1
|
Uchiyama H, Kudo T, Yamaguchi T, Obana N, Watanabe K, Abe K, Miyazaki H, Toyofuku M, Nomura N, Akeda Y, Nakao R. Mucosal adjuvanticity and mucosal booster effect of colibactin-depleted probiotic Escherichia coli membrane vesicles. Hum Vaccin Immunother 2024; 20:2337987. [PMID: 38658133 PMCID: PMC11057659 DOI: 10.1080/21645515.2024.2337987] [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: 11/21/2023] [Accepted: 03/29/2024] [Indexed: 04/26/2024] Open
Abstract
There is a growing interest in development of novel vaccines against respiratory tract infections, due to COVID-19 pandemic. Here, we examined mucosal adjuvanticity and the mucosal booster effect of membrane vesicles (MVs) of a novel probiotic E. coli derivative lacking both flagella and potentially carcinogenic colibactin (ΔflhDΔclbP). ΔflhDΔclbP-derived MVs showed rather strong mucosal adjuvanticity as compared to those of a single flagellar mutant strain (ΔflhD-MVs). In addition, glycoengineered ΔflhDΔclbP-MVs displaying serotype-14 pneumococcal capsular polysaccharide (CPS14+MVs) were well-characterized based on biological and physicochemical parameters. Subcutaneous (SC) and intranasal (IN) booster effects of CPS14+MVs on systemic and mucosal immunity were evaluated in mice that have already been subcutaneously prime-immunized with the same MVs. With a two-dose regimen, an IN boost (SC-IN) elicited stronger IgA responses than homologous prime-boost immunization (SC-SC). With a three-dose regimen, serum IgG levels were comparable among all tested regimens. Homologous immunization (SC-SC-SC) elicited the highest IgM responses among all regimens tested, whereas SC-SC-SC failed to elicit IgA responses in blood and saliva. Furthermore, serum IgA and salivary SIgA levels were increased with an increased number of IN doses administrated. Notably, SC-IN-IN induced not only robust IgG response, but also the highest IgA response in both serum and saliva among the groups. The present findings suggest the potential of a heterologous three-dose administration for building both systemic and mucosal immunity, e.g. an SC-IN-IN vaccine regimen could be beneficial. Another important observation was abundant packaging of colibactin in MVs, suggesting increased applicability of ΔflhDΔclbP-MVs in the context of vaccine safety.
Collapse
Affiliation(s)
- Hiroki Uchiyama
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
- Department of Vascular Surgery, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Toshifumi Kudo
- Department of Vascular Surgery, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Takehiro Yamaguchi
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Nozomu Obana
- Tsukuba Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kimihiro Abe
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Hidetaka Miyazaki
- Department of Oculoplastic, Orbital and Lacrimal Surgery, Aichi Medical University, Nagakute, Japan
- Department of Oral and Maxillofacial Surgery, Division of Oral Health Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Masanori Toyofuku
- Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Nobuhiko Nomura
- Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Yukihiro Akeda
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Ryoma Nakao
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| |
Collapse
|
2
|
Bayne C, Boutard M, Zaplana T, Tolonen AC. L-tryptophan and copper interactions linked to reduced colibactin genotoxicity in pks+ Escherichia coli. mSystems 2024:e0099224. [PMID: 39264195 DOI: 10.1128/msystems.00992-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Accepted: 08/06/2024] [Indexed: 09/13/2024] Open
Abstract
Colibactin, a nonribosomal peptide/polyketide produced by pks+ Enterobacteriaceae, is a virulence factor and putative carcinogen that damages DNA by interstrand crosslinking (ICL). While the clb genes for colibactin biosynthesis have been identified, studies are needed to elucidate the mechanisms regulating colibactin production and activity. Here we perform untargeted metabolomics of pks+ Escherichia coli cultures to identify L-tryptophan as a candidate repressor of colibactin activity. When pks+ E. coli is grown in a minimal medium supplemented with L-tryptophan in vitro ICL of plasmid DNA is reduced by >80%. L-tryptophan does not affect the transcription of clb genes but protects from copper toxicity and triggers the expression of genes to export copper to the periplasm where copper can directly inhibit the ClbP peptidase domain. Thus, L-tryptophan and copper interact and repress colibactin activity, potentially reducing its carcinogenic effects in the intestine. IMPORTANCE Colibactin is a small molecule produced by pks+ Enterobacteriaceae that damages DNA, leading to oncogenic mutations in human genomes. Colibactin-producing Escherichia coli (pks+) cells promote tumorigenesis in mouse models of colorectal cancer (CRC) and are elevated in abundance in CRC patient biopsies, making it important to identify the regulatory systems governing colibactin production. Here, we apply a systems biology approach to explore metabolite repression of colibactin production in pks+ E. coli. We identify L-tryptophan as a repressor of colibactin genotoxicity that stimulates the expression of genes to export copper to the periplasm where it can inhibit ClbP, the colibactin-activating peptidase. These results work toward an antibiotic-sparing, prophylactic strategy to inhibit colibactin genotoxicity and its tumorigenic effects in the intestine.
Collapse
Affiliation(s)
- Charlie Bayne
- Department of Pharmacology, University of California, San Diego, California, USA
| | - Magali Boutard
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Tom Zaplana
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Andrew C Tolonen
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| |
Collapse
|
3
|
Dhahi MAR. Analysis of the partial sequencing of clbA, clbB and clbQ in Escherichia coli isolates that produce colibactin and multilocus sequence typing. Sci Rep 2024; 14:17966. [PMID: 39095472 PMCID: PMC11297330 DOI: 10.1038/s41598-024-68867-w] [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: 04/05/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024] Open
Abstract
Colibactin, is a cyclomodulin expressed from polyketide synthase (pk) genomic islands. These bacterial toxins interfere with the eukaryotic cell cycle and induce DNA damage. The aim of the present study was to investigate the prevalence of colibactin production among E. coli strains recovered from different infections, determine the similarity of clb nucleotide sequences, and identify genotype of isolates using multilocus sequence typing(MLST). This was a prospective, cross-sectional study conducted from January 2022 to February 2023. A total of 117 clinical isolates were obtained from various sample types collected from outpatients and inpatients recruited to the Department of Bacteriology Labs in different hospitals in Baghdad, Iraq. clbA/clbR, clbB and clbP/clbQ were detected via conventional PCR, and partial sequencing of amplicons was performed via Sanger sequencing. For select isolates, MLST genotyping was performed. The most common phylogenetic group was B2 (61/106; 57.54%). Among the E. coli strains, 27/106 (25.47%) were clb + ve, and the most common type was clbB (13/27; 48.14%). Analysis of the partial sequencing of clb among the strains revealed high molecular similarity. Genotyping of 37 selected E. coli strains via MLST revealed 28 different genotypes. There was a high prevalence of colibactin production in phylogroup B2, and it seems that the clb + ve strains had conserved molecular structures. There was high genetic diversity among the strains tested.
