Protein versatility reflects the versatility of plant phenotypes, since proteins are directly involved in biological processes shaping plant phenotypes. Plant genome sequencing programs revealed a relatively low number of protein-coding genes (e.g., around 27,000 protein-coding genes in Arabidopsis thaliana genome) with respect to the number of different functional proteins present in plant cells, tissues, or even at whole-organism level [more than 100,000 different functional protein species and around 25 billion protein molecules are estimated to be present in Arabidopsis mesophyll cell by Heinemann et al. (2020)], thus, it is evident that complexity at the levels “gene” → “transcript” → “protein” rises due to the fact that a single gene can produce multiple functional proteins via an array of posttranscriptional and posttranslational modifications (Figure 1). It is, thus, evident that plant response to environmental cues at proteome level cannot be simply derived from transcriptome data. All proteins encoded by a single gene are termed proteoforms (Smith et al., 2013).

Basically, two major categories of functional proteins derived from a given gene can be distinguished: “protein isoforms,” which differ in their primary protein sequence, and “protein posttranslational modifications (PTMs),” which differ in modifications of side amino acid residues ranging from a few atoms (nitrosylation, carbonylation) to whole peptides (S-glutathionylation, ubiquitinylation, sumoylation). In addition, alterations in protein/enzyme conformation in response to ligand/substrate interaction can be considered another kind of proteoforms. Differences in primary protein sequences among protein isoforms lead to differential molecular weight (MW), while conjugation of charged molecules or residues leads to altered isoelectric point (pI) values in differential PTMs. Since differential protein isoforms and PTMs often acquire differential biological functions, studying different protein isoforms and PTMs is of high importance for understanding protein functions. Methods based on 2-DE and its modifications are suitable for studies on protein isoforms and PTMs because of protein separation according to pI and MW values. Moreover, some specialized 2-DE gel-based protocols on PTMs detection were developed including either specific staining such as phosphoprotein detection by ProQ Diamond stain or PTM-specific primary antibody such as immunoblot detection of carbonylated proteins modified by dinitrophenylhydrazine (DNPH) to dinitrophenylhydrazones by a specific primary antibody [Oxyblot kit; Levine et al. (1990)], biotin-switch technique (BST) for detection of S-nitrosylated proteins (Jaffrey and Snyder, 2001) or concanavalin A lectin blot for glycoprotein detection (Hashiguchi and Komatsu, 2016) and immunoprecipitation methods for S-glutathionylated proteins detection (Butturini et al., 2019). However, the dominant methods for proteoforms detection represent MS/MS-based approaches, such as TMT labeling for phosphoprotein detection. Recently, an excellent review on MS-based approaches used for PTM identifications was published by Virág et al. (2020). Since only a relatively small fraction of a given protein undergoes PTM, the modified proteins reveal low abundances and have to be enriched in the protein samples; for example, ZrO₂- or TiO₂-IMAC beads are used for phosphoprotein enrichment. Approaches of immune affinity chromatography using specific anti-PTM primary antibodies are also widely used for PTM enrichment. However, the differential accumulation patterns and biological functions of different proteoforms that raised from a single gene indicate an urgent need to study plant responses to environmental cues at the proteome and PTMome levels to understand the plant phenotype under stress.

Plants as sessile organisms have developed evolutionary mechanisms to adapt to adverse environmental conditions imposing stress responses. Stress-adaptive responses involve several alterations in plant water regime (dehydration stress), redox homeostasis (enhanced risk of redox stress as a consequence of alterations in plant metabolism leading to enhanced levels of RMS) and altered physio-biochemical properties of biomolecules (e.g., altered fluidity of cellular membranes under low or high temperatures). Proteomics studies found out that these alterations are underlied by differences at proteome level including not only differential protein relative accumulation, but also differential spectrum of proteoforms.

