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Lowry E, Mitchell A. Colibactin-induced damage in bacteria is cell contact independent. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.600066. [PMID: 38948699 PMCID: PMC11212979 DOI: 10.1101/2024.06.21.600066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The bacterial toxin colibactin, produced primarily by the B2 phylogroup of Escherichia coli, underlies some cases of colorectal cancers. Colibactin crosslinks DNA and induces genotoxic damage in both mammalian and bacterial cells. While the mechanisms facilitating colibactin delivery remain unclear, results from multiple studies supported a delivery model that necessitates cell-cell contact. We directly tested this requirement in bacterial cultures by monitoring the spatiotemporal dynamics of the DNA damage response using a fluorescent transcriptional reporter. We found that in mixed-cell populations, DNA damage saturated within twelve hours and was detectable even in reporter cells separated from colibactin producers by hundreds of microns. Experiments with distinctly separated producer and reporter colonies revealed that the intensity of DNA damage decays similarly with distance regardless of colony contact. Our work reveals that cell contact is inconsequential for colibactin delivery in bacteria and suggests that contact-dependence needs to be reexamined in mammalian cells as well. Importance Colibactin is a bacteria-produced toxin that binds and damages DNA. It has been widely studied in mammalian cells due to its potential role in tumorigenesis. However, fundamental questions about its impact in bacteria remain underexplored. We used E. coli as a model system to study colibactin toxicity in neighboring bacteria and directly tested if cell-cell contact is required for toxicity, as has previously been proposed. We found that colibactin can induce DNA damage in bacteria hundreds of microns away and that the intensity of DNA damage presents similarly regardless of cell-cell contact. Our work further suggests that the requirement for cell-cell contact for colibactin-induced toxicity also needs to be reevaluated in mammalian cells.
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2
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Lv C, Abdullah M, Chen W, Zhou N, Cheng Z, Chen Y, Li M, Simpson KW, Elsaadi A, Zhu Y, Lipkin SM, Chang YF. Genomic characterization of Escherichia coli harbor a polyketide synthase ( pks ) island associated with colorectal cancer (CRC) development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.16.599199. [PMID: 38948848 PMCID: PMC11212869 DOI: 10.1101/2024.06.16.599199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The E. coli strain harboring the polyketide synthase ( Pks) island encodes the genotoxin colibactin, a secondary metabolite reported to have severe implications for human health and for the progression of colorectal cancer. The present study involved whole-genome-wide comparison and phylogenetic analysis of pks harboring E. coli isolates to gain insight into the distribution and evolution of these organism. Fifteen E. coli strains isolated from patients with ulcerative colitis were sequenced, 13 of which harbored pks islands. In addition, 2,654 genomes from the public database were also screened for pks harboring E. coli genomes, 158 of which were pks -positive isolates. Whole-genome-wide comparison and phylogenetic analysis revealed that 171 (158+13) pks -positive isolates belonged to phylogroup B2, and most of the isolates associated to sequence types ST73 and ST95. One isolate from an ulcerative colitis (UC) patient was of the sequence type ST8303. The maximum likelihood tree based on the core genome of pks -positive isolates revealed horizontal gene transfer across sequence types and serotypes. Virulome and resistome analyses revealed the preponderance of virulence genes and a reduced number of antimicrobial genes in Pks -positive isolates. This study strongly contributes to understanding the evolution of pks islands in E. coli .
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Morgado S, Fonseca É, Freitas F, Caldart R, Vicente AC. In-depth analysis of Klebsiella aerogenes resistome, virulome and plasmidome worldwide. Sci Rep 2024; 14:6538. [PMID: 38503805 PMCID: PMC10951357 DOI: 10.1038/s41598-024-57245-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 03/15/2024] [Indexed: 03/21/2024] Open
Abstract
Klebsiella aerogenes is an emergent pathogen associated with outbreaks of carbapenem-resistant strains. To date, studies focusing on K. aerogenes have been small-scale and/or geographically restricted. Here, we analyzed the epidemiology, resistome, virulome, and plasmidome of this species based on 561 genomes, spanning all continents. Furthermore, we sequenced four new strains from Brazil (mostly from the Amazon region). Dozens of STs occur worldwide, but the pandemic clones ST93 and ST4 have prevailed in several countries. Almost all genomes were clinical, however, most of them did not carry ESBL or carbapenemases, instead, they carried chromosomal alterations (omp36, ampD, ampG, ampR) associated with resistance to β-lactams. Integrons were also identified, presenting gene cassettes not yet reported in this species (blaIMP, blaVIM, blaGES). Considering the virulence loci, the yersiniabactin and colibactin operons were found in the ICEKp10 element, which is disseminated in genomes of several STs, as well as an incomplete salmochelin cluster. In contrast, the aerobactin hypervirulence trait was observed only in one ST432 genome. Plasmids were common, mainly from the ColRNAI replicon, with some carrying resistance genes (mcr, blaTEM, blaNDM, blaIMP, blaKPC, blaVIM) and virulence genes (EAST1, senB). Interestingly, 172 genomes of different STs presented putative plasmids containing the colicin gene.
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Affiliation(s)
- Sergio Morgado
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil.
| | - Érica Fonseca
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
| | - Fernanda Freitas
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
| | - Raquel Caldart
- Centro de Ciências da Saúde, Universidade Federal de Roraima, Boa Vista, RR, 69300-000, Brazil
| | - Ana Carolina Vicente
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
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4
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de Souza JB, de Almeida Campos LA, Palácio SB, Brelaz-de-Castro MCA, Cavalcanti IMF. Prevalence and implications of pKs-positive Escherichia coli in colorectal cancer. Life Sci 2024; 341:122462. [PMID: 38281542 DOI: 10.1016/j.lfs.2024.122462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/13/2024] [Accepted: 01/23/2024] [Indexed: 01/30/2024]
Abstract
Colorectal cancer (CRC) remains a significant global health concern, necessitating continuous investigation into its etiology and potential risk factors. Recent research has shed light on the potential role of pKs-positive Escherichia coli (pKs + E. coli) and colibactin in the development and progression of CRC. Therefore, this review aimed to provide an updated analysis of the prevalence and implications of pKs + E. coli in colorectal cancer. We conducted a literature review search in major scientific databases to identify relevant studies exploring the association between pKs + E. coli and CRC. The search strategy included studies published up to the present date, and articles were carefully selected based on predefined inclusion criteria. Thus, the present study encompasses scientific evidence from clinical and epidemiological studies supporting the presence of pKs + E. coli in CRC patients, demonstrating a consistent and significant association in multiple studies. Furthermore, we highlighted the potential mechanisms by which colibactin may promote tumorigenesis and cancer progression within the colorectal mucosa, including the production of genotoxic virulence factors. Additionally, we explored current diagnostic methods for detecting pKs + E. coli in clinical settings, emphasizing the importance of accurate identification. Moreover, we discussed future strategies that could utilize the presence of this strain as a biomarker for CRC diagnosis and treatment. In conclusion, this review consolidated existing evidence on the prevalence and implications of pKs + E. coli in colorectal cancer. The findings underscore the importance of further research to elucidate the precise mechanisms linking this strain to CRC pathogenesis and to explore its potential as a therapeutic target or diagnostic marker. Ultimately, a better understanding of the role of pKs + E. coli in CRC may pave the way for innovative strategies in CRC management and patient care.
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Affiliation(s)
| | | | - Sarah Brandão Palácio
- Research, development and innovation subdivision (SDPI) of Chemical-Pharmaceutical Laboratory of Aeronautics (LAQFA), Rio de Janeiro, RJ, Brazil
| | | | - Isabella Macário Ferro Cavalcanti
- Keizo Asami Institute (iLIKA), Federal University of Pernambuco (UFPE), Recife, PE, Brazil; Academic Center of Vitória (CAV), Federal University of Pernambuco (UFPE), Vitória de Santo Antão, PE, Brazil.
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5
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Addington E, Sandalli S, Roe AJ. Current understandings of colibactin regulation. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001427. [PMID: 38314762 PMCID: PMC10924459 DOI: 10.1099/mic.0.001427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/12/2024] [Indexed: 02/07/2024]
Abstract
The biosynthetic machinery for the production of colibactin is encoded by 19 genes (clbA - S) within the pks pathogenicity island harboured by many E. coli of the B2-phylogroup. Colibactin is a potent genotoxic metabolite which causes DNA-damage and which has potential roles in microbial competition and fitness of pks+ bacteria. Colibactin has also been strongly implicated in the development of colorectal cancer. Given the genotoxicity of colibactin and the metabolic cost of its synthesis, the regulatory system governing the clb cluster is accordingly highly complex, and many of the mechanisms remain to be elucidated. In this review we summarise the current understanding of regulation of colibactin biosynthesis by internal molecular components and how these factors are modulated by signals from the external environment.
