rid="B32">El-Mounadi et&#xa0;al., 2020</xref>; <xref ref-type="bibr" rid="B141">Vu et&#xa0;al., 2020a</xref>). There are several prospective strategies in which the CRISPR-Cas-based genome editing technology can be applied to UPR research. For instance, researchers can employ CRISPR-Cas to knockout or knockdown UPR-related genes. By investigating how these engineered plants respond to ER stress and the phenotypes they exhibit, scientists can gain valuable insights into the role of the targeted genes in the UPR pathway (<xref ref-type="bibr" rid="B92">Mishiba et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B82">Liu et&#xa0;al., 2020</xref>). Furthermore, the CRISPR-Cas system holds potential for modifying <italic>cis</italic>-regulatory elements or promoter regions in the genome, which in turn control gene expression, to augment stress resilience and other desirable traits (<xref ref-type="bibr" rid="B74">Lim et&#xa0;al., 2022</xref>). In this review, we also discuss several promising applications and future prospects of employing the CRISPR-Cas-based genome editing technology for strategic modifications of genes associated with ER stress responses, aiming to improve stress tolerance, productivity, and crop quality.</p>
<sec id="s1_1">
<title>UPR in plant adaptation to biotic and abiotic stresses</title>
<p>Plant adaptation to environmental stress is a complex process that involves a range of molecular, physiological, and biochemical responses. In plant stress response research, the majority of investigations have focused on single biotic or abiotic elements; however, the simultaneous presence of both biotic and abiotic stresses can markedly influence plant growth, productivity, and viability (<xref ref-type="bibr" rid="B105">Park and Park, 2019</xref>). To cope with these multiple stresses, plants initiate a range of signaling pathways and regulatory processes to preserve homeostasis and adapt to changing environmental conditions. The UPR is one such mechanism; it is a conserved response found across eukaryotic organisms, including plants, and plays a critical role in cellular adaptation to stress (<xref ref-type="bibr" rid="B14">Chakraborty et&#xa0;al., 2016</xref>). The UPR has emerged as a crucial regulatory mechanism in plant adaptation to combined biotic and abiotic stresses, allowing plants to cope with the challenges posed by their environment.</p>
<p>Under heat stress conditions, protein folding becomes perturbed, and several ER membrane-associated transcription factors relay stress signals to the nucleus, which in turn activates stress-responsive genes (<xref ref-type="bibr" rid="B34">Fragkostefanakis et&#xa0;al., 2016</xref>; <xref ref-type="bibr" rid="B111">Reyes-Impellizzeri and Moreno, 2021</xref>). It has been discovered that in diverse plant species, such as <italic>Arabidopsis thaliana</italic> (Arabidopsis) and <italic>Zea mays</italic> (maize), heat stimulation causes IRE1 to splice <italic>bZIP60</italic> mRNA (<xref ref-type="bibr" rid="B28">Deng et&#xa0;al., 2011</xref>; <xref ref-type="bibr" rid="B65">Li et&#xa0;al., 2012</xref>; <xref ref-type="bibr" rid="B98">Neill et&#xa0;al., 2019</xref>). The expression of active bZIP60 also elevates the transcription of heat shock protein (HSP) genes, suggesting a link between the UPR and the heat shock response mechanism (<xref ref-type="bibr" rid="B70">Li et&#xa0;al., 2020c</xref>). The transcription factor bZIP28 regulates the expression of UPR-related genes in response to heat stress conditions via a proteolytic mechanism, which triggers the translocation of bZIP28 to the nucleus (<xref ref-type="bibr" rid="B51">Iwata et&#xa0;al., 2017</xref>). Drought and salt significantly impact plant development and yield. In response to salt stress, bZIP17 is cleaved by site-1 proteases (S1P) and translocated to the nucleus to activate UPR genes (<xref ref-type="bibr" rid="B84">Liu et&#xa0;al., 2007b</xref>). It has been shown that the transcription factors bZIP60 and bZIP17 orchestrate the expression of the molecular chaperone gene, luminal-binding protein 3 (BiP3), as well as several genes implicated in the response to salt stress conditions (<xref ref-type="bibr" rid="B45">Henriquez-Valencia et&#xa0;al., 2015</xref>). Elevated expression of BiP has been observed to augment drought tolerance in a variety of plant species, such as <italic>Glycine max</italic> (soybean), <italic>Nicotiana tabacum</italic> (tobacco), and Arabidopsis (<xref ref-type="bibr" rid="B23">Coutinho et&#xa0;al., 2019</xref>). Infection by pathogens has been shown to induce ER stress in plants, with the IRE1-bZIP60 signaling pathway playing a crucial role in mounting a defense against the fungal pathogen, <italic>Alternaria alternate</italic> (<xref ref-type="bibr" rid="B155">Xu et&#xa0;al., 2019</xref>). Plants with mutations in <italic>IRE1</italic> and <italic>bZIP60</italic> are more susceptible to bacterial and viral infections (<xref ref-type="bibr" rid="B95">Moreno et&#xa0;al., 2012</xref>). In <italic>Nicotiana benthamiana</italic>, UPR was activated by the Geminivirus satellite-encoded &#x3b2;C1, which induces the nuclear export of NbbZIP60 to evade the plant defense response (<xref ref-type="bibr" rid="B162">Zhang et&#xa0;al., 2023</xref>). Overall, these findings indicate that various biotic and abiotic factors can disrupt protein folding capacity and activate the UPR in plants. As environmental stresses continue to impact global agriculture, the role of the UPR in facilitating plant adaptation to combined biotic and abiotic stresses is becoming a more significant area of research. Investigating the function of the UPR in plants has the potential to enhance crop improvement and sustainable agriculture practices, making the study of UPR activation in response to stress in plants increasingly important for agricultural research.</p>
</sec>
</sec>
<sec id="s2">
<title>UPR pathways in plant cells: mechanisms and regulation</title>
<p>The UPR constitutes a crucial regulatory process in plant cells, which is activated upon the presence of misfolded or unfolded proteins stress (<xref ref-type="bibr" rid="B48">Howell, 2021</xref>). Comprehensive investigations have been conducted to elucidate the UPR pathways in a range of plant species, encompassing maize, <italic>Oryza sativa</italic> (rice), <italic>Solanum lycopersicum</italic> (tomato), soybean, tobacco, and Arabidopsis (<xref ref-type="bibr" rid="B86">Lu et&#xa0;al., 2012</xref>; <xref ref-type="bibr" rid="B25">Czekus et&#xa0;al., 2020</xref>; <xref ref-type="bibr" rid="B106">Pastor-Cantizano et&#xa0;al., 2020</xref>; <xref ref-type="bibr" rid="B26">Czekus et&#xa0;al., 2022</xref>; <xref ref-type="bibr" rid="B156">Yang et&#xa0;al., 2022</xref>). In plants, the UPR is mediated through two distinct signal transduction pathways. The initial pathway, referred to as the IRE1 pathway, is facilitated by IRE1 and involves two isoforms in Arabidopsis, IRE1a and IRE1b (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B59">Koizumi et&#xa0;al., 2001</xref>; <xref ref-type="bibr" rid="B100">Noh et&#xa0;al., 2002</xref>; <xref ref-type="bibr" rid="B95">Moreno et&#xa0;al., 2012</xref>). IRE1a and IRE1b possess homologous cytoplasmic regions characterized by the presence of a kinase domain, but exhibit functional divergence (<xref ref-type="bibr" rid="B100">Noh et&#xa0;al., 2002</xref>). IRE1a is primarily required for biotic stresses, while IRE1b plays a predominant role in abiotic stresses (<xref ref-type="bibr" rid="B28">Deng et&#xa0;al., 2011</xref>; <xref ref-type="bibr" rid="B1">Afrin et&#xa0;al., 2020</xref>). An additional isoform of IRE1, designated as IRE1C, has been identified as unique to plants (<xref ref-type="bibr" rid="B92">Mishiba et&#xa0;al., 2019</xref>). Recent evidence has shown that IRE1 promotes balanced cell expansion by restricting the Target of Rapamycin (TOR) kinase-dependent control of cellular differentiation (<xref ref-type="bibr" rid="B6">Angelos and Brandizzi, 2022</xref>). However, its precise role in the UPR remains to be elucidated. Under ER stress conditions, BiP binds to unfolded proteins, dissociating IRE1, which then undergoes trans-autophosphorylation and dimerization (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1</bold>
</xref>). The endonucleases IRE1a and IRE1b facilitate the removal of a 26-nucleotide intron from <italic>bZIP60</italic> mRNA, resulting in the production of the spliced variant <italic>bZIP60s</italic>, which encodes an active transcription factor (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B28">Deng et&#xa0;al., 2011</xref>; <xref ref-type="bibr" rid="B96">Nagashima et&#xa0;al., 2011</xref>; <xref ref-type="bibr" rid="B65">Li et&#xa0;al., 2012</xref>; <xref ref-type="bibr" rid="B95">Moreno et&#xa0;al., 2012</xref>; <xref ref-type="bibr" rid="B71">Li et&#xa0;al., 2022</xref>). Upon activation, bZIP60s translocates to the nucleus, where it promotes the expression of genes associated with ER stress (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B52">Iwata et&#xa0;al., 2008</xref>; <xref ref-type="bibr" rid="B28">Deng et&#xa0;al., 2011</xref>; <xref ref-type="bibr" rid="B96">Nagashima et&#xa0;al., 2011</xref>; <xref ref-type="bibr" rid="B95">Moreno et&#xa0;al., 2012</xref>; <xref ref-type="bibr" rid="B41">Hayashi et&#xa0;al., 2013</xref>; <xref ref-type="bibr" rid="B129">Sun et&#xa0;al., 2013</xref>; <xref ref-type="bibr" rid="B155">Xu et&#xa0;al., 2019</xref>). Under severe or prolonged ER stress, IRE1 also degrades many mRNAs on the ER membrane encoding secretory pathway proteins through a selective cleavage mechanism referred to as regulated IRE1-dependent decay (RIDD) (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B93">Mishiba et&#xa0;al., 2013</xref>; <xref ref-type="bibr" rid="B42">Hayashi et&#xa0;al., 2016</xref>). The recent findings indicate that AtIRE1 determines cell fate during ER stress by balancing the UPR and the ubiquitin-proteasome system (UPS) via a key pro-death component, phosphatase type 2CA (PP2CA)-interacting finger protein 1 (PIR1). However, the mechanism by which AtIRE1 regulates PIR1 remains unknown (<xref ref-type="bibr" rid="B58">Ko et&#xa0;al., 2023</xref>).</p>