Recently, it became evident that stress-induced alterations in protein relative abundance represent just one aspect of plant proteome stress responses, and that modifications at posttranscriptional and posttranslational levels leading to differential protein isoforms and PTMs, respectively, add another layer to the complexity and fine tuning of the plant stress response (Barua et al., 2019). The impacts of differential protein abundance patterns, structural modifications, such as isoforms and PTMs, cellular localization, and interacting partners in plant responses to environmental stresses were already discussed in recent reviews (Wang and Komatsu, 2016a; Kosová et al., 2018, 2021). Basic literature information on most studied protein PTMs in crop plants under abiotic stress was reviewed by Hashiguchi and Komatsu (2016) and Mustafa and Komatsu (2021) with a major focus on protein phosphorylation, glycosylation, acetylation, and succinylation, and by Wu et al. (2016) with a major focus on phosphorylation, ubiquitination and sumoylation, and most studied redox modifications such as protein carbonylation and S-nitrosylation. Recently, the role of PTMs in plant-pathogen interactions was reviewed by Gough and Sadanandom (2021) with a focus on phosphorylation, ubiquitination, and SUMoylation. Specialized reviews on plant protein phosphorylation under both abiotic and biotic stress signaling (Rampitsch and Bykova, 2012), rice phosphoproteomics studies (Ajadi et al., 2020), sumoylation (Benlloch and Lois, 2018), and nitrosylation (Romero-Puertas et al., 2013; Feng et al., 2019) were also published. A review focused on selected posttranscriptional and posttranslational regulations of drought and heat stress responses in plants with a focus on alternative splicing, RNA-mediated silencing, and ubiquitination and sumoylation protein modifications was published by Guerra et al. (2015).

The aim of this review is to provide a basic overview of the diversity and versatility of proteoforms derived from a single gene in order to emphasize the necessity of studying differences in protein isoforms and PTMs to understand protein biological functions. Proteoforms, i.e., multiple functional proteins derived from a single gene, highlight the necessity to study plant phenotypic response at proteome level, since it cannot be simply derived from transcriptome data. Examples of the impacts of diverse posttranscriptional and posttranslational modifications on the diversity of proteoforms arised from a single gene with respect to their biological functions are provided.

Protein isoforms can either arise from a single gene via posttranscriptional modifications such as alternative splicing or RNA editing or they can represent products of homologous genes including both orthologous and paralogous genes. Orthologous genes represent homologs of a given gene in genomes of another plant species, while paralogous genes represent homologous genes that are products of the local multiplication of a given sequence in a single genome. As an example of gene paralogs, cluster of CBF genes at Fr2 locus on the long arm of homoeologous group 5 chromosomes in Triticeae can be given (Tondelli et al., 2011). Several important crops, such as bread wheat, potato, oilseed rape, banana, and others, which are allopolyploids, contain whole sets of homeologous genomes; thus, they contain homeologous genes. Homeologs are pairs of genes that originated by speciation and are brought back together by allopolyploidization (Glover et al., 2016). In addition to sequence homeology, the array of protein isoforms can be significantly increased by the mechanism of alternative splicing, giving rise to multiple functional proteins from a single gene. Alternative splicing, thus, represents an efficient evolutionary mechanism of enhancing phenotypic variation in response to environmental cues (Shang et al., 2017). Mechanisms of isoform differentiation at the transcript level are not included in this study, since we focus on proteins and their biological functions.

Protein isoforms can reveal differential biological functions because of differential expression patterns, differential cellular localization, differential protein interaction partners, and others. Some examples of functional diversification of isoformic proteins are provided below:

Transcriptome and proteome reprogramming under stress: non-canonical histone isoforms were found to play important roles in transcriptome reprogramming under stress. Alterations in transcript expression between canonical H2A and cold-induced H2AZ histone isoforms affecting nucleosome structure and DNA wrapping underlying transcriptome remodeling under cold acclimation were observed in A. thaliana (Kumar and Wigge, 2010) as well as in winter barley crowns (Janská et al., 2011). At proteome level, Martinez-Seidel et al. (2021) reported differential ribosomal proteins paralogs underlying alterations at ribosomal level and proteome reprogramming in barley root tip meristems subjected to cold acclimation.