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Affiliation(s)
- Emily Addington
- School of Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Scotland, UK
| | - Sofia Sandalli
- School of Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Scotland, UK
| | - Andrew J. Roe
- School of Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Scotland, UK
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6
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Altshuller M, He X, MacKrell EJ, Wernke KM, Wong JWH, Sellés-Baiget S, Wang TY, Chou TF, Duxin JP, Balskus EP, Herzon SB, Semlow DR. The Fanconi anemia pathway repairs colibactin-induced DNA interstrand cross-links. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.30.576698. [PMID: 38352618 PMCID: PMC10862771 DOI: 10.1101/2024.01.30.576698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Colibactin is a secondary metabolite produced by bacteria present in the human gut and is implicated in the progression of colorectal cancer and inflammatory bowel disease. This genotoxin alkylates deoxyadenosines on opposite strands of host cell DNA to produce DNA interstrand cross-links (ICLs) that block DNA replication. While cells have evolved multiple mechanisms to resolve ("unhook") ICLs encountered by the replication machinery, little is known about which of these pathways promote resistance to colibactin-induced ICLs. Here, we use Xenopus egg extracts to investigate replication-coupled repair of plasmids engineered to contain site-specific colibactin-ICLs. We show that replication fork stalling at a colibactin-ICL leads to replisome disassembly and activation of the Fanconi anemia ICL repair pathway, which unhooks the colibactin-ICL through nucleolytic incisions. These incisions generate a DNA double-strand break intermediate in one sister chromatid, which can be repaired by homologous recombination, and a monoadduct ("ICL remnant") in the other. Our data indicate that translesion synthesis past the colibactin-ICL remnant depends on Polη and a Polκ-REV1-Polζ polymerase complex. Although translesion synthesis past colibactin-induced DNA damage is frequently error-free, it can introduce T>N point mutations that partially recapitulate the mutation signature associated with colibactin exposure in vivo. Taken together, our work provides a biochemical framework for understanding how cells tolerate a naturally-occurring and clinically-relevant ICL.
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Affiliation(s)
- Maria Altshuller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Xu He
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Elliot J. MacKrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kevin M. Wernke
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Joel W. H. Wong
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Selene Sellés-Baiget
- TheNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ting-Yu Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Julien P. Duxin
- TheNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Seth B. Herzon
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Daniel R. Semlow
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
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7
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Bosveli A, Griboura N, Kampouropoulos I, Kalaitzakis D, Montagnon T, Vassilikogiannakis G. The Rapid Synthesis of Colibactin Warhead Model Compounds Using New Metal-Free Photocatalytic Cyclopropanation Reactions Facilitates the Investigation of Biological Mechanisms. Chemistry 2023; 29:e202301713. [PMID: 37452669 DOI: 10.1002/chem.202301713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/06/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Herein, we report the synthesis of a series of colibactin warhead model compounds using two newly developed metal-free photocatalytic cyclopropanation reactions. These mild cyclopropanations expand the known applications of eosin within synthesis. A halogen atom transfer reaction mode has been harnessed so that dihalides can be used as the cyclopropanating agents. The colibactin warhead models were then used to provide new insight into two key mechanisms in colibactin chemistry. An explanation is provided for why the colibactin warhead sometimes undergoes a ring expansion-addition reaction to give fused cyclobutyl products while at other times nucleophiles add directly to the cyclopropyl unit (as when DNA adds to colibactin). Finally, we provide some evidence that Cu(II) chelated to colibactin may catalyze an important oxidation of the colibactin-DNA adduct. The Cu(I) generated as a result could then also play a role in inducing double strand breaks in DNA.
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Affiliation(s)
- Artemis Bosveli
- Department of Chemistry, University of Crete, Vasilika Vouton, 71003, Iraklion, Crete
| | - Nefeli Griboura
- Department of Chemistry, University of Crete, Vasilika Vouton, 71003, Iraklion, Crete
| | | | - Dimitris Kalaitzakis
- Department of Chemistry, University of Crete, Vasilika Vouton, 71003, Iraklion, Crete
| | - Tamsyn Montagnon
- Department of Chemistry, University of Crete, Vasilika Vouton, 71003, Iraklion, Crete
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8
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Tripathi P, Mousa JJ, Guntaka NS, Bruner SD. Structural basis of the amidase ClbL central to the biosynthesis of the genotoxin colibactin. Acta Crystallogr D Struct Biol 2023; 79:830-836. [PMID: 37561403 PMCID: PMC10478638 DOI: 10.1107/s2059798323005703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/28/2023] [Indexed: 08/11/2023] Open
Abstract
Colibactin is a genotoxic natural product produced by select commensal bacteria in the human gut microbiota. The compound is a bis-electrophile that is predicted to form interstrand DNA cross-links in target cells, leading to double-strand DNA breaks. The biosynthesis of colibactin is carried out by a mixed NRPS-PKS assembly line with several noncanonical features. An amidase, ClbL, plays a key role in the pathway, catalyzing the final step in the formation of the pseudodimeric scaffold. ClbL couples α-aminoketone and β-ketothioester intermediates attached to separate carrier domains on the NRPS-PKS assembly. Here, the 1.9 Å resolution structure of ClbL is reported, providing a structural basis for this key step in the colibactin biosynthetic pathway. The structure reveals an open hydrophobic active site surrounded by flexible loops, and comparison with homologous amidases supports its unusual function and predicts macromolecular interactions with pathway carrier-protein substrates. Modeling protein-protein interactions supports a predicted molecular basis for enzyme-carrier domain interactions. Overall, the work provides structural insight into this unique enzyme that is central to the biosynthesis of colibactin.
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Affiliation(s)
| | - Jarrod J. Mousa
- Department of Chemistry, University of Florida, Gainesville, FL 32601, USA
| | | | - Steven D. Bruner
- Department of Chemistry, University of Florida, Gainesville, FL 32601, USA
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9
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Dougherty MW, Valdés-Mas R, Wernke KM, Gharaibeh RZ, Yang Y, Brant JO, Riva A, Muehlbauer M, Elinav E, Puschhof J, Herzon SB, Jobin C. The microbial genotoxin colibactin exacerbates mismatch repair mutations in colorectal tumors. Neoplasia 2023; 43:100918. [PMID: 37499275 PMCID: PMC10413156 DOI: 10.1016/j.neo.2023.100918] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 07/29/2023]
Abstract
Certain Enterobacteriaceae strains contain a 54-kb biosynthetic gene cluster referred to as "pks" encoding the biosynthesis of a secondary metabolite, colibactin. Colibactin-producing E. coli promote colorectal cancer (CRC) in preclinical models, and in vitro induce a specific mutational signature that is also detected in human CRC genomes. Yet, how colibactin exposure affects the mutational landscape of CRC in vivo remains unclear. Here we show that colibactin-producing E. coli-driven colonic tumors in mice have a significantly higher SBS burden and a larger percentage of these mutations can be attributed to a signature associated with mismatch repair deficiency (MMRd; SBS15), compared to tumors developed in the presence of colibactin-deficient E. coli. We found that the synthetic colibactin 742 but not an inactive analog 746 causes DNA damage and induces transcriptional activation of p53 and senescence signaling pathways in non-transformed human colonic epithelial cells. In MMRd colon cancer cells (HCT 116), chronic exposure to 742 resulted in the upregulation of BRCA1, Fanconi anemia, and MMR signaling pathways as revealed by global transcriptomic analysis. This was accompanied by increased T>N single-base substitutions (SBS) attributed to the proposed pks+E. coli signature (SBS88), reactive oxygen species (SBS17), and mismatch-repair deficiency (SBS44). A significant co-occurrence between MMRd SBS44 and pks-associated SBS88 signature was observed in a large cohort of human CRC patients (n=2,945), and significantly more SBS44 mutations were found when SBS88 was also detected. Collectively, these findings reveal the host response mechanisms underlying colibactin genotoxic activity and suggest that colibactin may exacerbate MMRd-associated mutations.
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Affiliation(s)
- Michael W Dougherty
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Rafael Valdés-Mas
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, IL, Israel
| | - Kevin M Wernke
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Raad Z Gharaibeh
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Ye Yang
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Jason O Brant
- Department of Biostatistics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Alberto Riva
- Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Marcus Muehlbauer
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Eran Elinav
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, IL, Israel; Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Heidelberg, DE, Germany
| | - Jens Puschhof
- Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Heidelberg, DE, Germany
| | - Seth B Herzon
- Department of Biostatistics, University of Florida College of Medicine, Gainesville, FL, USA; Departments of Pharmacology and Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - Christian Jobin
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA; Department of Infectious Diseases and Immunology, University of Florida College of Medicine, Gainesville, FL, USA; Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, USA.