<fig id="f1" position="float">
<label>Figure&#xa0;1</label>
<caption>
<p>The UPR in plants: a signaling network coordinating ER homeostasis and stress adaptation. The UPR is activated by the accumulation of unfolded proteins in the ER due to various factors (top left of figure). BiP binds to unfolded proteins, leading to dissociation of IRE1a and IRE1b. Activated IRE1 then cleaves a specific intron from bZIP60u mRNA, generating bZIP60s mRNA. bZIP60s, a potent transcriptional activator, translocates to the nucleus and binds to UPREs and ERSEs in target gene promoters, inducing the expression of stress-responsive genes. In addition to its role in splicing bZIP60 mRNA, activated IRE1 is also involved in a process called Regulated IRE1-dependent decay (RIDD). Under conditions of chronic stress, IRE1 hyper-activates and cleaves additional mRNAs through RIDD. The bZIP17 and bZIP28 pathway is activated by ER stress in plants. Unfolded proteins bind to BiP, causing bZIP17 and bZIP28 to dissociate from the ER membrane. These transcription factors are transported to the Golgi, where proteolytic cleavage mediated by S1P and S2P enzymes releases their N-terminal domains. The N-terminal domains contain the necessary domains for their function as transcription factors. Upon translocation to the nucleus, they bind to ERSE-1 sequences in target gene promoters, inducing the expression of UPR-associated genes encoding ER chaperones and ERAD proteins involved in protein folding, quality control, and degradation within the ER. GCN2 is a kinase activated by dimerization and autophosphorylation in response to endoplasmic reticulum stress. It phosphorylates eIF2&#x3b1;, leading to widespread inhibition of mRNA translation. However, a specific group of uncapped mRNAs with upstream open reading frames (uORFs), such as TBF1 mRNA, are selectively translated. TBF1, a heat-shock factor-like transcription factor, binds to the <italic>TL1 cis</italic>-element, crucial for inducing BiP2 and CRT3. TBF1 also plays a role in coordinating developmental processes with stress responses, particularly in the growth-to-defense transition. During ER stress, ER chaperones assist in proper protein folding, while ERAD proteins eliminate irreversibly misfolded proteins. ERAD initiation involves OS9 recognizing the N-glycan on a misfolded protein and associating with Sel1L/Hrd3. The Hrd1-Sel1L/Hrd3-OS9 complex, along with UBC32, the E2 enzyme, promotes ubiquitination (Ub) of the misfolded protein for subsequent cytosolic degradation. This process helps restore ER homeostasis by removing unfolded proteins that could disrupt cellular functions.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-14-1271368-g001.tif"/>
</fig>
<p>The second pathway involves membrane-associated bZIP transcription factors bZIP17 and bZIP28, which are functional homologs of mammalian ATF6 (<xref ref-type="bibr" rid="B83">Liu et&#xa0;al., 2007a</xref>; <xref ref-type="bibr" rid="B84">Liu et&#xa0;al., 2007b</xref>). Under normal conditions, bZIP17/28 is retained in the ER due to its binding to the BiP protein (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B83">Liu et&#xa0;al., 2007a</xref>; <xref ref-type="bibr" rid="B127">Srivastava et&#xa0;al., 2013</xref>; <xref ref-type="bibr" rid="B126">Srivastava et&#xa0;al., 2014</xref>; <xref ref-type="bibr" rid="B45">Henriquez-Valencia et&#xa0;al., 2015</xref>). Under ER stress conditions, bZIP17 and bZIP28 dissociate from BiP, become mobilized, and undergo translocation to the Golgi apparatus through coat protein complex II (COPII) vesicle-mediated transport (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B125">Srivastava et&#xa0;al., 2012</xref>). In the Golgi apparatus, they undergo proteolytic processing by two resident site proteases, S1P and S2P, releasing their transcription factor (TF) domains (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B88">Manghwar and Li, 2022</xref>). Subsequently, these TF domains translocate to the nucleus, where they act as transcription factors, enhancing the expression of ER stress-associated genes (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B84">Liu et&#xa0;al., 2007b</xref>; <xref ref-type="bibr" rid="B72">Li et&#xa0;al., 2010</xref>; <xref ref-type="bibr" rid="B81">Liu et&#xa0;al., 2022</xref>). Nonetheless, a recent investigation has demonstrated that the activation of bZIP28 occurs through a sequential process involving S2P and as-yet-unidentified proteases, rather than S1P-mediated cleavage (<xref ref-type="bibr" rid="B130">Sun et&#xa0;al., 2015</xref>; <xref ref-type="bibr" rid="B51">Iwata et&#xa0;al., 2017</xref>). Both bZIP17 and bZIP28 can bind to ER stress response elements (ERSEs) and unfolded protein response elements (UPREs) at the promoter region of UPR-related genes, including BiPs (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B79">Liu and Howell, 2010</xref>; <xref ref-type="bibr" rid="B36">Gao et&#xa0;al., 2022</xref>). Moreover, bZIP28 can interact with Nuclear transcription factor Y (NF-Y) and form a transcriptional complex to upregulate UPR-related genes (<xref ref-type="bibr" rid="B79">Liu and Howell, 2010</xref>). Typically, bZIP17 and bZIP28 exhibit comparable activation patterns in response to ER stress inducers, including chemicals like tunicamycin (TM) or dithiothreitol (DTT), cadmium (Cd) as well as environmental stresses such as heat stress and viral infections (<xref ref-type="bibr" rid="B84">Liu et&#xa0;al., 2007b</xref>; <xref ref-type="bibr" rid="B72">Li et&#xa0;al., 2010</xref>; <xref ref-type="bibr" rid="B36">Gao et&#xa0;al., 2022</xref>; <xref ref-type="bibr" rid="B71">Li et&#xa0;al., 2022</xref>; <xref ref-type="bibr" rid="B27">De Benedictis et&#xa0;al., 2023</xref>). However, they show differences in sensitivity in certain environmental stresses. For instance, under salt stress conditions, bZIP17 elevates the expression of the chaperone BiP3, whereas bZIP28 participates in responses to pathogen infections (<xref ref-type="bibr" rid="B45">Henriquez-Valencia et&#xa0;al., 2015</xref>; <xref ref-type="bibr" rid="B109">Qiang et&#xa0;al., 2021</xref>).</p>
<p>Although the PERK pathway, which is present in mammals, has not been identified in plants, General Control Non-repressible 2 (GCN2) has been identified as an orthologue of the elF2&#x3b1; kinase that responds to both abiotic and biotic stresses (<xref ref-type="bibr" rid="B159">Yu et&#xa0;al., 2022</xref>). Recently, Arabidopsis GCN2 was shown to activate the translation of a heat-shock factor-like transcription factor, TL1-binding transcription factor 1 (TBF1), which contains upstream open reading frames (uORFs) within its 5&#x2019; untranslated region (5&#x2019; UTR) (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B77">Liu et&#xa0;al., 2019</xref>). This process is initiated in response to pathogen invasion, subsequently triggering specific transcriptional reprogramming through the expression of target genes (<xref ref-type="bibr" rid="B64">Lageix et&#xa0;al., 2008</xref>; <xref ref-type="bibr" rid="B104">Pajerowska-Mukhtar et&#xa0;al., 2012</xref>; <xref ref-type="bibr" rid="B77">Liu et&#xa0;al., 2019</xref>).</p>
<sec id="s2_1">
<title>Role in maintaining ER homeostasis and protein quality control</title>
<p>In situations of excessive or prolonged ER stress, where UPR mechanisms cannot restore protein folding, the ERAD system facilitates the clearance of terminally aberrant proteins, thus maintaining ER homeostasis (<xref ref-type="bibr" rid="B139">Vembar and Brodsky, 2008</xref>; <xref ref-type="bibr" rid="B50">Hwang and Qi, 2018</xref>). The ERAD comprises a multistep process, which includes the identification of cargo proteins, retro-translocation of substrates to the cytoplasm through an ER membrane channel, ubiquitination of ER proteins by ubiquitin enzymes, and subsequent degradation of ubiquitinated substrates via the 26S proteasome (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B20">Chen et&#xa0;al., 2020</xref>). The ERAD machinery has been extensively studied in yeast and mammals (<xref ref-type="bibr" rid="B157">Ye et&#xa0;al., 2001</xref>; <xref ref-type="bibr" rid="B116">Sato et&#xa0;al., 2009</xref>; <xref ref-type="bibr" rid="B9">Avci and Lemberg, 2015</xref>; <xref ref-type="bibr" rid="B38">Habeck et&#xa0;al., 2015</xref>; <xref ref-type="bibr" rid="B117">Schoebel et&#xa0;al., 2017</xref>). In recent years, several ERAD components have been identified and characterized in plants (<xref ref-type="bibr" rid="B19">Chen et&#xa0;al., 2022</xref>). The N-glycans of misfolded proteins are recognized by osteosarcoma amplified 9 (OS9), which associates with the suppressor enhancer Lin12 1 like (Sel1L)/HMG-CoA reductase degradation protein 3 (Hrd3)/HMG-CoA reductase degradation 1 (Hrd1) complex (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B31">Duwi Fanata et&#xa0;al., 2013</xref>). Protein associated with Hrd1-1/2 (PAWH1/2) interaction with EMS-mutagenized Bri1 suppressor 7 (EBS7) indirectly associates with Hrd1, regulating the stability and activity of the E3 ligase (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B85">Liu et&#xa0;al., 2015</xref>; <xref ref-type="bibr" rid="B75">Lin et&#xa0;al., 2019</xref>). Therefore, Hrd1 has the potential to target UBC32, an E2 enzyme located on the ER membrane of Arabidopsis. UBC32 is responsible for the ubiquitination of aberrant proteins that is induced by stress, leading to their subsequent degradation in the cytosol via the proteasome pathway (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B24">Cui et&#xa0;al., 2012</xref>; <xref ref-type="bibr" rid="B18">Chen et&#xa0;al., 2017</xref>; <xref ref-type="bibr" rid="B20">Chen et&#xa0;al., 2020</xref>).</p>