Collapse
|
4
|
Sadeghi M, Mestivier D, Sobhani I. Contribution of pks+ Escherichia coli ( E. coli) to Colon Carcinogenesis. Microorganisms 2024; 12:1111. [PMID: 38930493 PMCID: PMC11205849 DOI: 10.3390/microorganisms12061111] [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: 05/21/2024] [Revised: 05/24/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Colorectal cancer (CRC) stands as a significant global health concern, ranking second in mortality and third in frequency among cancers worldwide. While only a small fraction of CRC cases can be attributed to inherited genetic mutations, the majority arise sporadically due to somatic mutations. Emerging evidence reveals gut microbiota dysbiosis to be a contributing factor, wherein polyketide synthase-positive Escherichia coli (pks+ E. coli) plays a pivotal role in CRC pathogenesis. pks+ bacteria produce colibactin, a genotoxic protein that causes deleterious effects on DNA within host colonocytes. In this review, we examine the role of the gut microbiota in colon carcinogenesis, elucidating how colibactin-producer bacteria induce DNA damage, promote genomic instability, disrupt the gut epithelial barrier, induce mucosal inflammation, modulate host immune responses, and influence cell cycle dynamics. Collectively, these actions foster a microenvironment conducive to tumor initiation and progression. Understanding the mechanisms underlying pks+ bacteria-mediated CRC development may pave the way for mass screening, early detection of tumors, and therapeutic strategies such as microbiota modulation, bacteria-targeted therapy, checkpoint inhibition of colibactin production and immunomodulatory pathways.
Collapse
Affiliation(s)
- Mohammad Sadeghi
- EA7375–EC2M3: Early, Detection of Colonic Cancer by Using Microbial & Molecular Markers, Paris East Créteil University (UPEC), 94010 Créteil, France;
| | - Denis Mestivier
- EA7375–EC2M3: Early, Detection of Colonic Cancer by Using Microbial & Molecular Markers, Paris East Créteil University (UPEC), 94010 Créteil, France;
| | - Iradj Sobhani
- EA7375–EC2M3: Early, Detection of Colonic Cancer by Using Microbial & Molecular Markers, Paris East Créteil University (UPEC), 94010 Créteil, France;
- Department of Gastroenterology, Assistance Publique–Hôpitaux de Paris (APHP), Henri Mondor Hospital, 94010 Créteil, France
| |
Collapse
|
5
|
Long Q, Zhou W, Zhou H, Tang Y, Chen W, Liu Q, Bian X. Polyamine-containing natural products: structure, bioactivity, and biosynthesis. Nat Prod Rep 2024; 41:525-564. [PMID: 37873660 DOI: 10.1039/d2np00087c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Covering: 2005 to August, 2023Polyamine-containing natural products (NPs) have been isolated from a wide range of terrestrial and marine organisms and most of them exhibit remarkable and diverse activities, including antimicrobial, antiprotozoal, antiangiogenic, antitumor, antiviral, iron-chelating, anti-depressive, anti-inflammatory, insecticidal, antiobesity, and antioxidant properties. Their extraordinary activities and potential applications in human health and agriculture attract increasing numbers of studies on polyamine-containing NPs. In this review, we summarized the source, structure, classification, bioactivities and biosynthesis of polyamine-containing NPs, focusing on the biosynthetic mechanism of polyamine itself and representative polyamine alkaloids, polyamine-containing siderophores with catechol/hydroxamate/hydroxycarboxylate groups, nonribosomal peptide-(polyketide)-polyamine (NRP-(PK)-PA), and NRP-PK-long chain poly-fatty amine (lcPFAN) hybrid molecules.
Collapse
Affiliation(s)
- Qingshan Long
- Hunan Provincial Engineering and Technology Research Center for Agricultural Microbiology Application, Hunan Institute of Microbiology, Changsha, 410009, China.
| | - Wen Zhou
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural, Affairs, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Ying Tang
- Hunan Provincial Engineering and Technology Research Center for Agricultural Microbiology Application, Hunan Institute of Microbiology, Changsha, 410009, China.
| | - Wu Chen
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China.
| | - Qingshu Liu
- Hunan Provincial Engineering and Technology Research Center for Agricultural Microbiology Application, Hunan Institute of Microbiology, Changsha, 410009, China.
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Zou X, Hui Z, Shepherd RA, Zhao S, Wu Y, Shen Z, Pang C, Zhou S, Yu Z, Zhou J, Moore BS, Sanchez LM, Tang X. Unveiling a CAAX Protease-Like Protein Involved in Didemnin Drug Maturation and Secretion. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306044. [PMID: 38032137 PMCID: PMC10811503 DOI: 10.1002/advs.202306044] [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: 08/24/2023] [Revised: 10/29/2023] [Indexed: 12/01/2023]
Abstract
The assembly line biosynthesis of the powerful anticancer-antiviral didemnin cyclic peptides is proposed to follow a prodrug release mechanism in Tristella bacteria. This strategy commences with the formation of N-terminal prodrug scaffolds and culminates in their cleavage during the cellular export of the mature products. In this study, a comprehensive exploration of the genetic and biochemical aspects of the enzymes responsible for both the assembly and cleavage of the acylated peptide prodrug scaffolds is provided. This process involves the assembly of N-acyl-polyglutamine moieties orchestrated by the nonribosomal peptide synthetase DidA and the cleavage of these components at the post-assembly stage by DidK, a transmembrane CAAX hydrolase homolog. The findings not only shed light on the complex prodrug mechanism that underlies the synthesis and secretion of didemnin compounds but also offer novel insights into the expanded role of CAAX hydrolases in microbes. Furthermore, this knowledge can be leveraged for the strategic design of genome mining approaches aimed at discovering new bioactive natural products that employ similar prodrug biochemical strategies.