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10
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Jans M, Kolata M, Blancke G, Ciers M, Dohlman AB, Kusakabe T, Sze M, Thiran A, Berx G, Tejpar S, van Loo G, Iliev ID, Remaut H, Vereecke L. Colibactin-induced genotoxicity and colorectal cancer exacerbation critically depends on adhesin-mediated epithelial binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553526. [PMID: 37645947 PMCID: PMC10462063 DOI: 10.1101/2023.08.16.553526] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Various bacteria are suggested to contribute to colorectal cancer (CRC) development, including pks+ E. coli which produce the genotoxin colibactin that induces characteristic mutational signatures in host epithelial cells. It remains unclear how the highly unstable colibactin molecule is able to access host epithelial cells and its DNA to cause harm. Using the microbiota-dependent ZEB2-transgenic mouse model of invasive CRC, we found that pks+ E. coli drives CRC exacerbation and tissue invasion in a colibactin-dependent manner. Using isogenic mutant strains, we further demonstrate that CRC exacerbation critically depends on expression of the E. coli type-1 pilus adhesin FimH and the F9-pilus adhesin FmlH. Blocking bacterial adhesion using a pharmacological FimH inhibitor attenuates colibactin-mediated genotoxicity and CRC exacerbation. Together, we show that the oncogenic potential of pks+ E. coli critically depends on bacterial adhesion to host epithelial cells and is critically mediated by specific bacterial adhesins. Adhesin-mediated epithelial binding subsequently allows production of the genotoxin colibactin in close proximity to host epithelial cells, which promotes DNA damage and drives CRC development. These findings present promising therapeutic avenues for the development of anti-adhesive therapies aiming at mitigating colibactin-induced DNA damage and inhibiting the initiation and progression of CRC, particularly in individuals at risk for developing CRC.
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11
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Lozenov S, Krastev B, Nikolaev G, Peshevska-Sekulovska M, Peruhova M, Velikova T. Gut Microbiome Composition and Its Metabolites Are a Key Regulating Factor for Malignant Transformation, Metastasis and Antitumor Immunity. Int J Mol Sci 2023; 24:ijms24065978. [PMID: 36983053 PMCID: PMC10054493 DOI: 10.3390/ijms24065978] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/14/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
The genetic and metabolomic abundance of the microbiome exemplifies that the microbiome comprises a more extensive set of genes than the entire human genome, which justifies the numerous metabolic and immunological interactions between the gut microbiota, macroorganisms and immune processes. These interactions have local and systemic impacts that can influence the pathological process of carcinogenesis. The latter can be promoted, enhanced or inhibited by the interactions between the microbiota and the host. This review aimed to present evidence that interactions between the host and the gut microbiota might be a significant exogenic factor for cancer predisposition. It is beyond doubt that the cross-talk between microbiota and the host cells in terms of epigenetic modifications can regulate gene expression patterns and influence cell fate in both beneficial and adverse directions for the host's health. Furthermore, bacterial metabolites could shift pro- and anti-tumor processes in one direction or another. However, the exact mechanisms behind these interactions are elusive and require large-scale omics studies to better understand and possibly discover new therapeutic approaches for cancer.
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Affiliation(s)
- Stefan Lozenov
- Laboratory for Control and Monitoring of the Antibiotic Resistance, National Centre for Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd, 1504 Sofia, Bulgaria
| | - Boris Krastev
- Nadezhda Paradise Medical Center, 1330 Sofia, Bulgaria
| | - Georgi Nikolaev
- Department of Cell and Developmental Biology, Faculty of Biology, Sofia University "St. Kliment Ohridski", 1504 Sofia, Bulgaria
| | - Monika Peshevska-Sekulovska
- Department of Gastroenterology, University Hospital Lozenetz, Sofia, Medical Faculty, Sofia University "St. Kliment Ohridski", 1407 Sofia, Bulgaria
| | - Milena Peruhova
- Department of Gastroenterology, University Hospital Heart and Brain, 5804 Pleven, Bulgaria
| | - Tsvetelina Velikova
- Medical Faculty, Sofia University St. Kliment Ohridski, Kozyak 1 str., 1407 Sofia, Bulgaria
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12
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Zhou T, Ando T, Kudo A, Sato M, Miyoshi N, Mutoh M, Ishikawa H, Wakabayashi K, Watanabe K. Screening method toward ClbP-specific inhibitors. Genes Environ 2023; 45:8. [PMID: 36797758 PMCID: PMC9933310 DOI: 10.1186/s41021-023-00264-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/09/2023] [Indexed: 02/18/2023] Open
Abstract
BACKGROUND Colibactin is a genotoxin produced by Escherichia coli and other Enterobacteriaceae that is believed to increase the risk of colorectal cancer (CRC) of their symbiosis hosts, including human. A peptidase ClbP is the key enzyme for activation of colibactin. Inhibition of ClbP is considered to impede maturation of precolibactin into genotoxic colibactin. Therefore, ClbP-specific inhibitors could potentially prevent the onset of CRC, one of the leading causes of cancer-related deaths in the world. This study intends to establish an efficient screening system for identifying inhibitors that are specific to ClbP. METHODS Two types of assays were applied in the screening procedure: a probe assay and an LC-MS assay. For the probe assay, we employed the synthesized probe which we described in our previous report. This probe can be hydrolyzed efficiently by ClbP to release a fluorophore. Hence it was applied here for detection of inhibition of ClbP. For the LC-MS assay, formation of the byproduct of precolibactin maturation process, N-myristoyl-D-asparagine, was quantified using a liquid chromatography-mass spectrometry (LC-MS) technique. The probe assay can be performed much faster, while the LC-MS assay is more accurate. Therefore, our method employed the two assays in sequence to screen a large number of compounds for inhibition of ClbP. RESULTS A library of 67,965 standard compounds was evaluated by the screening method established in the current study, and one compound was found to show a moderate inhibitory activity against ClbP. CONCLUSION A simple screening method for ClbP-specific inhibitors was established. It was proven to be reliable and is believed to be useful in developing potential prophylactic agents for CRC.
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Affiliation(s)
- Tao Zhou
- Adenoprevent Co., Ltd., Shizuoka, 422-8526 Japan ,grid.469280.10000 0000 9209 9298Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526 Japan
| | - Takayuki Ando
- Department of Pharmaceutical and Food Science, Shizuoka Institution of Environment and Hygiene, Fujieda, 426-0083 Japan
| | - Akihiro Kudo
- Department of Pharmaceutical and Food Science, Shizuoka Institution of Environment and Hygiene, Fujieda, 426-0083 Japan
| | - Michio Sato
- grid.469280.10000 0000 9209 9298Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526 Japan
| | - Noriyuki Miyoshi
- grid.469280.10000 0000 9209 9298Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, 422-8526 Japan
| | - Michihiro Mutoh
- grid.272458.e0000 0001 0667 4960Department of Molecular-Targeting Cancer Prevention, Kyoto Prefectural University of Medicine, Kyoto, 602-8566 Japan
| | - Hideki Ishikawa
- grid.272458.e0000 0001 0667 4960Department of Molecular-Targeting Cancer Prevention, Kyoto Prefectural University of Medicine, Kyoto, 602-8566 Japan
| | - Keiji Wakabayashi
- grid.469280.10000 0000 9209 9298Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka, 422-8526 Japan
| | - Kenji Watanabe
- Adenoprevent Co., Ltd., Shizuoka, 422-8526, Japan. .,Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan.
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13
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Velilla JA, Kenney GE, Gaudet R. Structure and function of prodrug-activating peptidases. Biochimie 2023; 205:124-135. [PMID: 36803695 PMCID: PMC10030199 DOI: 10.1016/j.biochi.2022.07.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/25/2022] [Indexed: 11/11/2022]
Abstract
Bacteria protect themselves from the toxicity of antimicrobial metabolites they produce through several strategies. In one resistance mechanism, bacteria assemble a non-toxic precursor on an N-acyl-d-asparagine prodrug motif in the cytoplasm, then export it to the periplasm where a dedicated d-amino peptidase hydrolyzes the prodrug motif. These prodrug-activating peptidases contain an N-terminal periplasmic S12 hydrolase domain and C-terminal transmembrane domains (TMDs) of varying lengths: type I peptidases contain three transmembrane helices, and type II peptidases have an additional C-terminal ABC half-transporter. We review studies which have addressed the role of the TMD in function, the substrate specificity, and the biological assembly of ClbP, the type I peptidase that activates colibactin. We use modeling and sequence analyses to extend those insights to other prodrug-activating peptidases and ClbP-like proteins which are not part of prodrug resistance gene clusters. These ClbP-like proteins may play roles in the biosynthesis or degradation of other natural products, including antibiotics, may adopt different TMD folds, and have different substrate specificity compared to prodrug-activating homologs. Finally, we review the data supporting the long-standing hypothesis that ClbP interacts with transporters in the cell and that this association is important for the export of other natural products. Future investigations of this hypothesis as well as of the structure and function of type II peptidases will provide a complete account of the role of prodrug-activating peptidases in the activation and secretion of bacterial toxins.
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Affiliation(s)
- José A Velilla
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford St, Cambridge, MA, 02138, USA
| | - Grace E Kenney
- Department of Chemistry and Chemical Biology, Harvard University, 38 Oxford St, Cambridge, MA, USA
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford St, Cambridge, MA, 02138, USA.