<p>ERAD, an important proteolytic pathway crucial to protein quality control, appears as a key factor in various studies associated with the enhancement of plant resistance to environmental stresses, productivity increase, and quality improvement. ERAD is a significant mechanism in plants for responding to environmental stresses, showing resistance capabilities to heat stress, drought, and salinity (<xref ref-type="bibr" rid="B67">Li et&#xa0;al., 2017</xref>; <xref ref-type="bibr" rid="B128">Strasser, 2018</xref>). In various plant species, evolutionarily conserved homologous ERAD components appear to be associated with stress tolerance and plant defense pathways elucidated two evolutionarily conserved ERAD pathways, DOA10 and HRD1, responding to heat stress in Arabidopsis (<xref ref-type="bibr" rid="B80">Liu and Li, 2014</xref>; <xref ref-type="bibr" rid="B67">Li et&#xa0;al., 2017</xref>; <xref ref-type="bibr" rid="B128">Strasser, 2018</xref>; <xref ref-type="bibr" rid="B49">Huber et&#xa0;al., 2021</xref>). This study demonstrated that loss-of-function mutants exhibited a higher survival rate and lower electrolyte leakage compared to the wild-type plants, enhancing plant resistance to heat stress (<xref ref-type="bibr" rid="B67">Li et&#xa0;al., 2017</xref>; <xref ref-type="bibr" rid="B128">Strasser, 2018</xref>). ERAD influences plant productivity by managing ER stress caused by protein misfolding. In this context, <xref ref-type="bibr" rid="B101">Ohta and Takaiwa (2015)</xref> showed that OsHrd3 is necessary for maintaining the quality of ER-derived protein bodies in rice endosperm (<xref ref-type="bibr" rid="B101">Ohta and Takaiwa, 2015</xref>). Additionally, <xref ref-type="bibr" rid="B144">Wakasa et&#xa0;al. (2011)</xref> proposed the possibility of improving the protein quality of rice through the role of ER stress response and ERAD (<xref ref-type="bibr" rid="B144">Wakasa et&#xa0;al., 2011</xref>). However, further research is necessary for a comprehensive understanding of ERAD associated with enhancing plant stress resistance, productivity, and quality.</p>
</sec>
<sec id="s2_2">
<title>CRISPR-Cas system as a versatile genome editing tool in plants</title>
<p>The CRISPR-Cas system is an adaptive immune mechanism used by bacteria to defend against the invasion of bacteriophages (<xref ref-type="bibr" rid="B94">Mojica et&#xa0;al., 2005</xref>). The system comprises an endonuclease (Cas) and a guide RNA (gRNA) that together form a ribonucleoprotein complex. The Cas complex locates and binds to a target dsDNA with the help of the guidance of gRNA. Once the complex is activated, the Cas enzyme cleaves the phosphodiester bonds of both strands, creating a double-stranded break (DSB) in the target DNA (<xref ref-type="bibr" rid="B12">Barrangou et&#xa0;al., 2007</xref>). The cells repair the DSB using nonhomologous end-joining (NHEJ) or homologous recombination (HR) (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2A</bold>
</xref>), which may result in mutations or modifications in the DNA sequence, thereby achieving gene editing (<xref ref-type="bibr" rid="B53">Jinek et&#xa0;al., 2012</xref>; <xref ref-type="bibr" rid="B22">Cong et&#xa0;al., 2013</xref>; <xref ref-type="bibr" rid="B29">Dickinson et&#xa0;al., 2013</xref>; <xref ref-type="bibr" rid="B120">Schwank et&#xa0;al., 2013</xref>; <xref ref-type="bibr" rid="B138">Van Vu et&#xa0;al., 2019</xref>).</p>
<fig id="f2" position="float">
<label>Figure&#xa0;2</label>
<caption>
<p>CRISPR-Cas-Mediated Gene Editing. <bold>(A)</bold> CRISPR-Cas9-Mediated Gene Editing through Double-Stranded Break (DSB) Repair. The CRISPR-Cas complex cleaves both strands of the target DNA, resulting in a DSB. The repair of the DSB predominantly occurs through two pathways: nonhomologous end joining (NHEJ) and homologous recombination (HR). NHEJ usually restores the original DNA sequence, but it can lead to imperfect repair and DNA insertion or deletion mutations, particularly during intense DSB formation. HR precisely inserts the desired sequence (green sticks) into the genomic region using a DNA donor template with homologous ends to the DSB terminals. <bold>(B)</bold> DNA base editors for genome editing. Base editing involves a deaminase, usually fused with a Cas9 (nCas9<sup>D10A</sup>) nickase, to remove an amino group from a nucleobase on the non-target strand. The deaminated base is then repaired via base excision or nucleotide excision repair, resulting in base transitions or transversions. Depending on the type of deaminase used, base conversion can lead to transitions, such as cytidine deaminase for C/G to A/T in cytosine base editors (CBE), or A/T to G/C in adenine base editors (ABE). Adding uracil DNA N-glycosylase inhibitors (UGI) enhances CBE efficiency. Base transversions can be achieved by adding uracil DNA N-glycosylase (UNG) to CBE (C/G to G/C in CGBE), N-methylpurine N-glycosylase to ABE (A/T to C/G or T/A), or by using UNG alone (G/C to C/G or T/A with GYBE). <bold>(C)</bold> Prime editing for precise DNA modification. The prime editing utilizes a pegRNA and a reverse transcriptase (RT) enzyme fused to the C-terminal of a nCas9<sup>H840A</sup>. It copies genetic information from the 3&#x2019; extension of the pegRNA into the nicked end on the non-target strand. By introducing desired genetic changes within the RT template of the 3&#x2019; extension, prime editing enables precise genetic modifications at the target site. Prime editing allows for a wide range of precise DNA changes within a genome, including various types of base conversion, DNA insertion, and deletion.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-14-1271368-g002.tif"/>
</fig>
<p>Since its repurposing for customized DNA cleavages and subsequent gene editing in 2012, the CRISPR era has begun (<xref ref-type="bibr" rid="B53">Jinek et&#xa0;al., 2012</xref>). The technology, recognized for its potential in precise genome engineering, has proven valuable in agriculture and various other fields, paving the way for numerous applications and advancements (<xref ref-type="bibr" rid="B16">Chen et&#xa0;al., 2019</xref>). As of today, there are two classes, six types, and over 30 subtypes of the CRISPR-Cas system that function in DNA or RNA targeting or other activities (<xref ref-type="bibr" rid="B61">Koonin and Makarova, 2022</xref>). The system has not only been repurposed as molecular scissors but also for other applications such as transcriptional regulations (<xref ref-type="bibr" rid="B21">Cheng et&#xa0;al., 2013</xref>; <xref ref-type="bibr" rid="B108">Qi et&#xa0;al., 2013</xref>). Furthermore, the editing scope has expanded from single bases (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2B</bold>
</xref>) (<xref ref-type="bibr" rid="B60">Komor et&#xa0;al., 2016</xref>; <xref ref-type="bibr" rid="B37">Gaudelli et&#xa0;al., 2017</xref>; <xref ref-type="bibr" rid="B17">Chen et&#xa0;al., 2021</xref>; <xref ref-type="bibr" rid="B63">Kurt et&#xa0;al., 2021</xref>; <xref ref-type="bibr" rid="B134">Tong et&#xa0;al., 2023</xref>) to small DNA changes with prime editing (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2C</bold>
</xref>) (<xref ref-type="bibr" rid="B8">Anzalone et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B76">Lin et&#xa0;al., 2020</xref>) and microhomology-mediated precision short DNA replacement (<xref ref-type="bibr" rid="B133">Tien Van et&#xa0;al., 2022</xref>), extending to kilobase-gene targeting, thereby establishing it as a versatile tool for genome editing (<xref ref-type="bibr" rid="B29">Dickinson et&#xa0;al., 2013</xref>; <xref ref-type="bibr" rid="B120">Schwank et&#xa0;al., 2013</xref>; <xref ref-type="bibr" rid="B16">Chen et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B142">Vu et&#xa0;al., 2020b</xref>).</p>
<p>The CRISPR-Cas system has been extensively utilized in plant biology and crop engineering, with a wide range of applications developed for editing target genes in both monocot and dicot species (<xref ref-type="bibr" rid="B16">Chen et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B166">Zhu et&#xa0;al., 2020</xref>). These applications include simple edits with indel mutations as well as HR-based precise gene replacement (<xref ref-type="bibr" rid="B33">Feng et&#xa0;al., 2013</xref>; <xref ref-type="bibr" rid="B68">Li et&#xa0;al., 2013</xref>; <xref ref-type="bibr" rid="B99">Nekrasov et&#xa0;al., 2013</xref>; <xref ref-type="bibr" rid="B16">Chen et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B142">Vu et&#xa0;al., 2020b</xref>). Due to the versatility of the CRISPR system, it has emerged as a valuable tool for achieving high efficiency in gene editing in plants, proving to be a significant asset in advancing plant biology and crop improvement research (<xref ref-type="bibr" rid="B16">Chen et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B166">Zhu et&#xa0;al., 2020</xref>; <xref ref-type="bibr" rid="B133">Tien Van et&#xa0;al., 2022</xref>).</p>
</sec>
<sec id="s2_3">
<title>Exploring the versatility of CRISPR-Cas system in UPR pathways</title>
<p>The CRISPR-Cas system is a versatile tool with numerous applications, including gene functionalization and regulation. Cas9 complexes act like molecular scissors and can theoretically cleave any genomic site of interest if a PAM motif is present. Previously, researchers relied on knockout lines generated by T-DNA insertion, random mutagenesis, or RNA interference (RNAi)-based downregulation lines to assess gene function (<xref ref-type="bibr" rid="B47">Howell, 2013</xref>; <xref ref-type="bibr" rid="B107">Pucker et&#xa0;al., 2021</xref>). However, these methods have limitations such as complex T-DNA integration events (<xref ref-type="bibr" rid="B132">Tamura et&#xa0;al., 2016</xref>) or residual gene activity in downregulated lines (<xref ref-type="bibr" rid="B115">Santillan Martinez et&#xa0;al., 2020</xref>), which lead to complicated analysis. The emergence of CRISPR-Cas technology has revolutionized the study of gene function in plants, as knockout lines generated by CRISPR-Cas tools are more precise and cleaner than traditional methods (<xref ref-type="bibr" rid="B133">Tien Van et&#xa0;al., 2022</xref>). The CRISPR-Cas system is highly efficient, customizable, simple, and cost-effective, making it an accessible tool for labs worldwide (<xref ref-type="bibr" rid="B2">Ahmadzadeh et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B16">Chen et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B44">He et&#xa0;al., 2023</xref>).</p>