Collapse
Affiliation(s)
- Xiaolin Zou
- Institute of Chemical BiologyShenzhen Bay LaboratoryShenzhen518132China
| | - Zhen Hui
- Institute of Chemical BiologyShenzhen Bay LaboratoryShenzhen518132China
| | - Robert A. Shepherd
- Department of Chemistry and BiochemistryUniversity of California Santa CruzSanta CruzCA95064USA
| | - Shuaiqiang Zhao
- Institute of Chemical BiologyShenzhen Bay LaboratoryShenzhen518132China
| | - Yanfei Wu
- CAS Key Laboratory of Quantitative Engineering BiologyShenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055China
| | - Zhuanglin Shen
- CAS Key Laboratory of Quantitative Engineering BiologyShenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055China
| | - Cuiping Pang
- CAS Key Laboratory of Quantitative Engineering BiologyShenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055China
| | - Shipeng Zhou
- Institute of Chemical BiologyShenzhen Bay LaboratoryShenzhen518132China
| | - Zehai Yu
- Institute of Chemical BiologyShenzhen Bay LaboratoryShenzhen518132China
| | - Jiahai Zhou
- CAS Key Laboratory of Quantitative Engineering BiologyShenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055China
| | - Bradly S. Moore
- Scripps Institution of OceanographyUniversity of California San DiegoLa JollaCA92093USA
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California San DiegoLa JollaCA92093USA
| | - Laura M. Sanchez
- Department of Chemistry and BiochemistryUniversity of California Santa CruzSanta CruzCA95064USA
| | - Xiaoyu Tang
- Institute of Chemical BiologyShenzhen Bay LaboratoryShenzhen518132China
| |
Collapse
|
8
|
Valadbeigi M, Mahmoudifard M, Ganji SM, Mehrabian S. Study on the antibacterial effect of CuO nanoparticles on Klebsiella pneumonia bacteria: Efficient treatment for colorectal cancer. Biotechnol Appl Biochem 2023; 70:1785-1793. [PMID: 37264727 DOI: 10.1002/bab.2481] [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: 11/16/2022] [Accepted: 05/09/2023] [Indexed: 06/03/2023]
Abstract
Colorectal cancer (CRC) is a widespread type of cancer across the world. One efficient therapy approach is the use of antibiotic agents, but one of the main issues related to treating CRC is microbial resistance to antibiotics. As microbes are becoming more resistant to antibiotics and other traditional antimicrobial agents, nanobiotechnology has made it possible to employ nanomaterials with the aim of creating a new generation of antimicrobial agents. In the present study, we have assessed the antimicrobial potential of CuO nanoparticles (NPs) against gram-negative bacteria like Klebsiella pneumoniae carrying PKS genes responsible for encoding colibactin as the key factor for CRC development. For this purpose, the antibacterial effects of conventional antibacterial agents, including erythromycin, piperacillin, and ampicillin, as well as CuONPs, were compared on isolated strains from cancerous candidates. The obtained results revealed that isolates (K. pneumoniae) showed resistance toward the mentioned conventional antibiotics, but CuONPs showed efficient antibacterial properties against K. pneumonia with a MIC = 62 μg/mL. On the other hand, a synergistic antibacterial effect was obtained when CuONPs were used in combination with conventional antibiotics, which are ineffective when used alone. Therefore, CuONPs can be introduced as an excellent antimicrobial agent against K. pneumoniae bacteria in CRC, especially when they are combined with other antibiotics since they can activate the antimicrobial activity of the conventional antibiotics.
Collapse
Affiliation(s)
- Maria Valadbeigi
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Matin Mahmoudifard
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Shahla Mohammad Ganji
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Sedigheh Mehrabian
- Department of Microbiology, Faculty of Life Sciences, Azad Islamic University, North Tehran Branch, Tehran, Iran
| |
Collapse
|
9
|
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.
Collapse
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
| | | |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
DiBello M, Healy AR, Nikolayevskiy H, Xu Z, Herzon SB. Structure Elucidation of Secondary Metabolites: Current Frontiers and Lingering Pitfalls. Acc Chem Res 2023; 56:1656-1668. [PMID: 37220079 PMCID: PMC10468810 DOI: 10.1021/acs.accounts.3c00183] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Analytical methods allow for the structure determination of submilligram quantities of complex secondary metabolites. This has been driven in large part by advances in NMR spectroscopic capabilities, including access to high-field magnets equipped with cryogenic probes. Experimental NMR spectroscopy may now be complemented by remarkably accurate carbon-13 NMR calculations using state-of-the-art DFT software packages. Additionally, microED analysis stands to have a profound effect on structure elucidation by providing X-ray-like images of microcrystalline samples of analytes. Nonetheless, lingering pitfalls in structure elucidation remain, particularly for isolates that are unstable or highly oxidized. In this Account, we discuss three projects from our laboratory that highlight nonoverlapping challenges to the field, with implications for chemical, synthetic, and mechanism of action studies. We first discuss the lomaiviticins, complex unsaturated polyketide natural products disclosed in 2001. The original structures were derived from NMR, HRMS, UV-vis, and IR analysis. Owing to the synthetic challenges presented by their structures and the absence of X-ray crystallographic data, the structure assignments remained untested for nearly two decades. In 2021, the Nelson group at Caltech carried out microED analysis of (-)-lomaiviticin C, leading to the startling discovery that the original structure assignment of the lomaiviticins was incorrect. Acquisition of higher-field (800 MHz 1H, cold probe) NMR data as well as DFT calculations provided insights into the basis for the original misassignment and lent further support to the new structure identified by microED. Reanalysis of the 2001 data set reveals that the two structure assignments are nearly indistinguishable, underscoring the limitations of NMR-based characterization. We then discuss the structure elucidation of colibactin, a complex, nonisolable microbiome metabolite implicated in colorectal cancer. The colibactin biosynthetic gene cluster was detected in 2006, but owing to colibactin's instability and low levels of production, it could not be isolated or characterized. We used a combination of chemical synthesis, mechanism of action studies, and biosynthetic analysis to identify the substructures in colibactin. These studies, coupled with isotope labeling and tandem MS analysis of colibactin-derived DNA interstrand cross-links, ultimately led to a structure assignment for the metabolite. We then discuss the ocimicides, plant secondary metabolites that were studied as agents against drug-resistant P. falciparum. We synthesized the core structure of the ocimicides and found significant discrepancies between our experimental NMR spectroscopic data and that reported for the natural products. We determined the theoretical carbon-13 NMR shifts for 32 diastereomers of the ocimicides. These studies indicated that a revision of the connectivity of the metabolites is likely needed. We end with some thoughts on the frontiers of secondary metabolite structure determination. As modern NMR computational methods are straightforward to execute, we advocate for their systematic use in validating the assignments of novel secondary metabolites.