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14
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Velilla JA, Volpe MR, Kenney GE, Walsh RM, Balskus EP, Gaudet R. Structural basis of colibactin activation by the ClbP peptidase. Nat Chem Biol 2023; 19:151-158. [PMID: 36253550 PMCID: PMC9889268 DOI: 10.1038/s41589-022-01142-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 08/12/2022] [Indexed: 02/04/2023]
Abstract
Colibactin, a DNA cross-linking agent produced by gut bacteria, is implicated in colorectal cancer. Its biosynthesis uses a prodrug resistance mechanism: a non-toxic precursor assembled in the cytoplasm is activated after export to the periplasm. This activation is mediated by ClbP, an inner-membrane peptidase with an N-terminal periplasmic catalytic domain and a C-terminal three-helix transmembrane domain. Although the transmembrane domain is required for colibactin activation, its role in catalysis is unclear. Our structure of full-length ClbP bound to a product analog reveals an interdomain interface important for substrate binding and enzyme stability and interactions that explain the selectivity of ClbP for the N-acyl-D-asparagine prodrug motif. Based on structural and biochemical evidence, we propose that ClbP dimerizes to form an extended substrate-binding site that can accommodate a pseudodimeric precolibactin with its two terminal prodrug motifs in the two ClbP active sites, thus enabling the coordinated activation of both electrophilic warheads.
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Affiliation(s)
- José A Velilla
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Matthew R Volpe
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Grace E Kenney
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Richard M Walsh
- Harvard Cryo-EM Center for Structural Biology, Harvard Medical School, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
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15
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Gaab ME, Lozano PO, Ibañez D, Manese KD, Riego FM, Tiongco RE, Albano PM. A Meta-Analysis on the Association of Colibactin-Producing pks+ Escherichia coli with the Development of Colorectal Cancer. Lab Med 2023; 54:75-82. [PMID: 35960765 DOI: 10.1093/labmed/lmac072] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
OBJECTIVE Previous studies on the association between pks+Escherichia coli and colorectal cancer (CRC) demonstrated conflicting results. Hence, we performed a meta-analysis to obtain more precise estimates. METHODS Related literature was obtained from PubMed, ScienceDirect, Google Scholar, and Cochrane Library. Data were then extracted, summarized, and subjected to analysis using Review Manager 5.4 by computing for the pooled odds ratios at the 95% confidence interval. RESULTS Overall analysis showed that individuals carrying pks+E coli had a greater risk of developing CRC. Subgroup analysis further showed that individuals from Western countries carrying pks+E coli and individuals with pks+E coli in their tissue samples had increased risk of developing CRC. CONCLUSION Results of this meta-analysis suggest that individuals with pks+E coli have a greater risk of developing CRC. However, more studies are needed to confirm our claims.
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Affiliation(s)
- Marcianne Elaine Gaab
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
| | - Prim Olivette Lozano
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
| | - Danica Ibañez
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
| | - Korina Diane Manese
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
| | - Fatima May Riego
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
| | - Raphael Enrique Tiongco
- Department of Medical Technology, College of Allied Medical Professions, Angeles University Foundation, Angeles City, Philippines
| | - Pia Marie Albano
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines.,Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
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16
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Dougherty MW, Jobin C. Intestinal bacteria and colorectal cancer: etiology and treatment. Gut Microbes 2023; 15:2185028. [PMID: 36927206 PMCID: PMC10026918 DOI: 10.1080/19490976.2023.2185028] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/17/2023] [Indexed: 03/18/2023] Open
Abstract
The etiology of colorectal cancer (CRC) is influenced by bacterial communities that colonize the gastrointestinal tract. These microorganisms derive essential nutrients from indigestible dietary or host-derived compounds and activate molecular signaling pathways necessary for normal tissue and immune function. Associative and mechanistic studies have identified bacterial species whose presence may increase CRC risk, including notable examples such as Fusobacterium nucleatum, Enterotoxigenic Bacteroides fragilis, and pks+ E. coli. In recent years this work has expanded in scope to include aspects of host mutational status, intra-tumoral microbial heterogeneity, transient infection, and the cumulative influence of multiple carcinogenic bacteria after sequential or co-colonization. In this review, we will provide an updated overview of how host-bacteria interactions influence CRC development, how this knowledge may be utilized to diagnose or prevent CRC, and how the gut microbiome influences CRC treatment efficacy.
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Affiliation(s)
- Michael W. Dougherty
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Christian Jobin
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
- Department of Infectious Diseases and Immunology, University of Florida College of Medicine, Gainesville, FL, USA
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, USA
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17
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Enterotoxin tilimycin from gut-resident Klebsiella promotes mutational evolution and antibiotic resistance in mice. Nat Microbiol 2022; 7:1834-1848. [PMID: 36289400 PMCID: PMC9613472 DOI: 10.1038/s41564-022-01260-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 09/29/2022] [Indexed: 11/20/2022]
Abstract
Klebsiella spp. that secrete the DNA-alkylating enterotoxin tilimycin colonize the human intestinal tract. Numbers of toxigenic bacteria increase during antibiotic use, and the resulting accumulation of tilimycin in the intestinal lumen damages the epithelium via genetic instability and apoptosis. Here we examine the impact of this genotoxin on the gut ecosystem. 16S rRNA sequencing of faecal samples from mice colonized with Klebsiella oxytoca strains and mechanistic analyses show that tilimycin is a pro-mutagenic antibiotic affecting multiple phyla. Transient synthesis of tilimycin in the murine gut antagonized niche competitors, reduced microbial richness and altered taxonomic composition of the microbiota both during and following exposure. Moreover, tilimycin secretion increased rates of mutagenesis in co-resident opportunistic pathogens such as Klebsiella pneumoniae and Escherichia coli, as shown by de novo acquisition of antibiotic resistance. We conclude that tilimycin is a bacterial mutagen, and flares of genotoxic Klebsiella have the potential to drive the emergence of resistance, destabilize the gut microbiota and shape its evolutionary trajectory. Production of the enterotoxin tilimycin by gut-resident Klebsiella species can alter gut microbiota composition, induce mutational evolution and drive the emergence of antibiotic resistance in mice.
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18
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Mousa WK. The microbiome-product colibactin hits unique cellular targets mediating host–microbe interaction. Front Pharmacol 2022; 13:958012. [PMID: 36172175 PMCID: PMC9510844 DOI: 10.3389/fphar.2022.958012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/18/2022] [Indexed: 11/20/2022] Open
Abstract
The human microbiota produces molecules that are evolved to interact with the diverse cellular machinery of both the host and microbes, mediating health and diseases. One of the most puzzling microbiome molecules is colibactin, a genotoxin encoded in some commensal and extraintestinal microbes and is implicated in initiating colorectal cancer. The colibactin cluster was discovered more than 15 years ago, and most of the research studies have been focused on revealing the biosynthesis and precise structure of the cryptic encoded molecule(s) and the mechanism of carcinogenesis. In 2022, the Balskus group revealed that colibactin not only hits targets in the eukaryotic cell machinery but also in the prokaryotic cell. To that end, colibactin crosslinks the DNA resulting in activation of the SOS signaling pathway, leading to prophage induction from bacterial lysogens and modulation of virulence genes in pathogenic species. These unique activities of colibactin highlight its ecological role in shaping gut microbial communities and further consequences that impact human health. This review dives in-depth into the molecular mechanisms underpinning colibactin cellular targets in eukaryotic and prokaryotic cells, aiming to understand the fine details of the role of secreted microbiome chemistry in mediating host–microbe and microbe–microbe interactions. This understanding translates into a better realization of microbiome potential and how this could be advanced to future microbiome-based therapeutics or diagnostic biomarkers.
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Affiliation(s)
- Walaa K. Mousa
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- College of Pharmacy, Mansoura University, Mansoura, Egypt
- *Correspondence: Walaa K. Mousa,
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19
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Abstract
Bacterial genotoxins are peptide or protein virulence factors produced by several pathogens, which make single-strand breaks (SSBs) and/or double-strand DNA breaks (DSBs) in the target host cells. If host DNA inflictions are not resolved on time, host cell apoptosis, cell senescence, and/or even bacterial pathogen-related cancer may occur. Two multi-protein AB toxins, cytolethal distending toxin (CDT) produced by over 30 bacterial pathogens and typhoid toxin from Salmonella Typhi, as well as small polyketide-peptides named colibactin that causes the DNA interstrand cross-linking and subsequent DSBs is the most well-characterized bacterial genotoxins. Using these three examples, this review discusses the mechanisms by which these toxins deliver themselves into the nucleus of the target host cells and exert their genotoxic functions at the structural and functional levels.
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Affiliation(s)
- Liaoqi Du
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Jeongmin Song
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
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20
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Hirayama Y, Sato M, Watanabe K. Advancing the Biosynthetic and Chemical Understanding of the Carcinogenic Risk Factor Colibactin and Its Producers. Biochemistry 2022; 61:2782-2790. [PMID: 35723977 DOI: 10.1021/acs.biochem.2c00229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent studies have shown that Escherichia coli often carries a biosynthetic gene cluster termed either the pks island or the clb cluster that allows the production of a genotoxic polyketide-nonribosomal peptide hybrid secondary metabolite called colibactin. While the gene cluster is not always expressed, when the strain that resides in the colon produces the genotoxin, it is suspected to become a risk factor for colorectal cancer. Therefore, there is great interest in devising a simple method for the detection of colibactin-producing strains and understanding the detailed mechanism of how colibactin can induce oncogenesis, to develop convenient early screening methods and possible preventive treatments against colorectal cancer. However, the definitive chemical structure of colibactin remained elusive until recently, primarily due to its low yield and instability. In this review, we will briefly trace the recent studies leading to the identification of the structure of the active intact colibactin. Subsequently, we will describe our efforts toward developing simple methods for detecting colibactin producers, where we established methods based on the conventional polymerase chain reaction and loop-mediated isothermal amplification techniques. We also designed an activity-based fluorogenic probe for detecting colibactin-producing strains that could discern colibactin production levels among the E. coli strains screened. Using the probe, we isolated a wild-type high-colibactin-producing strain from a colorectal cancer tissue sample that proved to be valuable in identifying new colibactin metabolites and structurally characterizing them by nuclear magnetic resonance. Those techniques and the chemical insight they furnished should improve the fight against colorectal cancer.