<p>Although CRISPR-Cas has been used extensively for gene regulation and functionalization since its discovery in 2012, its application in studying ER stress response is relatively recent and began in 2019 (<xref ref-type="bibr" rid="B92">Mishiba et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B82">Liu et&#xa0;al., 2020</xref>). Even though a few CRISPR-Cas-related studies have been conducted in this field, there is still considerable potential for further functional exploration of genes involved in ER stress signaling using this technology (<xref ref-type="table" rid="T1">
<bold>Tables&#xa0;1</bold>
</xref>, <xref ref-type="table" rid="T2">
<bold>2</bold>
</xref>). Early research using CRISPR-Cas to study ER stress response focused on the Arabidopsis genes Protein Associated with PAWH1 and PAWH2 (<xref ref-type="table" rid="T1">
<bold>Table&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B75">Lin et&#xa0;al., 2019</xref>). These genes are essential components of the ERAD pathway (<xref ref-type="bibr" rid="B75">Lin et&#xa0;al., 2019</xref>) and play vital roles in mitigating environmental stress such as salinity (<xref ref-type="bibr" rid="B78">Liu et&#xa0;al., 2011</xref>). The PAWH genes were induced by ER stress and contributed to the stabilization of the UPR sensing complexes mediated by the EBS7 and Hrd1 (<xref ref-type="bibr" rid="B75">Lin et&#xa0;al., 2019</xref>). Additionally, the IRE1-mediated RNA splicing of <italic>AtbZIP60</italic> is a critical aspect of the UPR pathway in ER stress responses (<xref ref-type="bibr" rid="B159">Yu et&#xa0;al., 2022</xref>). To investigate the role of IRE1b in the signaling arm, the sensor domain-coding region of the gene was deleted using dual gRNA CRISPR-Cas9 complexes in the <italic>ire1a</italic>/<italic>c</italic> mutant background (<xref ref-type="table" rid="T1">
<bold>Table&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B92">Mishiba et&#xa0;al., 2019</xref>). The IRE1b-edited lines exhibited similar effects on BiP3 and PR-4 transcription as the <italic>ire1a</italic>/<italic>b</italic> mutant lines and bZIP60 RNA splicing as the <italic>ire1a</italic>/<italic>c</italic> mutants. However, there was no evidence of growth defects or seed set reductions in the mutant lines (<xref ref-type="table" rid="T1">
<bold>Table&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B92">Mishiba et&#xa0;al., 2019</xref>).</p>
<table-wrap id="T1" position="float">
<label>Table&#xa0;1</label>
<caption>
<p>Recent studies related to the UPR that used CRISPR-Cas9 tools.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="top" align="left">No.</th>
<th valign="top" align="left">Target gene</th>
<th valign="top" align="left">Plant species</th>
<th valign="top" align="left">Gene function</th>
<th valign="top" align="left">Impact</th>
<th valign="top" align="left">Reference</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left">
<bold>1</bold>
</td>
<td valign="top" align="left">
<italic>PAWH1</italic> and <italic>PAWH2</italic>
</td>
<td valign="top" align="left">
<italic>Arabidopsis thaliana</italic>
</td>
<td valign="top" align="left">Plant-specific components of ERAD complex</td>
<td valign="top" align="left">The <italic>pawh1pawh2</italic> double mutants suppressed the dwarf phenotype of the corresponding <italic>bri1-5</italic>
</td>
<td valign="top" align="left">(<xref ref-type="bibr" rid="B75">Lin et&#xa0;al., 2019</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">
<bold>2</bold>
</td>
<td valign="top" align="left">
<italic>IRE1B</italic>
</td>
<td valign="top" align="left">
<italic>Arabidopsis thaliana</italic>
</td>
<td valign="top" align="left">Splicing of bZIP60-encoding mRNA</td>
<td valign="top" align="left">Deletion of the IRE1B&#x2019;s sensor domain by CRISPR-Cas9 showed no growth defect and seed set reduction</td>
<td valign="top" align="left">(<xref ref-type="bibr" rid="B92">Mishiba et&#xa0;al., 2019</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">
<bold>3</bold>
</td>
<td valign="top" align="left">
<italic>OsNTL3</italic>
</td>
<td valign="top" align="left">
<italic>Oryza sativa</italic>
</td>
<td valign="top" align="left">Regulation the expression of OsbZIP74 and other UPR related-genes involved under heat stress conditions</td>
<td valign="top" align="left">The <italic>ntl3</italic> mutant plants showed more sensitive phenotype to heat stress treatment</td>
<td valign="top" align="left">(<xref ref-type="bibr" rid="B82">Liu et&#xa0;al., 2020</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">
<bold>4</bold>
</td>
<td valign="top" align="left">
<italic>IAN2</italic>, <italic>IAN3</italic>, <italic>IAN4</italic>, <italic>IAN5</italic>, <italic>IAN6</italic>, <italic>OsIAN1</italic>, and <italic>OsIAN2</italic>
</td>
<td valign="top" align="left">
<italic>Arabidopsis thaliana</italic> and <italic>Oryza sativa</italic>
</td>
<td valign="top" align="left">Regulation of the HSR, UPR, and cell death</td>
<td valign="top" align="left">The single mutants (<italic>ian3</italic>, <italic>ian5</italic>, <italic>ian6</italic>) and double mutants (<italic>ian2ian3</italic>, <italic>ian4ian5</italic>) showed less barren siliques along their main inflorescences than wild type</td>
<td valign="top" align="left">(<xref ref-type="bibr" rid="B87">Lu et&#xa0;al., 2021</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">
<bold>5</bold>
</td>
<td valign="top" align="left">
<italic>Sec23</italic> isoforms</td>
<td valign="top" align="left">
<italic>Physcomitrium patens</italic>
</td>
<td valign="top" align="left">Influencing ER to Golgi apparatus trafficking and secretion to the plasma membrane</td>
<td valign="top" align="left">The <italic>sec23d</italic> mutant showed smaller phenotype and fewer gametophores than the wild type, while the quintuple <italic>sec23abcfg</italic> mutant have no detectable growth defects</td>
<td valign="top" align="left">(<xref ref-type="bibr" rid="B15">Chang et&#xa0;al., 2022</xref>)</td>
</tr>
<tr>
<td valign="top" rowspan="2" align="left">
<bold>6</bold>
</td>
<td valign="top" align="left">
<italic>OsHLP1</italic>
</td>
<td valign="top" rowspan="2" align="left">
<italic>Oryza sativa</italic>
</td>
<td valign="top" align="left">OsHLP1 promotes disease resistance by compromising ER homeostasis when plants are infected by pathogens</td>
<td valign="top" align="left">The <italic>oshlp1</italic> mutant showed compromising blast disease resistance in rice</td>
<td valign="top" rowspan="2" align="left">(<xref ref-type="bibr" rid="B91">Meng et&#xa0;al., 2022</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">
<italic>OsNTL6</italic>
</td>
<td valign="top" align="left">ER homeostasis in rice during infection of <italic>Magnaporthe oryzae</italic>
</td>
<td valign="top" align="left">The <italic>osntl6</italic> mutant plants showed enhanced disease resistance compared with wild type plants</td>
</tr>
<tr>
<td valign="top" rowspan="2" align="left">
<bold>7</bold>
</td>
<td valign="top" align="left">
<italic>OsbZIP60</italic>
</td>
<td valign="top" rowspan="2" align="left">
<italic>Oryza sativa</italic>
</td>
<td valign="top" align="left">OsbZIP60 regulates the formation of grain chalkiness in rice via UPR</td>
<td valign="top" align="left">The <italic>osbzip60</italic> mutant plants showed high grain chalkiness rate and white floury endosperm</td>
<td valign="top" rowspan="2" align="left">(<xref ref-type="bibr" rid="B156">Yang et&#xa0;al., 2022</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">
<italic>OsbZIP50</italic>
</td>
<td valign="top" align="left">OsbZIP50 played an important role in the formation of grain chalkiness</td>
<td valign="top" align="left">The <italic>osbzip50</italic> mutant plants had high grain chalkiness rates</td>
</tr>
<tr>
<td valign="top" align="left">
<bold>8</bold>
</td>
<td valign="top" align="left">
<italic>NOBIRO6/TAF12b</italic>
</td>
<td valign="top" align="left">
<italic>Arabidopsis thaliana</italic>
</td>
<td valign="top" align="left">NOBIRO6/TAF12b contributes to UPR-associated root growth control</td>
<td valign="top" align="left">The <italic>nobiro6</italic> mutant plants rescue the root growth defect characteristic of the <italic>bzip17bzip28</italic> double mutant</td>
<td valign="top" align="left">(<xref ref-type="bibr" rid="B55">Kim et&#xa0;al., 2022a</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">
<bold>9</bold>
</td>
<td valign="top" align="left">
<italic>NbbZIP60</italic>
</td>
<td valign="top" align="left">
<italic>Nicotiana benthamiana</italic>
</td>
<td valign="top" align="left">Geminivirus satellite-encode &#x3b2;C1 activates UPR, induces bZIP60 nuclear export, and manipulates the expression of bZIP60 downstream genes to benefit virus infection</td>
<td valign="top" align="left">The <italic>nbbzip60</italic> mutant plants showed milder curling symptoms than the wild type plants after inoculating these plants with TYLCCNV/TYLCCNB through agro-infiltration.</td>
<td valign="top" align="left">(<xref ref-type="bibr" rid="B162">Zhang et&#xa0;al., 2023</xref>)</td>
</tr>
</tbody>
</table>
</table-wrap>
<table-wrap id="T2" position="float">
<label>Table&#xa0;2</label>
<caption>
<p>Recent promoter editing studies that used CRISPR-Cas9 tools.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="top" align="left">No.</th>