Collapse
Affiliation(s)
- Mikaela DiBello
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Alan R Healy
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Herman Nikolayevskiy
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Zhi Xu
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Seth B Herzon
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Departments of Pharmacology and Therapeutic Radiology, Yale School of Medicine, New Haven, Connecticut 06520, United States
| |
Collapse
|
12
|
Hallam JC, Sandalli S, Floria I, Turner NCA, Tang-Fichaux M, Oswald E, O'Boyle N, Roe AJ. D-Serine reduces the expression of the cytopathic genotoxin colibactin. MICROBIAL CELL (GRAZ, AUSTRIA) 2023; 10:63-77. [PMID: 36908282 PMCID: PMC9993432 DOI: 10.15698/mic2023.03.793] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 03/14/2023]
Abstract
Some Escherichia coli strains harbour the pks island, a 54 kb genomic island encoding the biosynthesis genes for a genotoxic compound named colibactin. In eukaryotic cells, colibactin can induce DNA damage, cell cycle arrest and chromosomal instability. Production of colibactin has been implicated in the development of colorectal cancer (CRC). In this study, we demonstrate the inhibitory effect of D-Serine on the expression of the pks island in both prototypic and clinically-associated colibactin-producing strains and determine the implications for cytopathic effects on host cells. We also tested a comprehensive panel of proteinogenic L-amino acids and corresponding D-enantiomers for their ability to modulate clbB transcription. Whilst several D-amino acids exhibited the ability to inhibit expression of clbB, D-Serine exerted the strongest repressing activity (>3.8-fold) and thus, we focussed additional experiments on D-Serine. To investigate the cellular effect, we investigated if repression of colibactin by D-Serine could reduce the cytopathic responses normally observed during infection of HeLa cells with pks + strains. Levels of γ-H2AX (a marker of DNA double strand breaks) were reduced 2.75-fold in cells infected with D-Serine treatment. Moreover, exposure of pks + E. coli to D-Serine during infection caused a reduction in cellular senescence that was observable at 72 h post infection. The recent finding of an association between pks-carrying commensal E. coli and CRC, highlights the necessity for the development of colibactin targeting therapeutics. Here we show that D-Serine can reduce expression of colibactin, and inhibit downstream cellular cytopathy, illuminating its potential to prevent colibactin-associated disease.
Collapse
Affiliation(s)
- Jennifer C. Hallam
- School of Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Sofia Sandalli
- School of Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Iris Floria
- School of Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Natasha C. A. Turner
- School of Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Min Tang-Fichaux
- IRSD, INSERM, INRAE, Université de Toulouse, ENVT, Toulouse, France
| | - Eric Oswald
- IRSD, INSERM, INRAE, Université de Toulouse, ENVT, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse, France
| | - Nicky O'Boyle
- School of Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
- School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
| | - Andrew J. Roe
- School of Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| |
Collapse
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
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.
Collapse
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.
| |
Collapse
|
15
|
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.
Collapse
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.
| |
Collapse
|
16
|
Volpe MR, Velilla JA, Daniel-Ivad M, Yao JJ, Stornetta A, Villalta PW, Huang HC, Bachovchin DA, Balbo S, Gaudet R, Balskus EP. A small molecule inhibitor prevents gut bacterial genotoxin production. Nat Chem Biol 2023; 19:159-167. [PMID: 36253549 PMCID: PMC9889270 DOI: 10.1038/s41589-022-01147-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 08/19/2022] [Indexed: 02/04/2023]
Abstract
The human gut bacterial genotoxin colibactin is a possible key driver of colorectal cancer (CRC) development. Understanding colibactin's biological effects remains difficult owing to the instability of the proposed active species and the complexity of the gut microbiota. Here, we report small molecule boronic acid inhibitors of colibactin biosynthesis. Designed to mimic the biosynthetic precursor precolibactin, these compounds potently inhibit the colibactin-activating peptidase ClbP. Using biochemical assays and crystallography, we show that they engage the ClbP binding pocket, forming a covalent bond with the catalytic serine. These inhibitors reproduce the phenotypes observed in a clbP deletion mutant and block the genotoxic effects of colibactin on eukaryotic cells. The availability of ClbP inhibitors will allow precise, temporal control over colibactin production, enabling further study of its contributions to CRC. Finally, application of our inhibitors to related peptidase-encoding pathways highlights the power of chemical tools to probe natural product biosynthesis.
Collapse
Affiliation(s)
- Matthew R. Volpe
- grid.38142.3c000000041936754XDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, MA USA
| | - José A. Velilla
- grid.38142.3c000000041936754XDepartment of Molecular and Cellular Biology, Harvard University, Cambridge, MA USA
| | - Martin Daniel-Ivad
- grid.38142.3c000000041936754XDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, MA USA
| | - Jenny J. Yao
- grid.38142.3c000000041936754XDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, MA USA
| | - Alessia Stornetta
- grid.17635.360000000419368657Masonic Cancer Center, University of Minnesota, Minneapolis, MN USA
| | - Peter W. Villalta
- grid.17635.360000000419368657Masonic Cancer Center, University of Minnesota, Minneapolis, MN USA ,grid.17635.360000000419368657Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN USA
| | - Hsin-Che Huang
- grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Daniel A. Bachovchin
- grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Silvia Balbo
- grid.17635.360000000419368657Masonic Cancer Center, University of Minnesota, Minneapolis, MN USA ,grid.17635.360000000419368657Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN USA
| | - Rachelle Gaudet
- grid.38142.3c000000041936754XDepartment of Molecular and Cellular Biology, Harvard University, Cambridge, MA USA
| | - Emily P. Balskus
- grid.38142.3c000000041936754XDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, MA USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard University, Cambridge, MA USA
| |
Collapse
|
17
|
Li Y, Washburn LA, Watanabe CMH. Thioester Capture Strategy for the Identification of Nonribosomal Peptide and Polyketide Intermediates. Methods Mol Biol 2023; 2670:267-284. [PMID: 37184710 DOI: 10.1007/978-1-0716-3214-7_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) are multi-domainal megasynthases. While they are capable of generating a structurally diverse array of metabolites of therapeutic relevance, their mere size and complex nature of their assembly (intermediates are tethered and enzyme bound) make them inherently difficult to characterize. In order to facilitate structural characterization of these metabolites, a thioester capture strategy that enables direct trapping and characterization of the thioester-bound enzyme intermediates was developed. Specifically, a synthetic Biotin-Cys agent was designed and utilized, enabling direct analysis by LCMS/MS and NMR spectroscopy. In the long term, the approach might facilitate the discovery of novel scaffolds from cryptic biosynthetic pathways, paving the way for the development of drug leads and therapeutic initiatives.
