Escherichia coli, which is part of the normal flora of the human gut, plays a significant yet complex role in regulating intestinal function (Crosby et al., 2019). However, certain strains of E. coli can cause disease in the host, impairing gut function and adversely affecting overall health (Kaper et al., 2004; Vila et al., 2016). The E. coli B2 serogroup harbors the pks gene cluster, which encodes colibactin, a molecule potentially involved in the pathogenicity of the disease-causing strains in the gut (Abram et al., 2021; Gatya Al-Mayahie et al., 2022). However, the mechanism underlying its production in E. coli is complex, and the function of the pks gene cluster remains to be fully elucidated. Recent findings suggest that colibactin can induce DNA damage and genomic instability in human intestinal cells, leading to cellular aging and increased intestinal permeability, and may be important in the development of colorectal cancer (CRC) (Dougherty and Jobin, 2021; Dubinsky et al., 2020; Miyasaka et al., 2024; Tang-Fichaux et al., 2021). Nevertheless, as a secondary metabolite of E. coli, colibactin is structurally unstable and difficult to isolate, presenting a significant challenge to investigating the mechanisms underlying its actions. Previous reviews on PKS Island have largely focused on the structure, regulatory mechanisms, and tumorigenic mechanisms of colibactin (Chagneau et al., 2022). However, these articles lack in-depth descriptions of the production of colibactin and its mechanisms of inducing colorectal cancer. This article delves into the origin of colibactin, its biosynthetic pathway, and the mechanisms by which it induces colorectal tumors, with a particular focus on unraveling the genetic aspects of colibactin-induced tumorigenesis, thereby providing a foundation for further investigation into the effects of colibactin on human diseases.

E. coli belongs to the family Enterobacteriaceae within the class γ-Proteobacteria. It primarily colonizes the intestines of humans and animals and inhibits the colonization of other bacteria (Crosby et al., 2019). Although it plays a vital role in the intestine, E. coli has also been isolated from patients with bloodstream and urinary tract infections. The actions of E. coli are multifaceted, colonizing the gastrointestinal tract as a commensal bacterium, while also acting as a pathogen to elicit a spectrum of symptoms in organs, such as the gastrointestinal and urinary systems (Kaper et al., 2004; Vila et al., 2016).

E. coli can be classified into distinct phylogenetic groups, namely A, B1, B2, D, E, F, and the closely related groups C and G based on its genetic characteristics and developmental traits (Abram et al., 2021). Group B2 is noted for the increased adherence and invasion of its strains into intestinal cells, potentially contributing to bacterial colonization in CRC tumor tissue. Strains of group B2 harbor virulence-associated genes, increasing their potential cytotoxicity, thereby leading to cell death and inflammatory responses (Gatya Al-Mayahie et al., 2022; Nouri et al., 2016).

Depending on the site of colonization, E. coli strains are categorized into extraintestinal pathogenic Enterobacteriaceae (ExPEC) and intestinal pathogenic Enterobacteriaceae (InPEC). ExPEC strains primarily colonize extraintestinal organs, such as the peritoneum, vagina, cervix, urinary tract, and bloodstream, causing infection at these sites (Jang et al., 2017; Sharma et al., 2016; Vogeleer et al., 2014). Conversely, InPEC strains primarily inhabit the gastrointestinal tract and are associated with gastrointestinal diseases, including diarrhea, constipation, inflammatory bowel disease, and irritable bowel syndrome. These strains produce toxins and are classified based on their pathogenic characteristics and mechanisms (Alizade et al., 2019; Jang et al., 2017). InPEC group strains frequently exhibit a regional distribution pattern, and their contamination of food and water frequently leads to outbreaks of related diseases in developing countries, but they rarely cause extraintestinal infections and are less likely to colonize a healthy host (Alizade et al., 2019; Farrokh et al., 2013; Flores-Mireles et al., 2015).

The most prominent subgroup within the InPEC group is colibactin-producing E. coli (pEPEC) (Oliero et al., 2022; Taoum et al., 2022). Recent evidence suggests that the colonization of pEPEC in the gastrointestinal tract may be a significant contributing factor to the development of gastrointestinal tumors. Moreover, E. coli strains isolated from patients with colonic tumors exhibit a significantly higher potential of colicin production (Tariq et al., 2022; Yoshikawa et al., 2020; Zhou S. et al., 2021; Zhou T. et al., 2021).