Differential gene copy number determining quantitative differences in gene expression and quantitative phenotypic traits: Knox et al. (2010) and Würschum et al. (2017) revealed that the quantitative differences in acquired frost tolerance achieved by winter vs. spring Triticeae genotypes are associated with a higher copy number of CBF genes encoded by frost-tolerant winter genotypes with respect to the spring ones.

Differential expression patterns and differential interaction protein partners: Hsc70 protein is known as a cochaperone involved in protein folding. Hsc70-1 and Hsc70-3 isoforms are constitutively expressed, while Hsc70-2 isoform is pathogen-inducible and forms a complex with SGT1 protein involved in R-gene mediated resistance (Noël et al., 2007).

RubisCO activase (RCA) is crucial for maintaining the high carboxylation activity of RubisCO, since it removes pentosephosphates inhibiting the formation of carbamate critical for RubisCO carboxylation activity from RubisCO active site. Wang et al. (2020) studied RCA isoforms in relatively heat-tolerant Rhododendron hainanense. It encodes 3 RCA homologous genes named RCA1, RCA2, and RCA3, and each of them can give rise to multiple isoforms via a mechanism of alternative splicing (RCA1, RCA2 and RCA3 can potentially encode 5, 3, and 2 isoforms, respectively). While RCA2 and RCA3 isoforms are constitutively expressed, RCA1 isoforms are heat-inducible (especially the RCA1-X1 isoform) and persist in plants in recovery following a heat stress treatment; thus, they seem to provide some type of epigenetic stress memory involved in heat stress acclimation; enhanced levels of RCA1 persisting in plants reveal an improvement effect on plant photosynthesis when exposed to stress (Wang et al., 2020).

Differential cellular localization: Differential functions were described for nuclear isoforms and cytoplasmic (plastid, mitochondrial) isoforms of glycolytic enzymes. The nuclear isoform of fructose-bisphosphate aldolase (FBA) is known to act as a DNA-binding protein involved in regulation of expression of its own gene as well as other genes (Ronai et al., 1992). The nuclear isoform of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is known to act as a tRNA-binding protein involved in tRNA export (Singh and Green, 1993). It has also been reported that FBA may be involved in the integration of intra- and extracellular signals associated with growth, development, and sugar biosynthesis (Li et al., 2012), and that non-the phosphorylating isoform of GAPDH may be involved in regulation of ROS levels (Bustos et al., 2008). The nuclear isoform of enolase encoded by Los2 locus in A. thaliana functions as a transcriptional repressor of STZ/ZAT10, which is a repressor of cold-inducible CBF pathway; the nuclear isoform of enolase, thus, acts as an indirect positive regulator of CBF pathway and CBF-regulated COR gene expression (Lee et al., 2002). Tonoplast-associated isoforms of aldolase and enolase are involved in the activation of V-ATPase in salt-treated Mesembryanthemum crystallinum plants, leading to Na⁺ vacuolar accumulation (Barkla et al., 2009).

Differential regulatory functions: Cytoplasmic eIF5A is known as a translation initiation factor involved in the regulation of protein biosynthesis. However, nuclear eIF5A isoforms named eIF5A-1 and eIF5A-2 were reported to be involved in the regulation of cell cycle with eIF5A-1 involved in a “switch” between cell proliferation and cell death, with eIF5A-1 leading to programmed cell death (PCD) while eIF5A-2 enhancing cell proliferation (Thompson et al., 2004).