Collapse
Affiliation(s)
- Yueying Li
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Lauren A Washburn
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Coran M H Watanabe
- Department of Chemistry, Texas A&M University, College Station, TX, USA.
| |
Collapse
|
18
|
Newly Discovered Mechanisms of Antibiotic Self-Resistance with Multiple Enzymes Acting at Different Locations and Stages. Antibiotics (Basel) 2022; 12:antibiotics12010035. [PMID: 36671236 PMCID: PMC9854587 DOI: 10.3390/antibiotics12010035] [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: 11/16/2022] [Revised: 12/13/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
Self-resistance determinants are essential for the biosynthesis of bioactive natural products and are closely related to drug resistance in clinical settings. The study of self-resistance mechanisms has long moved forward on the discovery of new resistance genes and the characterization of enzymatic reactions catalyzed by these proteins. However, as more examples of self-resistance have been reported, it has been revealed that the enzymatic reactions contribute to self-protection are not confined to the cellular location where the final toxic compounds are present. In this review, we summarize representative examples of self-resistance mechanisms for bioactive natural products functional at different cell locations to explore the models of resistance strategies involved. Moreover, we also highlight those resistance determinants that are widespread in nature and describe the applications of self-resistance genes in natural product mining to interrogate the landscape of self-resistance genes in drug resistance-related new drug discovery.
Collapse
|
19
|
The pks island: a bacterial Swiss army knife? Colibactin: beyond DNA damage and cancer. Trends Microbiol 2022; 30:1146-1159. [PMID: 35672224 DOI: 10.1016/j.tim.2022.05.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 01/13/2023]
Abstract
The structure and mode of action of colibactin with its potential involvement in cancer have been extensively studied but little is known about the intrinsic function of the biosynthetic gene cluster, coding for colibactin, as a bacterial genotoxin. Paradoxically, this pathogenicity island is also found in commensal and probiotic strains of Escherichia coli and in bacterial species colonizing olive trees and the digestive tract of bees. In this review, we summarize the available literature to address the following key questions. What does this genomic island really encode? What explains the extensive dissemination of this genetically mobile element? What do we really know about the biosynthetic and secretory pathways of colibactin? What is its inherent target/function?
Collapse
|
20
|
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.
Collapse
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,
| |
Collapse
|
21
|
Wong JJ, Ho FK, Choo PY, Chong KKL, Ho CMB, Neelakandan R, Keogh D, Barkham T, Chen J, Liu CF, Kline KA. Escherichia coli BarA-UvrY regulates the pks island and kills Staphylococci via the genotoxin colibactin during interspecies competition. PLoS Pathog 2022; 18:e1010766. [PMID: 36067266 PMCID: PMC9481169 DOI: 10.1371/journal.ppat.1010766] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 09/16/2022] [Accepted: 07/25/2022] [Indexed: 11/19/2022] Open
Abstract
Wound infections are often polymicrobial in nature, biofilm associated and therefore tolerant to antibiotic therapy, and associated with delayed healing. Escherichia coli and Staphylococcus aureus are among the most frequently cultured pathogens from wound infections. However, little is known about the frequency or consequence of E. coli and S. aureus polymicrobial interactions during wound infections. Here we show that E. coli kills Staphylococci, including S. aureus, both in vitro and in a mouse excisional wound model via the genotoxin, colibactin. Colibactin biosynthesis is encoded by the pks locus, which we identified in nearly 30% of human E. coli wound infection isolates. While it is not clear how colibactin is released from E. coli or how it penetrates target cells, we found that the colibactin intermediate N-myristoyl-D-Asn (NMDA) disrupts the S. aureus membrane. We also show that the BarA-UvrY two component system (TCS) senses the environment created during E. coli and S. aureus mixed species interaction, leading to upregulation of pks island genes. Further, we show that BarA-UvrY acts via the carbon storage global regulatory (Csr) system to control pks expression. Together, our data demonstrate the role of colibactin in interspecies competition and show that it is regulated by BarA-UvrY TCS during interspecies competition. Wound infections are often polymicrobial in nature and are associated with poor disease prognoses. Escherichia coli and Staphylococcus aureus are among the top five most cultured pathogens from wound infections. However, little is known about the polymicrobial interactions between E. coli and S. aureus during wound infections. In this study, we show that E. coli kills S. aureus both in vitro and in a mouse excisional wound model via the genotoxin, colibactin. We also show that the BarA-UvrY two component system (TCS) regulates the pks island during this mixed species interaction, acting through the carbon storage global regulatory (Csr) system to control colibactin production. Together, our data demonstrate the role of colibactin in interspecies competition and show that it is regulated by BarA-UvrY TCS during interspecies competition.