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Affiliation(s)
- Yuichiro Hirayama
- Department of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Tobetsu 061-0293, Japan
| | - Michio Sato
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
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21
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Fobofou SA, Savidge T. Microbial metabolites: cause or consequence in gastrointestinal disease? Am J Physiol Gastrointest Liver Physiol 2022; 322:G535-G552. [PMID: 35271353 PMCID: PMC9054261 DOI: 10.1152/ajpgi.00008.2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 01/31/2023]
Abstract
Systems biology studies have established that changes in gastrointestinal microbiome composition and function can adversely impact host physiology. Notable diseases synonymously associated with dysbiosis include inflammatory bowel diseases, cancer, metabolic disorders, and opportunistic and recurrent pathogen infections. However, there is a scarcity of mechanistic data that advances our understanding of taxonomic correlations with pathophysiological host-microbiome interactions. Generally, to survive a hostile gut environment, microbes are highly metabolically active and produce trans-kingdom signaling molecules to interact with competing microorganisms and the host. These specialized metabolites likely play important homeostatic roles, and identifying disease-specific taxa and their effector pathways can provide better strategies for diagnosis, treatment, and prevention, as well as the discovery of innovative therapeutics. The signaling role of microbial biotransformation products such as bile acids, short-chain fatty acids, polysaccharides, and dietary tryptophan is increasingly recognized, but little is known about the identity and function of metabolites that are synthesized by microbial biosynthetic gene clusters, including ribosomally synthesized and posttranslationally modified peptides (RiPPs), nonribosomal peptides (NRPs), polyketides (PKs), PK-NRP hybrids, and terpenes. Here we consider how bioactive natural products directly encoded by the human microbiome can contribute to the pathophysiology of gastrointestinal disease, cancer, autoimmune, antimicrobial-resistant bacterial and viral infections (including COVID-19). We also present strategies used to discover these compounds and the biological activities they exhibit, with consideration of therapeutic interventions that could emerge from understanding molecular causation in gut microbiome research.
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Affiliation(s)
- Serge Alain Fobofou
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas
| | - Tor Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas
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22
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Tang JW, Liu X, Ye W, Li ZR, Qian PY. Biosynthesis and bioactivities of microbial genotoxin colibactins. Nat Prod Rep 2022; 39:991-1014. [PMID: 35288725 DOI: 10.1039/d1np00050k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Covering: up to 2021Colibactin(s), a group of secondary metabolites produced by the pks island (clb cluster) of Escherichia coli, shows genotoxicity relevant to colorectal cancer and thus significantly affects human health. Over the last 15 years, substantial efforts have been exerted to reveal the molecular structure of colibactin, but progress is slow owing to its instability, low titer, and elusive and complex biosynthesis logic. Fortunately, benefiting from the discovery of the prodrug mechanism, over 40 precursors of colibactin have been reported. Some key biosynthesis genes located on the pks island have also been characterised. Using an integrated bioinformatics, metabolomics, and chemical synthesis approach, researchers have recently characterised the structure and possible biosynthesis processes of colibactin, thereby providing new insights into the unique biosynthesis logic and the underlying mechanism of the biological activity of colibactin. Early developments in the study of colibactin have been summarised in several previous reviews covering various study periods, whereas the two most recent reviews have focused primarily on the chemical synthesis of colibactin. The present review aims to provide an update on the biosynthesis and bioactivities of colibactin.
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Affiliation(s)
- Jian-Wei Tang
- Department of Ocean Science, Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China. .,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
| | - Xin Liu
- Department of Ocean Science, Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China. .,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
| | - Wei Ye
- Department of Ocean Science, Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China. .,State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Zhong-Rui Li
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Pei-Yuan Qian
- Department of Ocean Science, Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China. .,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
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23
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Ballén V, Gabasa Y, Ratia C, Sánchez M, Soto S. Correlation Between Antimicrobial Resistance, Virulence Determinants and Biofilm Formation Ability Among Extraintestinal Pathogenic Escherichia coli Strains Isolated in Catalonia, Spain. Front Microbiol 2022; 12:803862. [PMID: 35087504 PMCID: PMC8786794 DOI: 10.3389/fmicb.2021.803862] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/09/2021] [Indexed: 01/29/2023] Open
Abstract
Escherichia coli is a well-characterized bacterium highly prevalent in the human intestinal tract and the cause of many important infections. The aim of this study was to characterize 376 extraintestinal pathogenic E. coli strains collected from four hospitals in Catalonia (Spain) between 2016 and 2017 in terms of antimicrobial resistance, siderophore production, phylogroup classification, and the presence of selected virulence and antimicrobial resistance genes. In addition, the association between these characteristics and the ability to form biofilms was also analyzed. The strains studied were classified into four groups according to their biofilm formation ability: non-biofilm formers (15.7%), weak (23.1%), moderate (35.6%), and strong biofilm formers (25.6%). The strains were highly resistant to ciprofloxacin (48.7%), trimethoprim-sulfamethoxazole (47.9%), and ampicillin (38%), showing a correlation between higher resistance to ciprofloxacin and lower biofilm production. Seventy-three strains (19.4%) were ESBL-producers. However, no relationship between the presence of ESBL and biofilm formation was found. The virulence factor genes fimH (92%), pgaA (84.6%), and irp1 (77.1%) were the most prevalent in all the studied strains. A statistically significant correlation was found between biofilm formation and the presence of iroN, papA, fimH, sfa, cnf, hlyA, iutA, and colibactin-encoding genes clbA, clbB, clbN, and clbQ. Interestingly, a high prevalence of colibactin-encoding genes (19.9%) was observed. Colibactin is a virulence factor, which interferes with the eukaryotic cell cycle and has been associated with colorectal cancer in humans. Most colibactin-encoding E. coli isolates belonged to phylogroup B2, exhibited low antimicrobial resistance but moderate or high biofilm-forming ability, and were significantly associated with most of the virulence factor genes tested. Additionally, the analysis of their clonal relatedness by PFGE showed 48 different clusters, indicating a high clonal diversity among the colibactin-positive strains. Several studies have correlated the pathogenicity of E. coli and the presence of virulence factor genes; however, colibactin and its relationship to biofilm formation have been scarcely investigated. The increasing prevalence of colibactin in E. coli and other Enterobacteriaceae and the recently described correlation with biofilm formation, makes colibactin a promising therapeutic target to prevent biofilm formation and its associated adverse effects.
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Affiliation(s)
- Victoria Ballén
- ISGlobal, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Yaiza Gabasa
- ISGlobal, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Carlos Ratia
- ISGlobal, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Melany Sánchez
- ISGlobal, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Sara Soto
- ISGlobal, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
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24
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Bajaj JS, Shamsaddini A, Acharya C, Fagan A, Sikaroodi M, Gavis E, McGeorge S, Khoruts A, Fuchs M, Sterling RK, Lee H, Gillevet PM. Multiple bacterial virulence factors focused on adherence and biofilm formation associate with outcomes in cirrhosis. Gut Microbes 2022; 13:1993584. [PMID: 34743650 PMCID: PMC8582993 DOI: 10.1080/19490976.2021.1993584] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND & AIMS Altered gut microbiota is associated with poor outcomes in cirrhosis, including infections and hepatic encephalopathy (HE). However, the role of bacterial virulence factors (VFs) is unclear. Aim: Define association of VFs with cirrhosis severity and infections, their linkage with outcomes, and impact of fecal microbiota transplant (FMT). METHODS VF abundances were determined using metagenomic analysis in stools from controls and cirrhosis patients (compensated, HE-only, ascites-only, both and infected). Patients were followed for 90-day hospitalizations and 1-year death. Stool samples collected before/after a placebo-controlled FMT trial were also analyzed. Bacterial species and VFs for all species and selected pathogens (Escherichia, Klebsiella, Pseudomonas, Staphylococcus, Streptococcus, and Enterococcus spp) were compared between groups. Multi-variable analyses were performed for clinical biomarkers and VFs for outcome prediction. Changes in VFs pre/post-FMT and post-FMT/placebo were analyzed. Results: We included 233 subjects (40 controls, 43 compensated, 30 HE-only, 20 ascites-only, 70 both, and 30 infected). Decompensated patients, especially those with infections, had higher VFs coding for siderophores, biofilms, and adhesion factors versus the rest. Biofilm and adhesion VFs from Enterobacteriaceae and Enterococcus spp associated with death and hospitalizations independent of clinical factors regardless of when all VFs or selected pathogens were analyzed. FMT was associated with reduced VF post-FMT versus pre-FMT and post-placebo groups. CONCLUSIONS Virulence factors from multiple species focused on adhesion and biofilms increased with decompensation and infections, associated with death and hospitalizations independent of clinical factors, and were attenuated with FMT. Strategies focused on targeting multiple virulence factors could potentially impact outcomes in cirrhosis. PRESENTATIONS Portions of this manuscript were an oral presentation in the virtual International Liver Congress 2021. ABBREVIATIONS VF: virulence factors, HE: hepatic encephalopathy, FMT: Fecal microbiota transplant, PPI: proton pump inhibitors, LPS: lipopolysaccharides, VFDB: Virulence factor database, OTU: operational taxonomic units, SBP: spontaneous bacterial peritonitis, UTI: urinary tract infections, MRSA: methicillin resistant Staphylococcus aureus, VRE: vancomycin-resistant Enterococcus, MAAsLin2: Microbiome Multivariable Associations with Linear Models, LPS: lipopolysaccharides, AKI: acute kidney injury.