The hybrid non-ribosomal peptide synthetase-polyketide synthetase (NRPS-PKS) biosynthetic gene cluster, known as the pks or clb island, comprises 19 genes (clb A–S), which encode three PKSs, three NRPSs, two NRPS/PKS hybrids, MATE transporters, resistance genes, and nine additional trimming and accessory enzymes (Tang J. W. et al., 2022; Tang S. et al., 2022). These enzymes participate in the biosynthetic pathway of colibactin, a peptidoglycan-genotoxin polyketide (Kalantari et al., 2023; Wong et al., 2022; Xia et al., 2020). Colibactin is produced by specific strains of E. coli and related bacteria, such as Klebsiella pneumoniae, Citrobacter koseri, and Enterobacter cloacae, collectively known as pks + strains (colibactin-producing E. coli) (Kalantari et al., 2023; Tang J. W. et al., 2022; Tang S. et al., 2022). The pks island, containing virulence-associated genes, features a unique genetic locus and is often linked to mobile genetic elements. It is approximately 54–56 kb in size and may vary among different pks-positive strains. Moreover, the number of base pairs is not uniform. In bacteria, it can exist as a mobile element, such as transposons, plasmids, and other elements, facilitating transfer between different bacterial species. Alternatively, it can integrate into the genome of the bacterial species. It encodes a mixture of colibactin and other metabolites and intermediates, influencing host-pathogen interactions (Vizcaino et al., 2014).

The pks island is predominantly found in E. coli strains of the B2 group but is also present in strains from groups A and B1, each with distinct genetic structures, indicating multiple introduction mechanisms into E. coli. Recent studies indicated a higher prevalence of pks + E. coli in CRC patients than in healthy individuals. Nouri et al. (2021) identified pks in 23% of CRC patients compared to 7.1% in the control group, corroborating prior findings by Buc et al. (2013) who detected the gene in 39.5% of CRC patients and 12.9% of diverticulosis patients. Thus, the pks island is a potential biomarker for CRC development. Moreover, it is highly conserved across various Enterobacteriaceae species and performs diverse functions beyond its potential role in CRC development (Chagneau et al., 2022).

Research on colibactin began in 2006 when Nougayrede infected eukaryotic cells with E. coli B2, which blocked mitosis and induced megakaryocyte proliferation, characteristics associated with the widespread pks island. This island encodes numerous non-ribosomal peptide and polyketide synthetases, causing DNA double-strand breaks (DSBs) and activating DNA damage checkpoint pathways, which lead to cell cycle arrest and cell death (Nougayrède et al., 2006). As already mentioned, colibactin is linked to human health (Silpe et al., 2022). However, despite its significant biological activities, it has not been isolated and structurally characterized by traditional methods, and thus information on its chemical structure mainly comes from bioinformatics and biochemical analyses.

The instability, low yield, and complex biosynthetic process of colibactin have posed significant challenges for structural elucidation (Bian et al., 2013; Brotherton and Balskus, 2013). In vitro infection with E. coli harboring the clb island induces DSBs in human cells, resulting in cell cycle arrest and subsequent cell death (Nougayrède et al., 2006). Physiological studies indicate that clb + bacteria cause DNA damage and genomic instability in intestinal cells in vivo, leading to cellular senescence (Cougnoux et al., 2014; Secher et al., 2013), increased intestinal permeability (Payros et al., 2014), and colorectal tumor formation in chronic intestinal inflammation mouse models (Cougnoux et al., 2014; Tomkovich et al., 2017). Notably, evidence suggests that pEPEC is associated with CRC (Dougherty and Jobin, 2021; Dubinsky et al., 2020; Miyasaka et al., 2024; Tang-Fichaux et al., 2021).

Current research on colibactin has become relatively in-depth, with its role in inducing DSBs in DNA likely being an important mechanism for tumorigenesis, especially in CRC. Colibactin-related tumorigenic activities have also been detected in other tumors. Moreover, colibactin exhibits pathogenic effects in non-tumor diseases, but its elusive signaling pathways and a lack of full understanding of its mechanisms pose challenges. As an unstable secondary metabolite with low yield and a complex biosynthetic process, colibactin cannot be directly isolated from the producing E. coli, making structural elucidation and subsequent in-depth research on its mechanism of action highly challenging. Furthermore, the mechanisms by which E. coli produces colibactin, particularly the release and hydrolysis of colibactin, are not fully understood, highlighting the importance of further exploration of its biosynthetic mechanism for drug development.