Colibactin

Overview

Colibactin is a genotoxic secondary metabolite produced by certain gut bacteria. It belongs to a family of bacterial toxins known as cyclomodulins, which interfere with the eukaryotic cell cycle.^[1] First identified in 2006 from an Escherichia coli strain (IHE3034) that caused neonatal meningitis, colibactin gained attention for its ability to induce DNA damage in host cells.^[2][3] Unlike many toxins, colibactin’s exact chemical structure remained elusive for years because it is highly unstable and difficult to isolate. Researchers have since determined that it is synthesized by a 54-kilobase “pks” genomic island in the bacterial genome.^[4] This large gene cluster encodes a hybrid assembly line of enzymes that make colibactin, classifying it as a polyketide-nonribosomal peptide natural product.^[5][6]

Colibactin is a DNA-damaging (genotoxic) compound. When certain E. coli (and other bacteria) harboring the pks island infect eukaryotic cells, they trigger chromosomal instability and DNA double-strand breaks, ultimately causing cells to arrest in the G2/M phase of the cell cycle.^[7] Microscopically, affected cells become abnormally enlarged (a cytopathic effect known as megalocytosis), reflecting this cell-cycle arrest.^[8] In epithelial cells, such DNA damage often leads to cellular senescence (permanent growth arrest), whereas in immune cells it can prompt apoptosis (cell death). These effects hint at colibactin’s potential to undermine tissue integrity and immune surveillance. Colibactin-producing bacteria are not rare: the pks island is found in various members of the Enterobacteriaceae family (notably in certain strains of E. coli, as well as some Klebsiella pneumoniae, Enterobacter, and Citrobacter species).^[9] Strains carrying this island are often commensals in the gut microbiome but can also be opportunistic pathogens in blood, brain, or urinary infections. The prevalence of colibactin-producing strains in the human population and their linkage to disease have made colibactin a subject of intense study in microbiome and cancer research.^[10]

How is Colibactin Produced?

Colibactin is produced by a complex biosynthetic pathway encoded in the bacterial pks (or clb) gene cluster. This ~54 kb island comprises 19 genes (named clbA through clbS) that work together to assemble colibactin.^[11] The pathway is a hybrid polyketide synthase–nonribosomal peptide synthetase (PKS-NRPS) system, meaning the bacterium uses enzymes typically reserved for building fatty acid-like chains (PKS) and peptide-like molecules (NRPS) in an integrated assembly line. Through a stepwise process, this enzymatic machinery constructs a precursor molecule known as precolibactin. Key steps include activation of the synthase enzymes by a phosphopantetheinyl transferase (ClbA) and iterative chain elongation by modular PKS and NRPS proteins, which incorporate building blocks like amino acids (e.g. aspartate, cysteine) and acetate units into the growing metabolite.^[12] The pathway’s exact sequence is complex, but in simplified terms, multiple partial structures are synthesized and then dimerized to form precolibactin, a larger inactive precursor.

Mechanism of Action in Human Cells

Colibactin is a microbiome-derived genotoxin produced by pks-positive bacteria that damages host DNA through direct chemical reactivity. Its best-supported primary action is the creation of DNA lesions consistent with interstrand cross-links, which obstruct replication and transcription and can progress to double-strand breaks if not accurately repaired.^[13] Host cells typically respond by activating canonical DNA damage checkpoints, often resulting in G2/M cell-cycle arrest and downstream outcomes such as senescence or apoptosis depending on damage burden and cellular context.^[14] In addition to cross-linking, some evidence suggests secondary amplification mechanisms involving metal ion interactions, oxidative stress, and signalling changes that may further increase genotoxic pressure.^[15] When cells survive but repair is imperfect, colibactin exposure can be recorded as a characteristic mutational pattern, providing a genomic “fingerprint” that has been observed in experimental systems and in subsets of human cancers.

Link to Colorectal Cancer

Colibactin’s ability to damage DNA has made it a suspect in the development of colorectal cancer (CRC), and mounting evidence over the past decade supports a link between colibactin-producing bacteria and colorectal tumorigenesis. Epidemiological and microbiome studies have found that E. coli strains harboring the pks island are significantly enriched in the intestinal tracts of patients with colorectal neoplasia.^[16] For example, one study reported that about 23% of CRC patients carried pks-positive E. coli in their gut, compared to only 7% of healthy individuals.^[17] This association suggest that harboring colibactin-producing bacteria in the colon may increase one’s risk of developing cancer, and they raise the possibility of using the presence of the pks gene cluster as a biomarker for CRC risk.^[18] Notably, researchers showed that even transient exposure to colibactin-producing bacteria can accelerate tumor growth in mice. One mechanism by which this occurs is through colibactin-induced senescence in colon epithelial cells – senescent cells secrete pro-inflammatory and growth factors (a phenomenon known as the senescence-associated secretory phenotype, SASP) that can fertilize the surrounding tissue for tumor expansion.^[19] In other words, colibactin might not only initiate tumorigenic mutations but also create a local microenvironment that promotes cancer development.

Clinical and Research Relevance

The discovery of colibactin’s role in colorectal cancer carries significant clinical and research implications. One immediate consideration is whether the presence of colibactin-producing bacteria could serve as a screening tool or biomarker for CRC risk.^[20] If individuals harboring pks-positive strains are at higher risk, stool or colon biopsy tests for the clb genes might help identify those who could benefit from more vigilant colonoscopic surveillance. Indeed, the pks island has been proposed as a potential biomarker for early detection of colorectal cancer or its precursors. Another avenue is prevention and intervention: since colibactin is a microbial product, it might be possible to mitigate CRC risk by modulating the gut microbiome.^[21] This could involve targeting the colibactin-producing bacteria themselves (for example, using selective antibiotics or bacteriophages to eliminate pks-positive strains, or probiotics to outcompete them) or neutralizing the toxin’s effect. Encouraging proof-of-concept comes from a study that identified small-molecule inhibitors of ClbP, the enzyme required for colibactin activation.^[22] These drug-like compounds (which mimic ClbP’s natural substrates) were shown to block colibactin production; in laboratory experiments and mouse models, they almost completely suppressed colibactin-induced DNA damage and significantly reduced tumor formation in the colon.^[23] This demonstrates that pharmacologically targeting the colibactin pathway is feasible and can translate into decreased cancer-driving effects. In the future, such inhibitors might be developed into chemopreventive treatments for people at high risk of CRC (for instance, those with familial adenomatous polyposis or inflammatory bowel disease, where colibactin-producing E. coli often colonize lesions).

Research Feed

April 9, 2018

Microbes •

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