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Affiliation(s)
- Jasmohan S Bajaj
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA,CONTACT Jasmohan S Bajaj Division of Gastroenterology, Hepatology, and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, 1201 Broad Rock Boulevard, Richmond, Virginia23249, USA
| | | | - Chathur Acharya
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Andrew Fagan
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Masoumeh Sikaroodi
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
| | - Edith Gavis
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Sara McGeorge
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Alexander Khoruts
- Gastroenterology, Hepatology and Nutrition, Center for Immunology and Biotechnology Institute, University of Minnesota, Minneapolis, Minnesota, USA
| | - Michael Fuchs
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Richard K Sterling
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Hannah Lee
- Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
| | - Patrick M Gillevet
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
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25
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Mahapatra S, Mohanty S, Mishra R, Prasad P. An overview of cancer and the human microbiome. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 191:83-139. [DOI: 10.1016/bs.pmbts.2022.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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26
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Ngoepe MP, Clayton HS. Metal Complexes as DNA Synthesis and/or Repair Inhibitors: Anticancer and Antimicrobial Agents. PHARMACEUTICAL FRONTS 2021. [DOI: 10.1055/s-0041-1741035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
AbstractMedicinal inorganic chemistry involving the utilization of metal-based compounds as therapeutics has become a field showing distinct promise. DNA and RNA are ideal drug targets for therapeutic intervention in the case of various diseases, such as cancer and microbial infection. Metals play a vital role in medicine, with at least 10 metals known to be essential for human life and a further 46 nonessential metals having been involved in drug therapies and diagnosis. These metal-based complexes interact with DNA in various ways, and are often delivered as prodrugs which undergo activation in vivo. Metal complexes cause DNA crosslinking, leading to the inhibition of DNA synthesis and repair. In this review, the various interactions of metal complexes with DNA nucleic acids, as well as the underlying mechanism of action, were highlighted. Furthermore, we also discussed various tools used to investigate the interaction between metal complexes and the DNA. The tools included in vitro techniques such as spectroscopy and electrophoresis, and in silico studies such as protein docking and density-functional theory that are highlighted for preclinical development.
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Affiliation(s)
| | - Hadley S. Clayton
- Department of Chemistry, University of South Africa, Pretoria, South Africa
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27
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Ma S, Mandalapu D, Wang S, Zhang Q. Biosynthesis of cyclopropane in natural products. Nat Prod Rep 2021; 39:926-945. [PMID: 34860231 DOI: 10.1039/d1np00065a] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Covering: 2012 to 2021Cyclopropane attracts wide interests in the fields of synthetic and pharmaceutical chemistry, and chemical biology because of its unique structural and chemical properties. This structural motif is widespread in natural products, and is usually essential for biological activities. Nature has evolved diverse strategies to access this structural motif, and increasing knowledge of the enzymes forming cyclopropane (i.e., cyclopropanases) has been revealed over the last two decades. Here, the scientific literature from the last two decades relating to cyclopropane biosynthesis is summarized, and the enzymatic cyclopropanations, according to reaction mechanism, which can be grouped into two major pathways according to whether the reaction involves an exogenous C1 unit from S-adenosylmethionine (SAM) or not, is discussed. The reactions can further be classified based on the key intermediates required prior to cyclopropane formation, which can be carbocations, carbanions, or carbon radicals. Besides the general biosynthetic pathways of the cyclopropane-containing natural products, particular emphasis is placed on the mechanism and engineering of the enzymes required for forming this unique structure motif.
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Affiliation(s)
- Suze Ma
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | | | - Shu Wang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
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28
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Rosendahl Huber A, Van Hoeck A, Van Boxtel R. The Mutagenic Impact of Environmental Exposures in Human Cells and Cancer: Imprints Through Time. Front Genet 2021; 12:760039. [PMID: 34745228 PMCID: PMC8565797 DOI: 10.3389/fgene.2021.760039] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/05/2021] [Indexed: 12/25/2022] Open
Abstract
During life, the DNA of our cells is continuously exposed to external damaging processes. Despite the activity of various repair mechanisms, DNA damage eventually results in the accumulation of mutations in the genomes of our cells. Oncogenic mutations are at the root of carcinogenesis, and carcinogenic agents are often highly mutagenic. Over the past decade, whole genome sequencing data of healthy and tumor tissues have revealed how cells in our body gradually accumulate mutations because of exposure to various mutagenic processes. Dissection of mutation profiles based on the type and context specificities of the altered bases has revealed a variety of signatures that reflect past exposure to environmental mutagens, ranging from chemotherapeutic drugs to genotoxic gut bacteria. In this review, we discuss the latest knowledge on somatic mutation accumulation in human cells, and how environmental mutagenic factors further shape the mutation landscapes of tissues. In addition, not all carcinogenic agents induce mutations, which may point to alternative tumor-promoting mechanisms, such as altered clonal selection dynamics. In short, we provide an overview of how environmental factors induce mutations in the DNA of our healthy cells and how this contributes to carcinogenesis. A better understanding of how environmental mutagens shape the genomes of our cells can help to identify potential preventable causes of cancer.
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Affiliation(s)
- Axel Rosendahl Huber
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Arne Van Hoeck
- Oncode Institute, Utrecht, Netherlands
- Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Ruben Van Boxtel
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
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29
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Wernke KM, Tirla A, Xue M, Surovtseva YV, Menges FS, Herzon SB. Probing Microbiome Genotoxicity: A Stable Colibactin Provides Insight into Structure-Activity Relationships and Facilitates Mechanism of Action Studies. J Am Chem Soc 2021; 143:15824-15833. [PMID: 34524796 DOI: 10.1021/jacs.1c07559] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Colibactin is a genotoxic metabolite produced by commensal-pathogenic members of the human microbiome that possess the clb (aka pks) biosynthetic gene cluster. clb+ bacteria induce tumorigenesis in models of intestinal inflammation and have been causally linked to oncogenesis in humans. While colibactin is believed underlie these effects, it has not been possible to study the molecule directly due to its instability. Herein, we report the synthesis and biological studies of colibactin 742 (4), a stable colibactin derivative. We show that colibactin 742 (4) induces DNA interstrand-cross-links, activation of the Fanconi Anemia DNA repair pathway, and G2/M arrest in a manner similar to clb+E. coli. The linear precursor 9, which mimics the biosynthetic precursor to colibactin, also recapitulates the bacterial phenotype. In the course of this work, we discovered a novel cyclization pathway that was previously undetected in MS-based studies of colibactin, suggesting a refinement to the natural product structure and its mode of DNA binding. Colibactin 742 (4) and its precursor 9 will allow researchers to study colibactin's genotoxic effects independent of the producing organism for the first time.
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Affiliation(s)
- Kevin M Wernke
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Alina Tirla
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Mengzhao Xue
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Yulia V Surovtseva
- Yale Center for Molecular Discovery, Yale University, West Haven, Connecticut 06516, United States
| | - Fabian S Menges
- Chemical and Biophysical Instrumentation Center, Yale University, New Haven, Connecticut 06511, United States
| | - Seth B Herzon
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States.,Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520, United States
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30
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Escherichia coli small molecule metabolism at the host-microorganism interface. Nat Chem Biol 2021; 17:1016-1026. [PMID: 34552219 DOI: 10.1038/s41589-021-00807-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 04/30/2021] [Indexed: 12/20/2022]
Abstract
Escherichia coli are a common component of the human microbiota, and isolates exhibit probiotic, commensal and pathogenic roles in the host. E. coli members often use diverse small molecule chemistry to regulate intrabacterial, intermicrobial and host-bacterial interactions. While E. coli are considered to be a well-studied model organism in biology, much of their chemical arsenal has only more recently been defined, and much remains to be explored. Here we describe chemical signaling systems in E. coli in the context of the broader field of metabolism at the host-bacteria interface and the role of this signaling in disease modulation.