Collapse
Affiliation(s)
- Jun Jie Wong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate Programme, Nanyang Technological University, Singapore, Singapore
| | - Foo Kiong Ho
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Pei Yi Choo
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Kelvin K. L. Chong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Nanyang Technological University Institute for Health Technologies, Interdisciplinary Graduate School, Nanyang Technological University, Singapore, Singapore
| | - Chee Meng Benjamin Ho
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ramesh Neelakandan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Damien Keogh
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Timothy Barkham
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Laboratory Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - John Chen
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Chuan Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kimberly A. Kline
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
- * E-mail:
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Molecular basis of antibiotic self-resistance in a bee larvae pathogen. Nat Commun 2022; 13:2349. [PMID: 35487884 PMCID: PMC9054821 DOI: 10.1038/s41467-022-29829-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/30/2022] [Indexed: 11/08/2022] Open
Abstract
Paenibacillus larvae, the causative agent of the devastating honey-bee disease American Foulbrood, produces the cationic polyketide-peptide hybrid paenilamicin that displays antibacterial and antifungal activity. Its biosynthetic gene cluster contains a gene coding for the N-acetyltransferase PamZ. We show that PamZ acts as self-resistance factor in Paenibacillus larvae by deactivation of paenilamicin. Using tandem mass spectrometry, nuclear magnetic resonance spectroscopy and synthetic diastereomers, we identified the N-terminal amino group of the agmatinamic acid as the N-acetylation site. These findings highlight the pharmacophore region of paenilamicin, which we very recently identified as a ribosome inhibitor. Here, we further determined the crystal structure of PamZ:acetyl-CoA complex at 1.34 Å resolution. An unusual tandem-domain architecture provides a well-defined substrate-binding groove decorated with negatively-charged residues to specifically attract the cationic paenilamicin. Our results will help to understand the mode of action of paenilamicin and its role in pathogenicity of Paenibacillus larvae to fight American Foulbrood. The authors show that the N-acetyltransferase PamZ acts as a self-resistance factor disabling the antibacterial paenilamicin that is produced by the honey bee larvae pathogen Paenibacillus larvae.
Collapse
|
25
|
Chen J, Byun H, Liu R, Jung IJ, Pu Q, Zhu CY, Tanchoco E, Alavi S, Degnan PH, Ma AT, Roggiani M, Beld J, Goulian M, Hsiao A, Zhu J. A commensal-encoded genotoxin drives restriction of Vibrio cholerae colonization and host gut microbiome remodeling. Proc Natl Acad Sci U S A 2022; 119:e2121180119. [PMID: 35254905 PMCID: PMC8931321 DOI: 10.1073/pnas.2121180119] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 02/01/2022] [Indexed: 02/08/2023] Open
Abstract
SignificanceIn a polymicrobial battlefield where different species compete for nutrients and colonization niches, antimicrobial compounds are the sword and shield of commensal microbes in competition with invading pathogens and each other. The identification of an Escherichia coli-produced genotoxin, colibactin, and its specific targeted killing of enteric pathogens and commensals, including Vibrio cholerae and Bacteroides fragilis, sheds light on our understanding of intermicrobial interactions in the mammalian gut. Our findings elucidate the mechanisms through which genotoxins shape microbial communities and provide a platform for probing the larger role of enteric multibacterial interactions regarding infection and disease outcomes.
Collapse
Affiliation(s)
- Jiandong Chen
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Hyuntae Byun
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Rui Liu
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA 92521
| | - I-Ji Jung
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Qinqin Pu
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | | | - Ethan Tanchoco
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA 92521
| | - Salma Alavi
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA 92521
| | - Patrick H. Degnan
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA 92521
| | - Amy T. Ma
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102
| | - Manuela Roggiani
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Joris Beld
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102
| | - Mark Goulian
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Ansel Hsiao
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA 92521
| | - Jun Zhu
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| |
Collapse
|
26
|
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.
Collapse
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
| |
Collapse
|
27
|
Silpe JE, Wong JWH, Owen SV, Baym M, Balskus EP. The bacterial toxin colibactin triggers prophage induction. Nature 2022; 603:315-320. [PMID: 35197633 PMCID: PMC8907063 DOI: 10.1038/s41586-022-04444-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 01/18/2022] [Indexed: 12/11/2022]
Abstract
Colibactin is a chemically unstable small-molecule genotoxin that is produced by several different bacteria, including members of the human gut microbiome1,2. Although the biological activity of colibactin has been extensively investigated in mammalian systems3, little is known about its effects on other microorganisms. Here we show that colibactin targets bacteria that contain prophages, and induces lytic development through the bacterial SOS response. DNA, added exogenously, protects bacteria from colibactin, as does expressing a colibactin resistance protein (ClbS) in non-colibactin-producing cells. The prophage-inducing effects that we observe apply broadly across different phage-bacteria systems and in complex communities. Finally, we identify bacteria that have colibactin resistance genes but lack colibactin biosynthetic genes. Many of these bacteria are infected with predicted prophages, and we show that the expression of their ClbS homologues provides immunity from colibactin-triggered induction. Our study reveals a mechanism by which colibactin production could affect microbiomes and highlights a role for microbial natural products in influencing population-level events such as phage outbreaks.
Collapse
Affiliation(s)
- Justin E Silpe
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Joel W H Wong
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Siân V Owen
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Michael Baym
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, 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.
| |
Collapse
|
28
|
Abstract
The importance of the microbiota in the development of colorectal cancer (CRC) is increasingly evident, but identifying specific microbial features that influence CRC initiation and progression remains a central task for investigators. Studies determining the microbial mechanisms that directly contribute to CRC development or progression are revealing bacterial factors such as toxins that contribute to colorectal carcinogenesis. However, even when investigators have identified bacteria that express toxins, questions remain about the host determinants of a toxin's cancer-potentiating effects. For other cancer-correlating bacteria that lack toxins, the challenge is to define cancer-relevant virulence factors. Herein, we evaluate three CRC-correlating bacteria, colibactin-producing Escherichia coli, enterotoxigenic Bacteroides fragilis, and Fusobacterium nucleatum, for their virulence features relevant to CRC. We also consider the beneficial bioactivity of gut microbes by highlighting a microbial metabolite that may enhance CRC antitumor immunity. In doing so, we aim to elucidate unique and shared mechanisms underlying the microbiota's contributions to CRC and to accelerate investigation from target validation to CRC therapeutic discovery.