Different cofactors and cellular localizations: Upon stress, a risk of ROS production in aerobic metabolism increases because of imbalances between the kinetics of electrontransport processes (respiratory electron transport chain, photosynthetic electrontransport chain) and the following enzymatic reactions. To diminish the harmful effects of ROS overproduction, plants express a wide array of several redox metabolism-related enzymes in order to finely tune their final levels. ROS levels are, thus, controlled by different peroxiredoxin (Prx) and thioredoxin (Trx) isoforms ensuring a fine tuning of redox processes in photosynthesis and respiratory electron transport chains in inner chloroplast and mitochondrial membranes, respectively. Superoxide dismutase (SOD) isoforms represent a well-known ROS scavenging enzyme with different cofactor ions and cellular localizations: Cu/Zn-SOD-cytoplasmic; Fe-SOD-plastid; Mn-SOD-mitochondrial localization. Several isoforms of ROS-scavenging enzymes, thus, provide fine tuning and control of oxidative stress, which is ubiquitously associated with aerobic metabolism localized to semiautonomous organelles, i.e., photosynthetic and respiratory electron transport chains localized in inner chloroplast and mitochondrial membranes, respectively (Meyer et al., 2005; Dietz, 2016).

Different isoforms form different cellular structures and reveal differential protein-protein interactions: Kijima et al. (2018) studied differential actin isoforms in A. thaliana and found that the A. thaliana genome encodes eight actin isoforms, out of which three (AtACT2, AtACT7, and AtACT8) are expressed at the vegetative stage while the remaining five (AtACT1, AtACT3, AtACT4, AtACT11, and AtACT12) are expressed at reproductive stage. They also found out that two vegetative actin isoforms, AtACT2 and AtACT7, form different types of filaments, with AtACT2 forming thinner filaments while AtACT7 forming thick bundles. They also reveal a different expression upon stress and interact with different actin-binding proteins (ABPs).

Examples of functional diversification of plant protein isoforms in plant stress responses are given in Table 1.

Protein posttranslational modifications (PTMs) involve all modifications of side amino acid residues occurring in nascent proteins and ranging from a few atoms, such as carbonyl or nitrosyl groups to whole peptides such as S-glutathione, ubiquitin, and SUMO. Currently, over 300 different PTMs were reported, such as phosphorylation, N- and O-glycosylation; reactive molecular species (RMS)-related modifications, such as glycation, carbonylation, nitrosylation, and others; peptide modifications, such as ubiquitylation and sumoylation, as well as acylation modifications of lysine residues such as succinylation (Xu W. et al., 2017) and crotonylation (Xu Y. et al., 2017). Protein PTMs range from single-step spontaneous non-enzymatic amino acid modifications by RMS, such as protein carbonylation or nitrosylation to large PTMs resulting from highly coordinated multi-step enzymatic processes, such as protein N-glycosylation or ubiquitination. An overview of most studied PTMs, such as target amino acids and added functional groups, is given in Table 2. Since recent articles revealed differential alterations in plant total proteome and PTMome in response to a given biological process (He et al., 2020), it is necessary to study plant responses to a given cue such as environmental stresses at PTMome level. Different PTMs result in differential modulation of protein biological functions; for example, regarding E3 RING-type ubiquitin ligase PARKIN, it was reported that nitrosylation decreases while persulfidation increases its ubiquitination capacity in mammalian neurons (Vandiver et al., 2013).

When studying protein PTMs, it has to be kept in mind that only a fraction of a given protein undergoes a given PTM and that the given PTM could be reversible and transient, i.e., to occur for a limited time, as it is evident for proteins in signaling cascades associated with transient phosphorylation/dephosphorylation events or for some RMS-mediated PTMs, which act as a signal indicating plant protein damage under stress. Moreover, a given amino acid residue can undergo multiple PTMs depending on the kind of stress; thus, the problem of PTM crosstalk has to be studied. In addition, only a few studies dealt with the impacts of combined stress treatments, which are common in the field conditions on plant protein PTM patterns. The results of the few studies indicate that plant response to combined stress is associated with a unique PTM pattern in comparison to the effects of single stress factors (Hu et al., 2015b).