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31
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Kim CS, Turocy T, Moon G, Shine EE, Crawford JM. Escherichia coli-Derived γ-Lactams and Structurally Related Metabolites Are Produced at the Intersection of Colibactin and Fatty Acid Biosynthesis. Org Lett 2021; 23:6895-6899. [PMID: 34406772 PMCID: PMC10577019 DOI: 10.1021/acs.orglett.1c02461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Colibactin is a genotoxic hybrid polyketide-nonribosomal peptide that drives colorectal cancer initiation. While clinical data suggest colibactin genotoxicity in vivo is largely caused by the major DNA-cross-linking metabolite, the colibactin locus produces a diverse collection of metabolites with mostly unknown biological activities. Here, we describe 10 new colibactin pathway metabolites (1-10) that are dependent on its α-aminomalonyl-carrier protein. The most abundant metabolites, 1 and 2, were isolated and structurally characterized mainly by nuclear magnetic resonance spectroscopy to be γ-lactam derivatives, and the remaining related structures were inferred via shared biosynthetic logic. Our proposed formation of 1-10, which is supported by stereochemical analysis, invokes cross-talk between colibactin and fatty acid biosynthesis, illuminating further the complexity of this diversity-oriented pathway.
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Affiliation(s)
- Chung Sub Kim
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, Connecticut 06516, United States
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Tayah Turocy
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, Connecticut 06516, United States
| | - Gyuri Moon
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Emilee E. Shine
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, Connecticut 06516, United States
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06536, United States
- Present address: Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Jason M. Crawford
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, Connecticut 06516, United States
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06536, United States
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32
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Scherlach K, Hertweck C. Mining and unearthing hidden biosynthetic potential. Nat Commun 2021; 12:3864. [PMID: 34162873 PMCID: PMC8222398 DOI: 10.1038/s41467-021-24133-5] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 06/04/2021] [Indexed: 12/11/2022] Open
Abstract
Genetically encoded small molecules (secondary metabolites) play eminent roles in ecological interactions, as pathogenicity factors and as drug leads. Yet, these chemical mediators often evade detection, and the discovery of novel entities is hampered by low production and high rediscovery rates. These limitations may be addressed by genome mining for biosynthetic gene clusters, thereby unveiling cryptic metabolic potential. The development of sophisticated data mining methods and genetic and analytical tools has enabled the discovery of an impressive array of previously overlooked natural products. This review shows the newest developments in the field, highlighting compound discovery from unconventional sources and microbiomes. Natural products are an important source of bioactive compounds and have versatile applications in different fields, but their discovery is challenging. Here, the authors review the recent developments in genome mining for discovery of natural products, focusing on compounds from unconventional microorganisms and microbiomes.
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Affiliation(s)
- Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Jena, Germany. .,Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany.
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33
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Dougherty MW, Jobin C. Shining a Light on Colibactin Biology. Toxins (Basel) 2021; 13:346. [PMID: 34065799 PMCID: PMC8151066 DOI: 10.3390/toxins13050346] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/06/2021] [Accepted: 05/10/2021] [Indexed: 12/16/2022] Open
Abstract
Colibactin is a secondary metabolite encoded by the pks gene island identified in several Enterobacteriaceae, including some pathogenic Escherichia coli (E. coli) commonly enriched in mucosal tissue collected from patients with inflammatory bowel disease and colorectal cancer. E. coli harboring this biosynthetic gene cluster cause DNA damage and tumorigenesis in cell lines and pre-clinical models, yet fundamental knowledge regarding colibactin function is lacking. To accurately assess the role of pks+ E. coli in cancer etiology, the biological mechanisms governing production and delivery of colibactin by these bacteria must be elucidated. In this review, we will focus on recent advances in our understanding of colibactin's structural mode-of-action and mutagenic potential with consideration for how this activity may be regulated by physiologic conditions within the intestine.
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Affiliation(s)
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, FL 32610, USA;
- Department of Infectious Diseases and Inflammation, University of Florida, Gainesville, FL 32610, USA
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34
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Gut Microbiota as Potential Biomarker and/or Therapeutic Target to Improve the Management of Cancer: Focus on Colibactin-Producing Escherichia coli in Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13092215. [PMID: 34063108 PMCID: PMC8124679 DOI: 10.3390/cancers13092215] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/29/2021] [Accepted: 05/01/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Gut microbiota is emerging as new diagnostic and prognostic marker and/or therapeutic target to improve the management of cancer. This review aims to summarize microbial signatures that have been associated with digestive and other cancers. We report the clinical relevance of these microbial markers to predict the response to cancer therapy. Among these biomarkers, colibactin-producing E. coli are prevalent in the colonic mucosa of patients with colorectal cancer and they promote colorectal carcinogenesis in several pre-clinical models. Here we discuss the promising use of colibactin-producing E. coli as a new predictive factor and a therapeutic target in colon cancer management. Abstract The gut microbiota is crucial for physiological development and immunological homeostasis. Alterations of this microbial community called dysbiosis, have been associated with cancers such colorectal cancers (CRC). The pro-carcinogenic potential of this dysbiotic microbiota has been demonstrated in the colon. Recently the role of the microbiota in the efficacy of anti-tumor therapeutic strategies has been described in digestive cancers and in other cancers (e.g., melanoma and sarcoma). Different bacterial species seem to be implicated in these mechanisms: F. nucleatum, B. fragilis, and colibactin-associated E. coli (CoPEC). CoPEC bacteria are prevalent in the colonic mucosa of patients with CRC and they promote colorectal carcinogenesis in susceptible mouse models of CRC. In this review, we report preclinical and clinical data that suggest that CoPEC could be a new factor predictive of poor outcomes that could be used to improve cancer management. Moreover, we describe the possibility of using these bacteria as new therapeutic targets.
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35
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Strakova N, Korena K, Karpiskova R. Klebsiella pneumoniae producing bacterial toxin colibactin as a risk of colorectal cancer development - A systematic review. Toxicon 2021; 197:126-135. [PMID: 33901549 DOI: 10.1016/j.toxicon.2021.04.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/24/2021] [Accepted: 04/11/2021] [Indexed: 12/12/2022]
Abstract
Microbiota can significantly contribute to colorectal cancer initiation and development. It was described that E. coli harbouring polyketide synthase (pks) genes can synthetize bacterial toxin colibactin, which was first described by Nougayrede's group in 2006. E. coli positive for pks genes were overrepresented in colorectal cancer biopsies and, therefore, prevalence and the effect of pks positive bacteria as a risk factor in colorectal cancer development is in our interest. Interestingly, pks gene cluster in E. coli shares a striking 100% sequence identity with K. pneumoniae, suggesting that their function and regulation are conserved. Moreover, K. pneumoniae can express a variety of virulence factors, including capsules, siderophores, iron-scavenging systems, adhesins and endotoxins. It was reported that pks cluster and thereby colibactin is also related to the hypervirulence of K. pneumoniae. Acquisition of the pks locus is associated with K. pneumoniae gut colonisation and mucosal invasion. Colibactin also increases the likelihood of serious complications of bacterial infections, such as development of meningitis and potentially tumorigenesis. Even though K. pneumoniae is undoubtedly a gut colonizer, the role of pks positive K. pneumoniae in GIT has not yet been investigated. It seems that CRC-distinctive microbiota is already present in the early stages of cancer development and, therefore, microbiome analysis could help to discover the early stages of cancer, which are crucial for effectiveness of anticancer therapy. We hypothesize, that pks positive K. pneumoniae can be a potential biomarker of tumour prevalence and anticancer therapy response.
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Affiliation(s)
- Nicol Strakova
- Laboratory of Zoonoses and Antibiotic Resistance, Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Brno, Hudcova 296/70, Brno, Czech Republic.
| | - Kristyna Korena
- Laboratory of Zoonoses and Antibiotic Resistance, Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Brno, Hudcova 296/70, Brno, Czech Republic
| | - Renata Karpiskova
- Laboratory of Zoonoses and Antibiotic Resistance, Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Brno, Hudcova 296/70, Brno, Czech Republic
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36
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Zhou T, Hirayama Y, Tsunematsu Y, Suzuki N, Tanaka S, Uchiyama N, Goda Y, Yoshikawa Y, Iwashita Y, Sato M, Miyoshi N, Mutoh M, Ishikawa H, Sugimura H, Wakabayashi K, Watanabe K. Isolation of New Colibactin Metabolites from Wild-Type Escherichia coli and In Situ Trapping of a Mature Colibactin Derivative. J Am Chem Soc 2021; 143:5526-5533. [PMID: 33787233 DOI: 10.1021/jacs.1c01495] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Colibactin is a polyketide-nonribosomal peptide hybrid secondary metabolite that can form interstrand cross-links in double-stranded DNA. Colibactin-producing Escherichia coli has also been linked to colorectal oncogenesis. Thus, there is a strong interest in understanding the role colibactin may play in oncogenesis. Here, using the high-colibactin-producing wild-type E. coli strain we isolated from a clinical sample with the activity-based fluorescent probe we developed earlier, we were able to identify colibactin 770, which was recently identified and proposed as the complete form of colibactin, along with colibactin 788, 406, 416, 420, and 430 derived from colibactin 770 through structural rearrangements and solvolysis. Furthermore, we were able to trap the degrading mature colibactin species by converting the diketone moiety into quinoxaline in situ in the crude culture extract to form colibactin 860 at milligram scale. This allowed us to determine the stereochemically complex structure of the rearranged form of an intact colibactin, colibactin 788, in detail. Furthermore, our study suggested that we were capturing only a few percent of the actual colibactin produced by the microbe, providing a crude quantitative insight into the inherent instability of this compound. Through the structural assignment of colibactins and their degradative products by the combination of LC-HRMS and NMR spectroscopies, we were able to elucidate further the fate of inherently unstable colibactin, which could help acquire a more complete picture of colibactin metabolism and identify key DNA adducts and biomarkers for diagnosing colorectal cancer.