Collapse
Affiliation(s)
- Slater L. Clay
- Department of Immunology and Infectious Diseases and Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard T.H. Chan Microbiome in Public Health Center, Boston, Massachusetts, USA
| | - Diogo Fonseca-Pereira
- Department of Immunology and Infectious Diseases and Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard T.H. Chan Microbiome in Public Health Center, Boston, Massachusetts, USA
| | - Wendy S. Garrett
- Department of Immunology and Infectious Diseases and Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard T.H. Chan Microbiome in Public Health Center, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
29
|
Hueber A, Petitfils C, Le Faouder P, Langevin G, Guy A, Galano JM, Durand T, Martin JF, Tabet JC, Cenac N, Bertrand-Michel J. Discovery and quantification of lipoamino acids in bacteria. Anal Chim Acta 2022; 1193:339316. [PMID: 35058001 DOI: 10.1016/j.aca.2021.339316] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/04/2021] [Accepted: 11/21/2021] [Indexed: 11/15/2022]
Abstract
Improving knowledge about metabolites produced by the microbiota is a key point to understand its role in human health and disease. Among them, lipoamino acid (LpAA) containing asparagine and their derivatives are bacterial metabolites which could have an impact on the host. In this study, our aim was to extend the characterization of this family. We developed a semi-targeted workflow to identify and quantify new candidates. First, the sample preparation and analytical conditions using liquid chromatography (LC) coupled to high resolution mass spectrometry (HRMS) were optimized. Using a theoretical homemade database, HRMS raw data were manually queried. This strategy allowed us to find 25 new LpAA conjugated to Asn, Gln, Asp, Glu, His, Leu, Ile, Lys, Phe, Trp and Val amino acids. These metabolites were then fully characterized by MS2, and compared to the pure synthesized standards to validate annotation. Finally, a quantitative method was developed by LC coupled to a triple quadrupole instrument, and linearity and limit of quantification were determined. 14 new LpAA were quantified in gram positive bacteria, Lactobacilus animalis, and 12 LpAA in Escherichia coli strain Nissle 1917.
Collapse
Affiliation(s)
- Amandine Hueber
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France; I2MC, Université de Toulouse, Inserm, Université Toulouse 3 Paul Sabatier, Toulouse, France; IRSD, Université de Toulouse, INSERM, INRA, INPENVT, Université de Toulouse 3 Paul Sabatier, Toulouse, France
| | - Camille Petitfils
- IRSD, Université de Toulouse, INSERM, INRA, INPENVT, Université de Toulouse 3 Paul Sabatier, Toulouse, France
| | - Pauline Le Faouder
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France; I2MC, Université de Toulouse, Inserm, Université Toulouse 3 Paul Sabatier, Toulouse, France
| | - Geoffrey Langevin
- Institut des Biomolécules Max Mousseron IBMM, UMR 5247 CNRS, Université de Montpellier-ENSCM, Montpellier, France
| | - Alexandre Guy
- Institut des Biomolécules Max Mousseron IBMM, UMR 5247 CNRS, Université de Montpellier-ENSCM, Montpellier, France
| | - Jean-Marie Galano
- Institut des Biomolécules Max Mousseron IBMM, UMR 5247 CNRS, Université de Montpellier-ENSCM, Montpellier, France
| | - Thierry Durand
- Institut des Biomolécules Max Mousseron IBMM, UMR 5247 CNRS, Université de Montpellier-ENSCM, Montpellier, France
| | - Jean-François Martin
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France; Toxalim (Research Centre in Food Toxicology), INRAE UMR 1331, ENVT, INP-Purpan, Paul Sabatier University (UPS), Toulouse, France
| | - Jean-Claude Tabet
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France; Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191, Gif sur Yvette, France; Sorbonne Université, Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), F-75005, Paris, France
| | - Nicolas Cenac
- IRSD, Université de Toulouse, INSERM, INRA, INPENVT, Université de Toulouse 3 Paul Sabatier, Toulouse, France
| | - Justine Bertrand-Michel
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France; I2MC, Université de Toulouse, Inserm, Université Toulouse 3 Paul Sabatier, Toulouse, France.
| |
Collapse
|
30
|
Wu L, Zhang Q, Deng Z, Yu Y. From solo to duet, intersections of natural product assembly with self-resistance. Nat Prod Rep 2022; 39:919-925. [PMID: 34989738 DOI: 10.1039/d1np00064k] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: up to 2021Self-resistance mechanisms adopted by natural product producers have long been recognized and studied as a standalone system separated from the assembly machinery. However, as more examples of self-resistance have been characterized in detail, it has been revealed that self-resistance could associate with the assembly machinery to fulfill the task of biosynthesis. This review summarizes different self-resistance mechanisms showing a common feature: intersection with natural product assembly. Furthermore, their possible evolutionary origin and synthetic biology applications are discussed.
Collapse
Affiliation(s)
- Linrui Wu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
| | - Qian Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
| | - Yi Yu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
| |
Collapse
|
31
|
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: 8] [Impact Index Per Article: 2.7] [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.
Collapse
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
| |
Collapse
|
32
|
Washburn LA, Nepal KK, Watanabe CMH. A Capture Strategy for the Identification of Thio-Templated Metabolites. ACS Chem Biol 2021; 16:1737-1744. [PMID: 34423966 DOI: 10.1021/acschembio.1c00437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nonribosomal peptide synthetase and polyketide synthase systems are home to complex enzymology and produce compounds of great therapeutic value. Despite this, they have continued to be difficult to characterize due to their substrates remaining enzyme-bound by a thioester bond. Here, we have developed a strategy to directly trap and characterize the thioester-bound enzyme intermediates and applied the strategy to the azinomycin biosynthetic pathway. The approach was initially applied in vitro to evaluate its efficacy and subsequently moved to an in situ system, where a protein of interest was isolated from the native organism to avoid needing to supply substrates. When the nonribosomal peptide synthetase AziA3 was isolated from Streptomyces sahachiroi, the capture strategy revealed AziA3 functions in the late stages of epoxide moiety formation of the azinomycins. The strategy was further validated in vitro with a nonribosomal peptide synthetase involved in colibactin biosynthesis. In the long term, this method will be utilized to characterize thioester-bound metabolites within not only the azinomycin biosynthetic pathway but also other cryptic metabolite pathways.