<th valign="top" align="left">Target gene</th>
<th valign="top" align="left">Plant species</th>
<th valign="top" align="left">Promoter edited regions</th>
<th valign="top" align="left">Impact</th>
<th valign="top" align="left">Reference</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left">
<bold>1</bold>
</td>
<td valign="top" align="left">
<italic>OsRAV2</italic>
</td>
<td valign="top" align="left">
<italic>Oryza sativa</italic>
</td>
<td valign="top" align="left">Mutation in the <italic>GT-1</italic> element regions of <italic>OsRAV2</italic>
</td>
<td valign="top" align="left">Induced salt stress response</td>
<td valign="top" align="left">(<xref ref-type="bibr" rid="B30">Duan et&#xa0;al., 2016</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">
<bold>2</bold>
</td>
<td valign="top" align="left">
<italic>ARGOS8</italic>
</td>
<td valign="top" align="left">
<italic>Maize</italic>
</td>
<td valign="top" align="left">Mutation of negative maize GOS2 promoter of <italic>ARGOS8</italic>
</td>
<td valign="top" align="left">Enhanced drought stress conditions in the field</td>
<td valign="top" align="left">(<xref ref-type="bibr" rid="B121">Shi et&#xa0;al., 2017</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">
<bold>3</bold>
</td>
<td valign="top" align="left">
<italic>SWEET11/13/14</italic>
</td>
<td valign="top" align="left">
<italic>Oryza sativa</italic>
</td>
<td valign="top" align="left">Mutation in the <italic>EBEs</italic> in the <italic>SWEET11/13/14</italic> promoters</td>
<td valign="top" align="left">Improved <italic>Xanthomonas oryzae</italic> pv. <italic>Oryzae</italic> resistance</td>
<td valign="top" align="left">(<xref ref-type="bibr" rid="B102">Oliva et&#xa0;al., 2019</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">
<bold>4</bold>
</td>
<td valign="top" align="left">
<italic>LsGGP2</italic>
</td>
<td valign="top" align="left">
<italic>Lactuca sativa</italic>
</td>
<td valign="top" align="left">Mutation in the uORFs of <italic>LsGGP2</italic>
</td>
<td valign="top" align="left">Increased tolerance to oxidative stress and ascorbate content</td>
<td valign="top" align="left">(<xref ref-type="bibr" rid="B163">Zhang et&#xa0;al., 2018</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">
<bold>5</bold>
</td>
<td valign="top" align="left">
<italic>AtTBF1</italic>
</td>
<td valign="top" align="left">
<italic>Arabidopsis thaliana</italic>
</td>
<td valign="top" align="left">Strategy of mutation in the uORFs of <italic>AtTBF1</italic>
</td>
<td valign="top" align="left">Expectation in response to pathogen attack</td>
<td valign="top" align="left">(<xref ref-type="bibr" rid="B143">Vuong et&#xa0;al., 2023</xref>)</td>
</tr>
</tbody>
</table>
</table-wrap>
<p>In rice, the IRE1-mediated RNA splicing in ER stress responses is also conserved, and the OsbZIP74 (also known as OsbZIP50) is the ortholog of AtbZIP60 (<xref ref-type="bibr" rid="B86">Lu et&#xa0;al., 2012</xref>). Modified OsbZIP74 is transported to the nucleus and upregulates UPR-related genes, including several membrane-associated NAC transcription factors. In a recent study, researchers utilized the CRISPR-Cas9 gene-editing system to generate knockout mutants of OsNTL3, confirming its role as a transcriptional activator of OsbZIP74 (<xref ref-type="table" rid="T1">
<bold>Table&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B82">Liu et&#xa0;al., 2020</xref>). The investigation also showed that OsbZIP74 positively regulates the transcription of OsNTL3 under heat stress conditions. Additionally, the study revealed that the loss of OsNTL3 function results in increased heat sensitivity in rice seedlings (<xref ref-type="table" rid="T1">
<bold>Table&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B82">Liu et&#xa0;al., 2020</xref>). <italic>OsbZIP60</italic> has been identified as a critical regulator of grain chalkiness, a stress-related phenotype in rice (<xref ref-type="bibr" rid="B43">Hayashi et&#xa0;al., 2012</xref>; <xref ref-type="bibr" rid="B131">Takahashi et&#xa0;al., 2012</xref>; <xref ref-type="bibr" rid="B156">Yang et&#xa0;al., 2022</xref>). To understand the role of <italic>OsbZIP60</italic> in managing this response, <italic>osbzip60</italic> knockout mutants were created using CRISPR-Cas9 gene-editing technology. In these mutants, upregulation of several chaperone genes, including <italic>OsbZIP50</italic>, <italic>OsBiP1</italic>, <italic>OsBiP2</italic>, and <italic>OsBiP3</italic>, was observed, leading to varying degrees of grain chalkiness. This result indicates that <italic>OsbZIP60</italic> plays a critical role in regulating rice grain chalkiness and maintaining ER homeostasis (<xref ref-type="table" rid="T1">
<bold>Table&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B156">Yang et&#xa0;al., 2022</xref>). In another study, the roles of two bZIP transcription factors, bZIP17 and bZIP28, in the UPR pathway were explored (<xref ref-type="bibr" rid="B83">Liu et&#xa0;al., 2007a</xref>; <xref ref-type="bibr" rid="B84">Liu et&#xa0;al., 2007b</xref>). The <italic>bzip17bzip28</italic> double mutant displayed stress-related phenotypes, including severe dwarfism, low germination rate, and short roots, compared to the wild-type plant (<xref ref-type="bibr" rid="B57">Kim et&#xa0;al., 2018</xref>). To unravel the underlying mechanisms associated with the observed stress-related phenotypes, a suppressor mutant named <italic>nobiro6</italic> was created within the <italic>bzip17bzip28</italic> background using CRISPR-Cas9 technology. This triple mutant, <italic>bzip17bzip28nbr6</italic>, demonstrated a partial rescue of root growth, highlighting the role of NOBIRO6/TAF12b as a transcription cofactor in UPR-associated root growth control (<xref ref-type="table" rid="T1">
<bold>Table&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B56">Kim et&#xa0;al., 2022b</xref>). In a recent study aiming to understand the role of NbbZIP60 in plant defense responses to pathogens, <italic>nbbzip60</italic> knockout mutants were generated using CRISPR/Cas9-based technology (<xref ref-type="bibr" rid="B162">Zhang et&#xa0;al., 2023</xref>). These knockout mutant plants showed a reduced amount of viral DNA, leading to milder leaf curling symptoms compared to wild-type plants under virus infection (<xref ref-type="table" rid="T1">
<bold>Table&#xa0;1</bold>
</xref>). These findings highlight how CRISPR-Cas9 technology is enabling a deeper understanding of UPR in plants, opening avenues for enhancing plant stress resistance.</p>
</sec>
<sec id="s2_4">
<title>CRISPR-Cas mediated dissection of ER stress and plant responses to biotic stresses</title>
<p>The CRISPR-Cas system offers a significant advantage in generating multiple gene mutations through multiplexing methods with multiple gRNAs. For instance, it was used to generate various mutated variants in single and combinations of UPR-related genes encoding for immune-associated nucleotide-binding (IAN) proteins in Arabidopsis (<xref ref-type="table" rid="T1">
<bold>Table&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B87">Lu et&#xa0;al., 2021</xref>). In the study, IAN2 to IAN6 were found to be located at a single locus on chromosome 1 by genome-wide association study (GWAS) (<xref ref-type="bibr" rid="B87">Lu et&#xa0;al., 2021</xref>). The efficient CRISPR-Cas9 system was used to create single, double, triple, and quadruple IAN gene mutations that were crucial for gene functionalization. Interestingly, the <italic>ian</italic> mutants, particularly the <italic>ian6</italic> knockout lines, exhibited enhanced heat tolerance during the reproductive stage in both Arabidopsis and rice (<xref ref-type="table" rid="T1">
<bold>Table&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B87">Lu et&#xa0;al., 2021</xref>). The IAN6 protein has been discovered to localize to the ER, where it suppresses HSP and UPR-related gene expression and promotes programmed cell death during the reproductive stage (<xref ref-type="table" rid="T1">
<bold>Table&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B87">Lu et&#xa0;al., 2021</xref>). In a similar manner, multiplexed editing has been effectively used to generate combined knockout mutations in genes associated with COPII-mediated vesicle trafficking from the ER to the Golgi apparatus (<xref ref-type="bibr" rid="B15">Chang et&#xa0;al., 2022</xref>). The COPII complex is involved in transporting bZIP28 proteins to the Golgi for processing and subsequent release into the cytosol during ER stress (<xref ref-type="bibr" rid="B125">Srivastava et&#xa0;al., 2012</xref>; <xref ref-type="bibr" rid="B47">Howell, 2013</xref>). In plants, Sec23 and Sec24 combine with Sar1 to form the inner layer of COPII vesicles. Several isoforms of the Sec23 were shown to form distinct ER exit sites with differential effects on protein trafficking and growth (<xref ref-type="bibr" rid="B158">Yoshihisa et&#xa0;al., 1993</xref>; <xref ref-type="bibr" rid="B161">Zeng et&#xa0;al., 2015</xref>). The <italic>sec23d</italic> mutant significantly hindered ER-to-Golgi transport, whereas the quintuple <italic>sec23abcfg</italic> mutant primarily impacted protein secretion to the plasma membrane (<xref ref-type="table" rid="T1">
<bold>Table&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B15">Chang et&#xa0;al., 2022</xref>).</p>
<p>Plant responses to biotic stress, such as those induced by phytopathogens, require the maintenance of ER homeostasis. In rice, OsHLP1, which is induced by Magnaporthe oryzae infection, has been shown to interact with OsNTL6. This interaction suppresses the accumulation of OsNTL6, leading to the activation of genes involved in plant immunity and resulting in enhanced disease resistance (<xref ref-type="bibr" rid="B91">Meng et&#xa0;al., 2022</xref>). CRISPR-Cas9 knockout mutants of OsHLP1 displayed reduced disease resistance, suggesting that OsHLP1 positively regulates blast resistance in rice (<xref ref-type="table" rid="T1">