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Affiliation(s)
- Tao Zhou
- Adenoprevent Co., Ltd., Shizuoka 422-8526, Japan
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Yuichiro Hirayama
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Yuta Tsunematsu
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Nanami Suzuki
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Seiji Tanaka
- National Institute of Health Sciences, Kawasaki 210-9501, Japan
| | - Nahoko Uchiyama
- National Institute of Health Sciences, Kawasaki 210-9501, Japan
| | - Yukihiro Goda
- National Institute of Health Sciences, Kawasaki 210-9501, Japan
| | - Yuko Yoshikawa
- School of Veterinary Medicine, Faculty of Veterinary Science, Nippon Veterinary and Life Science University, Tokyo 180-8602, Japan
| | - Yuji Iwashita
- Department of Tumor Pathology, Hamamatsu University School of Medicine, Shizuoka 431-3192, Japan
| | - Michio Sato
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Noriyuki Miyoshi
- Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Michihiro Mutoh
- Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Hideki Ishikawa
- Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Haruhiko Sugimura
- Department of Tumor Pathology, Hamamatsu University School of Medicine, Shizuoka 431-3192, Japan
| | - Keiji Wakabayashi
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Kenji Watanabe
- Adenoprevent Co., Ltd., Shizuoka 422-8526, Japan
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
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37
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Abstract
The human microbiome encodes a second genome that dwarfs the genetic capacity of the host. Microbiota-derived small molecules can directly target human cells and their receptors or indirectly modulate host responses through functional interactions with other microbes in their ecological niche. Their biochemical complexity has profound implications for nutrition, immune system development, disease progression, and drug metabolism, as well as the variation in these processes that exists between individuals. While the species composition of the human microbiome has been deeply explored, detailed mechanistic studies linking specific microbial molecules to host phenotypes are still nascent. In this review, we discuss challenges in decoding these interaction networks, which require interdisciplinary approaches that combine chemical biology, microbiology, immunology, genetics, analytical chemistry, bioinformatics, and synthetic biology. We highlight important classes of microbiota-derived small molecules and notable examples. An understanding of these molecular mechanisms is central to realizing the potential of precision microbiome editing in health, disease, and therapeutic responses.
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Affiliation(s)
- Emilee E Shine
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06536, USA; .,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA.,Current affiliation: Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Jason M Crawford
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06536, USA; .,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA.,Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
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38
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Williams PC, Wernke KM, Tirla A, Herzon SB. Employing chemical synthesis to study the structure and function of colibactin, a "dark matter" metabolite. Nat Prod Rep 2020; 37:1532-1548. [PMID: 33174565 PMCID: PMC7700718 DOI: 10.1039/d0np00072h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Covering: 2015 to 2020 The field of natural products is dominated by a discovery paradigm that follows the sequence: isolation, structure elucidation, chemical synthesis, and then elucidation of mechanism of action and structure-activity relationships. Although this discovery paradigm has proven successful in the past, researchers have amassed enough evidence to conclude that the vast majority of nature's secondary metabolites - biosynthetic "dark matter" - cannot be identified and studied by this approach. Many biosynthetic gene clusters (BGCs) are expressed at low levels, or not at all, and in some instances a molecule's instability to fermentation or isolation prevents detection entirely. Here, we discuss an alternative approach to natural product identification that addresses these challenges by enlisting synthetic chemistry to prepare putative natural product fragments and structures as guided by biosynthetic insight. We demonstrate the utility of this approach through our structure elucidation of colibactin, an unisolable genotoxin produced by pathogenic bacteria in the human gut.
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Affiliation(s)
- Peyton C Williams
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.
| | - Kevin M Wernke
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.
| | - Alina Tirla
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.
| | - Seth B Herzon
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA. and Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520, USA
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39
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Vacante M, Ciuni R, Basile F, Biondi A. Gut Microbiota and Colorectal Cancer Development: A Closer Look to the Adenoma-Carcinoma Sequence. Biomedicines 2020; 8:E489. [PMID: 33182693 PMCID: PMC7697438 DOI: 10.3390/biomedicines8110489] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 12/13/2022] Open
Abstract
There is wide evidence that CRC could be prevented by regular physical activity, keeping a healthy body weight, and following a healthy and balanced diet. Many sporadic CRCs develop via the traditional adenoma-carcinoma pathway, starting as premalignant lesions represented by conventional, tubular or tubulovillous adenomas. The gut bacteria play a crucial role in regulating the host metabolism and also contribute to preserve intestinal barrier function and an effective immune response against pathogen colonization. The microbiota composition is different among people, and is conditioned by many environmental factors, such as diet, chemical exposure, and the use of antibiotic or other medication. The gut microbiota could be directly involved in the development of colorectal adenomas and the subsequent progression to CRC. Specific gut bacteria, such as Fusobacterium nucleatum, Escherichia coli, and enterotoxigenic Bacteroides fragilis, could be involved in colorectal carcinogenesis. Potential mechanisms of CRC progression may include DNA damage, promotion of chronic inflammation, and release of bioactive carcinogenic metabolites. The aim of this review was to summarize the current knowledge on the role of the gut microbiota in the development of CRC, and discuss major mechanisms of microbiota-related progression of the adenoma-carcinoma sequence.
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Affiliation(s)
- Marco Vacante
- Department of General Surgery and Medical-Surgical Specialties, University of Catania, Via S. Sofia 78, 95123 Catania, Italy; (R.C.); (F.B.); (A.B.)
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40
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Lopez LR, Bleich RM, Arthur JC. Microbiota Effects on Carcinogenesis: Initiation, Promotion, and Progression. Annu Rev Med 2020; 72:243-261. [PMID: 33052764 DOI: 10.1146/annurev-med-080719-091604] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Carcinogenesis is a multistep process by which normal cells acquire genetic and epigenetic changes that result in cancer. In combination with host genetic susceptibility and environmental exposures, a prominent procarcinogenic role for the microbiota has recently emerged. In colorectal cancer (CRC), three nefarious microbes have been consistently linked to cancer development: (a) Colibactin-producing Escherichia coli initiates carcinogenic DNA damage, (b) enterotoxigenic Bacteroides fragilis promotes tumorigenesis via toxin-induced cell proliferation and tumor-promoting inflammation, and (c) Fusobacterium nucleatum enhances CRC progression through two adhesins, Fap2 and FadA, that promote proliferation and antitumor immune evasion and may contribute to metastases. Herein, we use these three prominent microbes to discuss the experimental evidence linking microbial activities to carcinogenesis and the specific mechanisms driving this stepwise process. Precisely defining mechanisms by which the microbiota impacts carcinogenesis at each stage is essential for developing microbiota-targeted strategies for the diagnosis, prognosis, and treatment of cancer.
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Affiliation(s)
- Lacey R Lopez
- Department of Microbiology and Immunology, The University of North Carolina, Chapel Hill, North Carolina 27599, USA; ,
| | - Rachel M Bleich
- Department of Biology, Appalachian State University, Boone, North Carolina 28608, USA;
| | - Janelle C Arthur
- Department of Microbiology and Immunology, The University of North Carolina, Chapel Hill, North Carolina 27599, USA; , .,Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Center for Gastrointestinal Biology and Disease, The University of North Carolina, Chapel Hill, North Carolina 27599, USA
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Ilazi A, Huang B, de Almeida Campos V, Gademann K. Synthesis of Colibactin Pyrrolidono[3,4- d]pyridones via Regioselective C(sp 3)-H Activation. Org Lett 2020; 22:6858-6862. [PMID: 32815372 DOI: 10.1021/acs.orglett.0c02385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The synthesis of pyrrolidono[3,4-d]pyridones of relevance to putative genotoxic colibactin structures featuring a doubly conjugated 1,6-Michael acceptor system is reported. We investigated and implemented a highly selective Pd-catalyzed C(sp3)-H activation reaction as a key step and further functionalized the pyridone core. Evaluating the role of this structural unit of relevance to colibactin, we found that this structure displayed a high degree of stability toward both acidic conditions and nucleophiles.
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Affiliation(s)
- Agron Ilazi
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH 8057 Zürich, Switzerland
| | - Bin Huang
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH 8057 Zürich, Switzerland
| | - Valery de Almeida Campos
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH 8057 Zürich, Switzerland
| | - Karl Gademann
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH 8057 Zürich, Switzerland
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