The concept of PTM “writers,” “erasers,” and “readers” was proposed by Leutert et al. (2021). PTM mechanisms consist of “writers,” i.e., enzymes catalyzing the addition of the PTM group to a target amino acid residue (kinases, ubiquitin ligases, acylases,…); “erasers,” i.e., enzymes catalyzing reversible removal of a given PTM from a target amino acid residue (phosphatases, deubiquitinases, deacetylases,…); and “readers,” i.e., all proteins interacting with the given PTM.

Accumulation of the data from tandem MS/MS identifications on protein PTMs led to the development of specific databases and prediction tools for most studied PTMs. Plant protein PTMs are specifically mapped by the Plant PTM Viewer¹, an integrative PTM resource database providing data on 19 PTM types (Willems et al., 2019), which currently contains PTMs data from five plant species, A. thaliana (165,279 PTMs in 55,988 proteins), Chlamydomonas reinhardtii (18,070 PTMs in 5,951 proteins), Oryza sativa ssp. japonica (56,606 PTMs in 19,500 proteins), Triticum aestivum (53,580 PTMs in 25,150 proteins), and Zea mays (143,869 PTMs in 37,099 proteins) (accessed 3rd November, 2021). MultiPTMs prediction tools, such as PTMscape (Li et al., 2018) and PTM-ssMP web server (Liu et al., 2018) utilizing information on site-specific profiles and enabling the identification of potential target motifs for multiple kinds of PTMs such as phosphorylation, acetylation, methylation, O-glycosylation, ubiquitination, and sumoylation, are available. Moreover, prediction tools for the most studied PTMs, such as PhosphoSitePlus (PSP) (Hornbeck et al., 2015), PHOSIDA (Gnad et al., 2011) for phosphoprotein detection, and UbiSite, as a web tool for ubiquitination prediction (Huang et al., 2016), etc., are available.

A brief overview of major high-throughput proteomic studies focused on stress-responsive PTMomes is provided in Table 3. In addition to the PTMs described below, other PTMs, such as protein C-terminal amidation or monomeric and polymeric ADP-ribosylation (MARylation and PARylation, linear or branched), are emerging to play an important role in plant innate immunity and plant-bacterial pathogen interactions. However, elucidation of their roles in plant responses to bacterial pathogens and biotic stress deserves further study (Feng et al., 2016).

In addition to covalent PTMs, non-covalent protein modifications such as protein/enzyme cofactors and/or substrates resulting in different protein/enzyme conformations represent a further level leading to novel functional proteoforms. Proteins/enzymes with multiple cofactors/substrates, probably the most studied plant enzyme with multiple substrates and multiple catalytic functions, is RubisCO, i.e., ribulose-1,5-bisphosphate carboxylase/oxygenase, which can bind either CO₂ or O₂ as competing substrate and, thus, catalyze either carboxylation or oxygenation of the substrate ribulose-1,5-bisphosphate. RubisCO needs RubisCO activase (RCA) to activate the RubisCO active site for CO₂ binding.

Enzymes can modify their affinity to a substrate based on ambient substrate concentration. In oligomeric enzymes with multiple catalytic sites, allosteric effect occurs, i.e., transition of the catalytic site from a low-affinity state to a high-affinity state is transmitted from one subunit to the other. Allosteric regulation, thus, means the spatial effect of the subunit on the others in oligomeric enzymes. This type of regulation of the affinity of the binding site is not possible in monomeric enzymes. However, it was also found that in monomeric enzymes, such as glucokinase, increasing glucose concentration as a substrate leads to an increased shift of the enzyme from low-affinity to high-affinity state analogously to the allosteric regulation in oligomeric enzymes (Whittington et al., 2015). As substrate concentration increases, the probability of encountering other substrate molecules after turnover also increases, thus preventing the enzyme from relaxing back to the low-affinity state. This time-dependent shift in the ratio of low-affinity to high-affinity enzyme proteoforms with respect to increased substrate concentration is called allokairy (Hilser et al., 2015). Mnemonical enzymes are monomeric enzymes that can retain high-affinity conformation after product release when substrate levels increase in an ambient environment (Ricard et al., 1974). The shifts between enzyme low-affinity and high-affinity states, such as allokairy in monomeric human glucokinase, play an important role in disease development (Whittington et al., 2015). However, to the best of our knowledge, no analogous research has been published for plant enzymes.