<bold>Table&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B91">Meng et&#xa0;al., 2022</xref>). In contrast, the OsNTL6 protein acts as a negative regulator of blast disease resistance; overexpression lines led to increased <italic>Magnaporthe oryzae</italic> infection, while knockout lines generated using CRISPR-Cas9 showed reduced infection compared to wild-type plants (<xref ref-type="table" rid="T1">
<bold>Table&#xa0;1</bold>
</xref>) (<xref ref-type="bibr" rid="B91">Meng et&#xa0;al., 2022</xref>). Recent application of CRISPR-Cas technology in studying ER stress and plant responses to biotic stress has provided valuable insights into critical components of these pathways (<xref ref-type="bibr" rid="B75">Lin et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B92">Mishiba et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B82">Liu et&#xa0;al., 2020</xref>; <xref ref-type="bibr" rid="B87">Lu et&#xa0;al., 2021</xref>; <xref ref-type="bibr" rid="B15">Chang et&#xa0;al., 2022</xref>; <xref ref-type="bibr" rid="B91">Meng et&#xa0;al., 2022</xref>). By using CRISPR-Cas to edit the genome of plants, researchers can generate mutations in UPR-related genes to study their function and determine their role in the UPR pathway. Overall, the CRISPR-Cas system has revolutionized the field of genetics and has significant implications for the study of gene function in plants, including UPR-related genes.</p>
</sec>
<sec id="s3_1">
<title>Enhancing stress tolerance and crop improvement through the CRISPR-Cas mediated modification of <italic>cis</italic>-regulatory elements</title>
<p>
<italic>Cis</italic>-regulatory elements (CREs) are noncoding DNA sequences that incorporate transcription factors and other molecular binding sites, such as promoters and enhancers, which influence transcription (<xref ref-type="bibr" rid="B148">Wittkopp and Kalay, 2011</xref>; <xref ref-type="bibr" rid="B150">Wolter et&#xa0;al., 2019</xref>). The promoter regions of most plant UPR-related genes contain a consensus <italic>cis</italic>-acting element known as the ERSE and/or the UPRE (<xref ref-type="bibr" rid="B79">Liu and Howell, 2010</xref>; <xref ref-type="bibr" rid="B47">Howell, 2013</xref>; <xref ref-type="bibr" rid="B97">Nawkar et&#xa0;al., 2017</xref>). Several studies have underscored the significant potential of crop improvement through the editing of regulatory sequences to adjust gene expression levels, thereby generating novel phenotypic variants (<xref ref-type="bibr" rid="B149">Wolter and Puchta, 2018</xref>; <xref ref-type="bibr" rid="B150">Wolter et&#xa0;al., 2019</xref>). For instance, the <italic>RAV2</italic> gene, which is transcriptionally induced by salt stress in rice, was subjected to CRISPR-Cas-mediated engineering to modify the <italic>GT-1</italic> element in the promoter, revealing that the <italic>GT-1</italic> element directly governs the salt stress response (<xref ref-type="table" rid="T2">
<bold>Table&#xa0;2</bold>
</xref>) (<xref ref-type="bibr" rid="B30">Duan et&#xa0;al., 2016</xref>; <xref ref-type="bibr" rid="B69">Li et&#xa0;al., 2020b</xref>). In maize, ARGOS8, a negative regulator of ethylene responses, enhances drought tolerance (<xref ref-type="table" rid="T2">
<bold>Table&#xa0;2</bold>
</xref>) (<xref ref-type="bibr" rid="B122">Shi et&#xa0;al., 2015</xref>). Plants edited with CRISPR-Cas9 to replace the native promoter region of the <italic>ARGOS8</italic> gene with the <italic>GOS2</italic> promoter demonstrated increased grain yield under drought stress conditions in the field (<xref ref-type="table" rid="T2">
<bold>Table&#xa0;2</bold>
</xref>) (<xref ref-type="bibr" rid="B122">Shi et&#xa0;al., 2015</xref>; <xref ref-type="bibr" rid="B121">Shi et&#xa0;al., 2017</xref>; <xref ref-type="bibr" rid="B146">Wang et&#xa0;al., 2022</xref>). Similarly, the removal of a regulatory fragment containing a transcription-activator-like effector (TALe)-Binding Element (EBE) in the promoter of <italic>SWEET11</italic> via CRISPR/Cas resulted in improved disease resistance in rice, without affecting fertility (<xref ref-type="table" rid="T2">
<bold>Table&#xa0;2</bold>
</xref>) (<xref ref-type="bibr" rid="B66">Li et&#xa0;al., 2020a</xref>). This development presents a clear advantage over the sterile phenotype of the <italic>Ossweet11</italic> knockout mutant, which is unsuitable for crop improvement. Recently, genome editing of EBEs in <italic>SWEET</italic> promoter genes led to broad-spectrum bacterial blight resistance in rice (<xref ref-type="table" rid="T2">
<bold>Table&#xa0;2</bold>
</xref>) (<xref ref-type="bibr" rid="B102">Oliva et&#xa0;al., 2019</xref>). While predicting the effects of gene expression regulation by manipulation of various CREs, including ERSEs and UPREs, and the resulting phenotypic changes could be difficult, the modification of CREs by CRISPR-Cas holds the potential to be a critical strategy not only for studying UPR signaling pathways, but also for breeding plants with stress tolerance and desirable traits (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3A</bold>
</xref>).</p>
<fig id="f3" position="float">
<label>Figure&#xa0;3</label>
<caption>
<p>Strategies for prospective editing of ER stress signaling components to enhance stress tolerance. <bold>(A)</bold> CRISPR-Cas9 can be effectively employed to edit the promoter region of target genes in order to modulate gene expression. The promoter region contains important <italic>cis</italic>-regulatory elements (CRE, brown and ocher boxes), endoplasmic reticulum stress response elements (ERSEs, blue boxes), and unfolded protein response elements (UPREs, green box). These elements act as enhancers or repressors, playing a crucial role in regulating the transcriptional activity of the gene. By utilizing a multiplex genome editing approach, multiple single-guide RNAs (sgRNAs) can be designed to specifically target distinct ERSEs and UPREs within the promoter region. The CRISPR-Cas9 system, guided by these sgRNAs, induces double-strand breaks at the desired sites in the promoter region, leading to DNA repair mechanisms that can introduce stochastic mutations. These stochastic mutations occurring in the promoter region lead to the generation of alleles with diverse patterns and levels of gene expression. Certain mutations may enhance gene expression, while others may repress it. Implementing this method has the potential to generate a spectrum of phenotypic variations across different lines. <bold>(B)</bold> CRISPR-Cas9 can be used to manipulate gene translation by targeting upstream open reading frames (uORFs). By utilizing the CRISPR-Cas9 system, specific mutations can be introduced into the start codon region of uORFs, disrupting their inhibitory effects on translation. The translation process of messenger RNA (mRNA) begins when small (light blue) and large (light green) ribosomal subunits scan the mRNA from its 5&#x2032; cap (represented by a dark brown circle). The initiation codon, represented by a yellow box, serves as the starting point for translation. However, if the mRNA contains an upstream open reading frame (uORF) represented by a pink rectangle, the ribosome can stall at the uORF. This stalling event leads to the repression of translation of the main open reading frame (mORF) indicated by a blue rectangle. Consequently, the reduced translation of the mORF results in a decreased production of protein products, represented by orange circles. The mutated initiation codon (red rectangle) within uORF regions using the CRISPR-Cas9 inhibits ribosome stalling, resulting in increased production of proteins encoded by the mORF. <bold>(C)</bold> Strategy to generate truncated UBC32 using CRISPR-Cas9-mediated knockout to enhance BR signaling by stabilizing structurally imperfect, yet biochemically active, bri1 peptides to achieve stress tolerance. The strategy to enhance brassinosteroid (BR) signaling and improve stress tolerance involves the generation of a truncated form of the <italic>ubiquitin-conjugating enzyme 32</italic> (<italic>UBC32</italic>) gene using CRISPR-Cas9-mediated knockout. <italic>UBC32</italic> is responsible for encoding an E2 ubiquitin-conjugating enzyme that plays a crucial role in the degradation of the biochemically active but structurally incomplete brassinosteroid insensitive 1 (<italic>bri1</italic>: <italic>bri1-5</italic> or <italic>bri1-9</italic>) peptide. Through the process of ubiquitination, UBC32 targets the <italic>bri1-5</italic> or <italic>bri1-9</italic> peptide for 26S proteasome-mediated degradation in the cytosol. However, utilizing the CRISPR-Cas9 to disrupt UBC32 allows for a reduction in the ubiquitination of <italic>bri1-5</italic> or <italic>bri1-9</italic> peptide, leading to increased stability of the peptide. This enhanced stability contributes to the amplification of BR signaling, thereby improving stress tolerance in plants.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-14-1271368-g003.tif"/>
</fig>
</sec>
<sec id="s3_2">
<title>Upstream open reading frames as regulatory elements and CRISPR-Cas9 applications for crop improvement</title>
<p>The uORFs are essential regulatory elements located in the 5&#x2019; UTR of main open reading frames (mORFs). Recent bioinformatics analyses estimate that approximately 35% of total plant transcripts contain uORFs (<xref ref-type="bibr" rid="B123">Silva et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B73">Li et&#xa0;al., 2021</xref>). These uORFs are known to act as inhibitors, repressing the initiation of mORF translation via ribosome stalling (<xref ref-type="bibr" rid="B123">Silva et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B164">Zhang et&#xa0;al., 2020</xref>). A recent research indicates that uORFs possess the ability to regulate gene expression in response to environmental stresses, as they control specific master regulators involved in stress responses (<xref ref-type="bibr" rid="B164">Zhang et&#xa0;al., 2020</xref>). Under adverse environmental conditions, stress-responsive transcripts containing uORFs are upregulated, suggesting that CRISPR-Cas9-mediated uORF editing could be a promising approach to enhance gene expression for crop trait improvement (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3B</bold>
</xref>) (<xref ref-type="bibr" rid="B136">Um et&#xa0;al., 2021</xref>). For example, the application of CRISPR-Cas9 editing to the uORF of LsGGP2 in <italic>Lactuca sativa</italic> (lettuce) has yielded promising results, demonstrating increased tolerance to oxidative stress and a substantial 150% increase in ascorbate content (<xref ref-type="table" rid="T2">
<bold>Table&#xa0;2</bold>
</xref> and <xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3B</bold>
</xref>) (<xref ref-type="bibr" rid="B163">Zhang et&#xa0;al., 2018</xref>). Similarly, in Arabidopsis, TBF1 plays a critical role in the growth-to-defense transition in response to pathogen attack (<xref ref-type="table" rid="T2">
<bold>Table&#xa0;2</bold>
</xref>) (<xref ref-type="bibr" rid="B135">Traubenik et&#xa0;al., 2021</xref>). Under normal conditions, two uORFs in TBF1 inhibit AtTBF1 translation; however, upon pathogen infection, these inhibitory effects are relieved, allowing TBF1 to regulate and induce the expression of defense-related genes (<xref ref-type="table" rid="T2">
<bold>Table&#xa0;2</bold>
</xref> and <xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3B</bold>
</xref>) (<xref ref-type="bibr" rid="B104">Pajerowska-Mukhtar et&#xa0;al., 2012</xref>). These findings suggest that CRISPR-Cas-based gene editing can be used to remove or generate uORF sequences in target genes. This strategy can be used to increase or decrease protein translation levels, and applied to develop crops with improved traits, including stress resistance (<xref ref-type="bibr" rid="B143">Vuong et&#xa0;al., 2023</xref>). In conclusion, CRISPR-Cas9-mediated uORF editing represents a promising avenue for enhancing plant resilience to environmental stresses and advancing crop trait improvement.</p>
</sec>
</sec>
<sec id="s4">
<title>Strategies for enhancing ER stress tolerance in plants using CRISPR-Cas9</title>
<p>Regulating plant responses to ER stress is essential for enhancing crop productivity and survival rates. To address this gap, we propose several strategies for using CRISPR-Cas tools to enhance ER stress tolerance in plants. One approach involves editing genes that directly or indirectly regulate the UPR signaling pathway. However, it is important to note that a thorough understanding of the roles of the targeted genes is necessary for designing an effective editing strategy. The most straightforward method for breeding ER stress tolerance using CRISPR-Cas complexes involves introducing indel mutations into the coding sequences of targeted genes and selecting knockout lines. The fundamental concept behind employing simple indel mutations to improve crop performance is to target genes known to regulate a specific response or trait. This method has been proven to be effective in improving crop performance (<xref ref-type="bibr" rid="B16">Chen et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B141">Vu et&#xa0;al., 2020a</xref>; <xref ref-type="bibr" rid="B166">Zhu et&#xa0;al., 2020</xref>). However, it is necessary to ensure that the targeted knockout mutants have minimal negative impact on plant morphology, agronomical traits, growth, development, and yield. A minimal trade-off in growth, development, and yield may be acceptable if the benefits to other agronomic traits are highly significant. Genes that directly or indirectly regulate the UPR signaling pathway could be targets for gene editing to confer ER stress tolerance in plants. However, fundamental studies are necessary to identify the specific genes that are suitable for the editing approach, and it is crucial to ensure that the benefits outweigh any potential trade-offs.</p>
<p>UPR regulators play a crucial role in maintaining ER homeostasis in both normal and stress conditions. Identifying genes involved in ERAD pathways is of great importance. One such gene is <italic>UBC32</italic>, which is involved in the ERAD-mediated quality control process through ubiquitination-associated protein degradation. The mutation of <italic>UBC32</italic> results in the accumulation of structurally abnormal <italic>bri1-5</italic> and <italic>bri1-9</italic> mutant forms of brassinosteroid insensitive 1 (BRI1). Despite their structural abnormalities, these mutant forms still retain the biochemical activity of the BRI1 receptor, subsequently enhancing brassinosteroid (BR) signaling (<xref ref-type="bibr" rid="B24">Cui et&#xa0;al., 2012</xref>). The <italic>ubc32</italic> single and <italic>bri1-5/9 ubc32</italic> double mutant lines shows improved salt stress tolerance compared to the wild-type control (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3C</bold>
</xref>) (<xref ref-type="bibr" rid="B24">Cui et&#xa0;al., 2012</xref>; <xref ref-type="bibr" rid="B165">Zhou et&#xa0;al., 2021</xref>). Interestingly, the <italic>ubc32</italic> single mutant Arabidopsis demonstrates a phenotype similar to the wild-type (WT) Col-0 when grown under normal conditions (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3C</bold>
</xref>) (<xref ref-type="bibr" rid="B165">Zhou et&#xa0;al., 2021</xref>). These findings suggest that <italic>UBC32</italic> could be a promising target for enhancing stress tolerance via CRISPR-Cas9-mediated knockout. By employing gRNAs to direct CRISPR-Cas9, cleavage of the UBC32 coding sequence can be achieved. This results in indel mutations that cause premature termination of translation and truncation of the UBC32 polypeptide chain, which may ultimately enhance salt tolerance by affecting BR signaling.</p>
<sec id="s4_1">
<title>Enhancing plant stress tolerance through CRISPR-Cas editing of key regulatory genes</title>
<p>Plant growth and development are significantly influenced by environmental conditions such as light (<xref ref-type="bibr" rid="B10">Bae and Choi, 2008</xref>; <xref ref-type="bibr" rid="B54">Kami et&#xa0;al., 2010</xref>; <xref ref-type="bibr" rid="B103">Paik and Huq, 2019</xref>). Suboptimal lighting conditions can trigger ER stress responses, which can lead to cellular dysfunction and ultimately affect plant growth and survival (<xref ref-type="bibr" rid="B90">Mawphlang and Kharshiing, 2017</xref>; <xref ref-type="bibr" rid="B3">Ahn et&#xa0;al., 2022</xref>). The connection between light and UPR has been shown to be mediated by ELONGATED HYPOCOTYL 5 (HY5), a bZIP factor previously known as a master regulator of light signaling (<xref ref-type="bibr" rid="B35">Gangappa and Botto, 2016</xref>). HY5 acts as an important transcription factor in both light signaling and the UPR pathway. In the dark, HY5 is targeted for degradation by the E3 ubiquitin ligase COP1, which marks HY5 with ubiquitin and targets it for degradation by the 26S proteasome (<xref ref-type="bibr" rid="B5">Ang et&#xa0;al., 1998</xref>; <xref ref-type="bibr" rid="B154">Xu et&#xa0;al., 2016</xref>). However, in the presence of light or under ER stress conditions, HY5 is stabilized and can regulate the expression of UPR-related genes (<xref ref-type="bibr" rid="B97">Nawkar et&#xa0;al., 2017</xref>). The <italic>HY5</italic> gene has been identified as a critical regulator of stress resistance in plants (<xref ref-type="bibr" rid="B152">Xiao et&#xa0;al., 2021</xref>). Therefore, the utilization of CRISPR-Cas-based gene editing technology for the generation and characterization of crops carrying HY5 alleles may present a promising and compelling direction for further scientific investigation. Under various stress conditions, the levels and activity of HY5 protein increase, leading to enhanced expression of downstream genes. Overexpression or complete removal of the <italic>HY5</italic> gene may result in significant trade-off in the phenotypes of edited lines, due to the important role of HY5 in multiple processes, such as photomorphogenesis. Consequently, generating mutants with HY5 alleles that maintain a certain level of expression could be an interesting approach for developing crops that efficiently respond to various stresses. The CRISPR-Cas-mediated generation of crops with HY5 alleles could be achieved by targeting the <italic>cis</italic>-regulatory elements of the <italic>HY5</italic> gene. This approach has already been shown to be effective in previous studies (<xref ref-type="bibr" rid="B114">Rodriguez-Leal et&#xa0;al., 2017</xref>). Additionally, introducing CRISPR-Cas-mediated precise modification of the DNA binding bZIP domain or the COP1 binding domain in HY5 may be alternative strategies to alter HY5 functions. Such a strategy could be readily implemented through CRISPR-Cas-based gene targeting or prime editing (<xref ref-type="bibr" rid="B138">Van Vu et&#xa0;al., 2019</xref>). In summary, the regulatory function of HY5 in various stress responses makes it a promising target for enhancing stress tolerance in plants via CRISPR-Cas-based gene editing. By generating mutant alleles of HY5, it might be possible to indirectly alter the expression of downstream genes, including UPR-related genes, and consequently enhance the resistance of plants to various stresses.</p>