Proteins are directly involved in plant responses to environmental cues. Mechanisms of posttranscriptional and posttranslational modifications of protein primary sequence and encoded amino acid residues, respectively, resulting in multiple functional proteins (proteoforms) derived from a single gene. Mechanisms of posttranscriptional and posttranslational modifications increase phenotypic variability with respect to genetic information encoded by the genome. Duplications of local genomic regions, as well as whole genome duplications, and the presence of multiple genomes in polyploid species lead to paralogous and orthologous genes, respectively, which can undergo functional diversifications represented by differential expression patterns. From a biochemical point of view, the twenty gene-encoded amino acids represent a very diverse set of chemical species such as non-polar (hydrophobic) amino acids with aliphatic (alanine, leucine, isoleucine, valine) or aromatic (phenylalanine) side chains as well as both acidic (aspartic and glutamic acid) and basic (lysine, arginine, asparagine, glutamine) groups. The coded amino acids can, thus, undergo several modifications resulting in altered properties. Some PTMs represent a result of a series of spatially and temporally coordinated enzymatic reactions (phosphorylation, N-glycosylation, succinylation, crotonylation, ubiquitination, sumoylation), while others occur spontaneously (PTMs arising from reactions with RMS such as oxidation, glycation, and S-nitrosylation). The level of spontaneous PTMs rises under environmental stress because of imbalances in cellular metabolism, leading to enhanced formation of reactive molecular species (RMS). RMS-mediated PTMs can result in loss of target protein biological activity, but they also serve as a signal-inducing stress response (Chaki et al., 2011, 2013; Camejo et al., 2013; Mock and Dietz, 2016).

It has to be summarized that PTMs represent a modification of only a relatively small fraction of the given protein; moreover, the modification is often reversible and/or transient, and the resulting PTM, thus, acts as a transient signal of the given stress cue, which is the case of phosphorylation and RMS-induced PTMs. Several proteins can undergo multiple PTMs under the given stress treatment, e.g., calreticulin was reported to undergo both phosphorylation and N-glycosylation in cold-treated rice leaf sheaths (Komatsu et al., 2009). Moreover, the same protein can undergo the same kind of PTM in different target motifs under different stress treatments; for example, differential phosphomotifs were identified in the same phosphoproteins in maize phosphoproteome under drought, heat, and their combination (Hu et al., 2015b). All these factors determine the protein’s biological activity.

The major roles of differential protein isoforms and PTMs in plant cells subjected to stress could be summarized as follows (Table 4):

Signaling and signal transduction: Stress-induced signal is transduced and amplified via reversible phosphorylation in protein kinase cascade. The reversibility of phosphorylation enables efficient regulation of signal spread and switching off of it when target cellular mechanisms are activated (Yamaguchi-Shinozaki and Shinozaki, 2006).

Transcriptome/proteome reprogramming under stress: Expression of differential histone isoforms and PTMs underlying modular reprogramming of plant transcriptome under stress enables expression of whole arrays of newly induced transcripts (Kumar and Wigge, 2010; Janská et al., 2011); ribosomal isoforms underlying proteome reprogramming under stress (Martinez-Seidel et al., 2021).

PTMs of histones and transcription-associated proteins determine the preparedness of stress memory-related genes to prompt transcription under repeated stress events resulting in enhanced stress tolerance. Stress memory mechanisms include both target gene repressions, such as FLC repression in A. thaliana by H3K9me2 and H3K27me3 followed by polycomb group proteins binding (Sung and Amasino, 2005), and target genes activation such as H3K4me3 and H3 acetylation in association with VRN1 gene activation in Triticeae following vernalization fulfillment (Oliver et al., 2009).

Differential isoforms and PTMs underlie differential enzymatic kinetics/activity and protein-protein interactions under stress treatments. These modifications are crucial for the final protein biological function. For example, the level of O-GlcNAc modification at Thr17 in TaGRP2 glycine-rich RNA binding protein determines its interaction with VER2 Jacalin lectin protein, resulting in TaGRP2 dissociation from VRN1 pre-mRNA first intron and induction of VRN1 transcript accumulation (Xiao et al., 2014). Phosphorylation of penultimate Thr in plasma membrane H⁺-ATPase leads to binding to phosphorylated C-terminus in 14-3-3 protein involved in the regulation of stomatal aperture in guard cells of A. thaliana rosette leaves (Hayashi et al., 2011). In salinity signaling, a physical interaction of myristoylated Ca²⁺-binding protein SOS3 with a Ser/Thr protein kinase SOS2 leads to SOS3-SOS2 complex formation and SOS2-mediated phosphorylation of SOS1 plasma membrane-localized Na⁺/H⁺ antiporter, resulting in its activation (Sanchez-Barrena et al., 2007). In addition, it was found that SOS2 activity is modulated by the phosphorylation status of 14-3-3 protein. Phosphorylated 14-3-3 protein inhibits SOS2 kinase activity, while 14-3-3 dephosphorylation upon salt stress leads to SOS2 activation (Yu et al., 2016).

Differential peroxiredoxin (Prx) and thioredoxin (Trx) isoforms finely tune redox reactions at the end of electrontransport chains in inner membranes of chloroplast and mitochondria. RubisCO activase (RCA) isoforms were found to finely tune RubisCO activity in heat-treated Rhododendron (Wang et al., 2020).

Besides modulation of enzyme activity, protein isoforms and PTMs are also involved in the modulation of structural protein properties such as chaperone Hsc70 isoforms determining other protein conformations and interactions (Noël et al., 2007), and actin isoforms underlying altered thickness of actin filaments (Kijima et al., 2018); altered patterns of N-glycosylation in cell wall proteins were found in salt-treated A. thaliana (Liu et al., 2021).

It can be concluded that protein isoforms and PTMs are involved in a broad scale of biological processes ranging from cell signaling, transcriptome reprogramming, protein expression, and protein/enzyme function/activity to stress memory mechanisms. Proteoforms represent most probably a universal means of how plants can modulate their biological processes in response to environmental cues; however, the current state of knowledge is far from being complete. Some examples of cellular processes affected by protein isoforms and PTMs in plant responses to environmental stresses are given in Figure 2.

Mechanisms of protein posttranscriptional and posttranslational modifications, thus, represent an efficient means of enhancing biological variability in response to variability in an ambient environment. It is, thus, becoming evident that just the sole identification of protein primary sequence encoded by a given gene does not fully define protein final structure and biological activity. In plants, the study of proteoforms is in its beginnings; however, from comparisons of the diversity of some plant proteins, such as Arabidopsis actin isoforms, with their human homologs, i.e., non-muscle actins, it is evident that plant isoforms reveal greater sequence variability than human isoforms that may reflect the greater diversity of environmental factors that plants, as sessile organisms, have to face during their life cycle (Kijima et al., 2018). When interpreting proteomic results, we have to consider differential proteoforms that can be derived from the identified protein and can reveal differential biological functions. The study of proteoforms, thus, indicates that proteome represents a specific level of an organism that cannot be derived from the simple transformation of the transcriptome. The study of proteoforms also represents a key to understanding the versatility of plant responses to environmental cues such as abiotic and biotic stresses.

KK outlined the idea and prepared the draft manuscript text. PV prepared the figures and tables. PV, MK, IP, and JR actively searched for relevant literature, suggested comments on the manuscript draft, and read and approved the final version of the manuscript. All authors contributed to the article and approved the submitted version.

The 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.

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