<p>Cadmium, a hazardous heavy metal, significantly impacts plants by interfering with crucial processes such as water and nutrient uptake, photosynthesis, calcium signaling, and genome maintenance. This interference leads to stunted growth, diminished yield, and in severe cases, plant death (<xref ref-type="bibr" rid="B151">Xi et&#xa0;al., 2016</xref>; <xref ref-type="bibr" rid="B27">De Benedictis et&#xa0;al., 2023</xref>). Recent studies have demonstrated that knockout of the supernumerary aleurone 1 (SAL1) enzyme can mitigate the toxicity of cadmium in Arabidopsis plants (<xref ref-type="bibr" rid="B151">Xi et&#xa0;al., 2016</xref>). SAL1, also known as FIERY1, is a well-established regulator of stress response signaling. This enzyme possesses 3&#x2019;(2&#x2019;),5&#x2019;-bisphosphate nucleotidase and inositol polyphosphate 1-phosphatase functions (<xref ref-type="bibr" rid="B110">Quintero et&#xa0;al., 1996</xref>; <xref ref-type="bibr" rid="B153">Xiong et&#xa0;al., 2001</xref>; <xref ref-type="bibr" rid="B147">Wilson et&#xa0;al., 2009</xref>), and is implicated in leaf morphogenesis (<xref ref-type="bibr" rid="B113">Robles et&#xa0;al., 2010</xref>). These findings suggest that targeting SAL1 using CRISPR-Cas-based techniques could be a promising approach to alleviating cadmium toxicity and other environmental stresses in crop plants. By knocking out SAL1, plants may be better equipped to cope with environmental stresses, leading to improved crop yields and sustainability. In conclusion, the recent discovery of the role of SAL1 in mitigating cadmium-induced toxicity and ER stress responses offers an exciting opportunity for enhancing the sustainability of crop production. By utilizing CRISPR-Cas-based techniques to target SAL1 and other regulators of ER stress responses, crop plants may exhibit increased resilience to environmental stresses, ultimately leading to enhanced crop yield and quality. Taken together, the proposed strategies for improving crop stress tolerance through genetic modification present a promising opportunity for enhancing plant tolerance and agricultural productivity. By targeting key genes involved in stress responses, such as <italic>UBC32</italic>, <italic>HY5</italic>, and <italic>SAL1</italic>, it may be possible to develop crops that are better adapted to challenging environmental conditions. However, further research is necessary to identify the optimal genes for modification and ensure that the benefits outweigh any potential drawbacks.</p>
</sec>
</sec>
<sec id="s5">
<title>Concluding remarks</title>
<p>The UPR mechanism plays a vital role in facilitating the growth and survival of plants under unfavorable environmental conditions (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1</bold>
</xref>). Despite the extensive research on the molecular mechanism of plant UPR, the adoption of CRISPR-Cas-based gene editing technology has been slow. This has limited the potential for developing crops with resistance to a variety of adverse biological and non-biological environmental conditions, including ER stress. Consequently, it is imperative to actively consider the use of CRISPR-Cas technology to study the functions of genes involved in ER stress responses and expand the scope of plant gene editing (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2</bold>
</xref>). Understanding how UPR is activated and regulated, as well as the consequences of such regulation, can provide valuable insights into the development of crops with resistance to various stresses. As plants continue to face unpredictable environmental stresses that can significantly impact crop yield and quality, the adoption of CRISPR-Cas-based gene knockout of UPR-related genes is of great importance. In this review, we summarize the current understanding of ER stress signaling and regulation, as well as the recent advances in CRISPR-Cas technology for ER stress research (<xref ref-type="table" rid="T1">
<bold>Tables&#xa0;1</bold>
</xref>, <xref ref-type="table" rid="T2">
<bold>2</bold>
</xref>). Additionally, we discuss the prospects of using CRISPR-Cas-based gene editing for crop breeding, particularly in the development of crop varieties with enhanced ER stress tolerance (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3</bold>
</xref>). We hope that our review will help expand research in this field and attract attention to the potential of CRISPR-Cas technology for studying gene functions related to ER stress responses and expanding the scope of plant gene editing. In this review, we summarize the current understanding of ER stress signaling and regulation, as well as the recent progress made in CRISPR-Cas technology for ER stress studies (<xref ref-type="table" rid="T1">
<bold>Tables&#xa0;1</bold>
</xref>, <xref ref-type="table" rid="T2">
<bold>2</bold>
</xref>). We also discuss the future prospects of using CRISPR-Cas-based gene editing for crop breeding, particularly in the development of crop varieties with enhanced stress tolerance We hope that our review will help propel the field and attract attention to the potential of CRISPR-Cas technology for studying gene functions related to ER stress responses.</p>
</sec>
<sec id="s6" sec-type="author-contributions">
<title>Author contributions</title>
<p>BV: Conceptualization, Methodology, Writing &#x2013; original draft, Writing &#x2013; review &amp; editing. TV: Conceptualization, Funding acquisition, Methodology, Supervision, Writing &#x2013; original draft, Writing &#x2013; review &amp; editing. JY: Writing &#x2013; original draft. NN: Writing &#x2013; original draft. KK: Writing &#x2013; original draft. J-YK: Conceptualization, Funding acquisition, Methodology, Supervision, Writing &#x2013; original draft, Writing &#x2013; review &amp; editing. KL: Conceptualization, Funding acquisition, Methodology, Supervision, Writing &#x2013; original draft, Writing &#x2013; review &amp; editing.</p>
</sec>
</body>
<back>
<sec id="s7" sec-type="funding-information">
<title>Funding</title>
<p>The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by the National Research Foundation of Korea (2020R1I1A1A01072130, 2020M3A9I4038352, 2020R1A6A1A03044344, 2021R1A5A8029490, 2022R1A2C3010331, 2021R1A2C1013516, and 2022R1I1A1A01071947), the Cooperative Research Program for Agriculture Science and Technology Development (Project No. PJ016236), and the Program for New Plant Breeding Techniques (NBT, Grant PJ016867022022), Rural Development Administration (RDA), Korea. BV and NN were supported by the BK4 program funded by the Ministry of Education of Korea.</p>
</sec>
<ack>
<title>Acknowledgments</title>
<p>We apologize to colleagues whose work could not be included owing to space constraints. All the figures were created with BioRender under a paid subscription.</p>
</ack>
<sec id="s9" sec-type="COI-statement">
<title>Conflict of interest</title>
<p>Author J-YK is employed by Nulla Bio Inc.</p>
<p>The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p>
</sec>
<sec id="s10" sec-type="disclaimer">
<title>Publisher&#x2019;s note</title>
<p>All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.</p>
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<glossary>
<title>Glossary</title>
<table-wrap position="anchor">
<table frame="hsides">
<tbody>
<tr>
<td>ATF6</td>
<td>activating transcription factor 6</td>
</tr>
<tr>
<td>BiP3</td>
<td>luminal-binding protein 3</td>
</tr>
<tr>
<td>BR</td>
<td>brassinosteroid</td>
</tr>
<tr>
<td>BRI1</td>
<td>brassinosteroid insensitive 1</td>
</tr>
<tr>
<td>bZIP</td>
<td>basic leucine zipper protein</td>
</tr>
<tr>
<td>Cd</td>
<td>cadmium</td>
</tr>
<tr>
<td>COPII</td>
<td>coat protein complex II</td>
</tr>
<tr>
<td>CREs</td>
<td>
<italic>cis</italic>-regulatory elements</td>
</tr>
<tr>
<td>Hrd1</td>
<td>HMG-CoA reductase degradation protein 1</td>
</tr>
<tr>
<td>DSB</td>
<td>double-stranded break</td>
</tr>
<tr>
<td>DTT</td>
<td>dithiothreitol</td>
</tr>
<tr>
<td>EBS7</td>
<td>EMS-mutagenized Bri1 suppressor 7</td>
</tr>
<tr>
<td>ER</td>
<td>endoplasmic reticulum</td>
</tr>
<tr>
<td>ERAD</td>
<td>ER-associated protein degradation</td>
</tr>
<tr>
<td>ERSE</td>
<td>ER stress response element</td>
</tr>
<tr>
<td>GCN2</td>
<td>general control non-repressible 2</td>
</tr>
<tr>
<td>gRNA</td>
<td>guide RNA</td>
</tr>
<tr>
<td>GWAS</td>
<td>genome-wide association study</td>
</tr>
<tr>
<td>HR</td>
<td>homologous recombination</td>
</tr>
<tr>
<td>Hrd1</td>
<td>HMG-CoA reductase degradation protein 1</td>
</tr>
<tr>
<td>Hrd1</td>
<td>HMG-CoA reductase degradation 3</td>
</tr>
<tr>
<td>HSP</td>
<td>heat shock protein</td>
</tr>
<tr>
<td>IRE1</td>
<td>inositol requiring enzyme 1</td>
</tr>
<tr>
<td>IAN</td>
<td>immune-associated nucleotide-binding</td>
</tr>
<tr>
<td>HY5</td>
<td>elongated hypocotyl 5</td>
</tr>
<tr>
<td>mORFs</td>
<td>main open reading frames</td>
</tr>
<tr>
<td>NHEJ</td>
<td>nonhomologous end-joining</td>
</tr>
<tr>
<td>NBT</td>
<td>new breeding techniques</td>
</tr>
<tr>
<td>NF-Y</td>
<td>Nuclear transcription factor Y</td>
</tr>
<tr>
<td>OS9</td>
<td>osteosarcoma amplified 9</td>
</tr>
<tr>
<td>PAWH1</td>
<td>protein associated with Hrd1-1</td>
</tr>
<tr>
<td>PERK</td>
<td>double-stranded RNA-activated protein kinase (PKR)-like endoplasmic reticulum kinase</td>
</tr>
<tr>
<td>PIR1</td>
<td>phosphatase type 2CA (PP2CA)-interacting finger protein 1</td>
</tr>
<tr>
<td>RIDD</td>
<td>regulated IRE1-dependent decay</td>
</tr>
<tr>
<td>RNAi</td>
<td>RNA interference</td>
</tr>
<tr>
<td>SAL1</td>
<td>supernumerary aleurone 1</td>
</tr>
<tr>
<td>Sel1L</td>
<td>suppressor enhancer Lin12 1 like</td>
</tr>
<tr>
<td>S1P</td>
<td>site-1 proteases</td>
</tr>
<tr>
<td>TBF1</td>
<td>TL1-binding transcription factor 1</td>
</tr>
<tr>
<td>TF</td>
<td>transcription factor</td>
</tr>
<tr>
<td>TOR</td>
<td>Target of rapamycin</td>
</tr>
<tr>
<td>TM</td>
<td>tunicamycin</td>
</tr>
<tr>
<td>UBC32</td>
<td>ubiquitin-conjugating enzyme 32</td>
</tr>
<tr>
<td>uORFs</td>
<td>upstream open reading frames</td>
</tr>
<tr>
<td>UPR</td>
<td>unfolded protein response</td>
</tr>
<tr>
<td>UPRE</td>
<td>unfolded protein response element</td>
</tr>
<tr>
<td>UPS</td>
<td>ubiquitin-proteasome system</td>
</tr>
<tr>
<td>UTR</td>
<td>untranslated region</td>
</tr>
<tr>
<td>XBP1.</td>
<td>X-box binding protein 1</td>
</tr>
</tbody>
</table>
</table-wrap>
</glossary>
</back>
</article>