Collapse
Affiliation(s)
- Lauren A. Washburn
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Keshav K. Nepal
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Coran M. H. Watanabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| |
Collapse
|
33
|
Tsunematsu Y, Hosomi K, Kunisawa J, Sato M, Shibuya N, Saito E, Murakami H, Yoshikawa Y, Iwashita Y, Miyoshi N, Mutoh M, Ishikawa H, Sugimura H, Miyachi M, Wakabayashi K, Watanabe K. Mother-to-infant transmission of the carcinogenic colibactin-producing bacteria. BMC Microbiol 2021; 21:235. [PMID: 34429063 PMCID: PMC8386082 DOI: 10.1186/s12866-021-02292-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 08/09/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The Escherichia coli strain that is known to produce the genotoxic secondary metabolite colibactin is linked to colorectal oncogenesis. Therefore, understanding the properties of such colibactin-positive E. coli and the molecular mechanism of oncogenesis by colibactin may provide us with opportunities for early diagnosis or prevention of colorectal oncogenesis. While there have been major advances in the characterization of colibactin-positive E. coli and the toxin it produces, the infection route of the clb + strain remains poorly characterized. RESULTS We examined infants and their treatments during and post-birth periods to examine potential transmission of colibactin-positive E. coli to infants. Here, analysis of fecal samples of infants over the first month of birth for the presence of a colibactin biosynthetic gene revealed that the bacterium may be transmitted from mother to infant through intimate contacts, such as natural childbirth and breastfeeding, but not through food intake. CONCLUSIONS Our finding suggests that transmission of colibactin-positive E. coli appears to be occurring at the very early stage of life of the newborn and hints at the possibility of developing early preventive measures against colorectal cancer.
Collapse
Affiliation(s)
- Yuta Tsunematsu
- Department of Pharmaceutical Sciences, University of Shizuoka, 422-8526, Shizuoka, Japan
| | - Koji Hosomi
- Laboratory of Vaccine Materials, Center for Vaccine and Adjuvant Research, Laboratory of Gut Environmental System, Health and Nutrition (NIBIOHN), National Institutes of Biomedical Innovation, 567-0085, Ibaraki-city, Japan
| | - Jun Kunisawa
- Laboratory of Vaccine Materials, Center for Vaccine and Adjuvant Research, Laboratory of Gut Environmental System, Health and Nutrition (NIBIOHN), National Institutes of Biomedical Innovation, 567-0085, Ibaraki-city, Japan
| | - Michio Sato
- Department of Pharmaceutical Sciences, University of Shizuoka, 422-8526, Shizuoka, Japan
| | - Noriko Shibuya
- Department of Pediatrics, Maternal and Child Health Center, Aiiku Clinic, 106-8580, Tokyo, Japan
| | - Emiko Saito
- Department of Human Nutrition, Tokyo Kasei Gakuin University, 194-0292, Tokyo, Japan
| | - Haruka Murakami
- Department of Physical Activity Research, Health and Nutrition (NIBIOHN), National Institutes of Biomedical Innovation, 162-8636, Tokyo, Japan
| | - Yuko Yoshikawa
- School of Veterinary Medicine, Faculty of Veterinary Science, Nippon Veterinary and Life Science University, 180-8602, Tokyo, Japan
| | - Yuji Iwashita
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 431- 3192, Shizuoka, Japan
| | - Noriyuki Miyoshi
- Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, 422-8526, Shizuoka, Japan
| | - Michihiro Mutoh
- Department of Molecular-Targeting Cancer Prevention, Kyoto Prefectural University of Medicine, 602-8566, Kyoto, Japan
| | - Hideki Ishikawa
- Department of Molecular-Targeting Cancer Prevention, Kyoto Prefectural University of Medicine, 602-8566, Kyoto, Japan
| | - Haruhiko Sugimura
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 431- 3192, Shizuoka, Japan
| | - Motohiko Miyachi
- Department of Physical Activity Research, Health and Nutrition (NIBIOHN), National Institutes of Biomedical Innovation, 162-8636, Tokyo, Japan
| | - Keiji Wakabayashi
- Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, 422-8526, Shizuoka, Japan
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, 422-8526, Shizuoka, Japan.
| |
Collapse
|
34
|
Abstract
The probiotic Escherichia coli strain Nissle 1917 (DSM 6601, Mutaflor), generally considered beneficial and safe, has been used for a century to treat various intestinal diseases. However, Nissle 1917 hosts in its genome the pks pathogenicity island that codes for the biosynthesis of the genotoxin colibactin. Colibactin is a potent DNA alkylator, suspected to play a role in colorectal cancer development. We show in this study that Nissle 1917 is functionally capable of producing colibactin and inducing interstrand cross-links in the genomic DNA of epithelial cells exposed to the probiotic. This toxicity was even exacerbated with lower doses of the probiotic, when the exposed cells started to divide again but exhibited aberrant anaphases and increased gene mutation frequency. DNA damage was confirmed in vivo in mouse models of intestinal colonization, demonstrating that Nissle 1917 produces the genotoxin in the gut lumen. Although it is possible that daily treatment of adult humans with their microbiota does not produce the same effects, administration of Nissle 1917 as a probiotic or as a chassis to deliver therapeutics might exert long-term adverse effects and thus should be considered in a risk-versus-benefit evaluation. IMPORTANCE Nissle 1917 is sold as a probiotic and considered safe even though it has been known since 2006 that it harbors the genes for colibactin synthesis. Colibactin is a potent genotoxin that is now linked to causative mutations found in human colorectal cancer. Many papers concerning the use of this strain in clinical applications ignore or elude this fact or misleadingly suggest that Nissle 1917 does not induce DNA damage. Here, we demonstrate that Nissle 1917 produces colibactin in vitro and in vivo and induces mutagenic DNA damage. This is a serious safety concern that must not be ignored in the interests of patients, the general public, health care professionals, and ethical probiotic manufacturers.
Collapse
|
35
|
Li P, Chen M, Tang W, Guo Z, Zhang Y, Wang M, Horsman GP, Zhong J, Lu Z, Chen Y. Initiating polyketide biosynthesis by on-line methyl esterification. Nat Commun 2021; 12:4499. [PMID: 34301953 PMCID: PMC8302727 DOI: 10.1038/s41467-021-24846-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 07/09/2021] [Indexed: 12/04/2022] Open
Abstract
Aurantinins (ARTs) are antibacterial polyketides featuring a unique 6/7/8/5-fused tetracyclic ring system and a triene side chain with a carboxyl terminus. Here we identify the art gene cluster and dissect ART’s C-methyl incorporation patterns to study its biosynthesis. During this process, an apparently redundant methyltransferase Art28 was characterized as a malonyl-acyl carrier protein O-methyltransferase, which represents an unusual on-line methyl esterification initiation strategy for polyketide biosynthesis. The methyl ester bond introduced by Art28 is kept until the last step of ART biosynthesis, in which it is hydrolyzed by Art9 to convert inactive ART 9B to active ART B. The cryptic reactions catalyzed by Art28 and Art9 represent a protecting group biosynthetic logic to render the ART carboxyl terminus inert to unwanted side reactions and to protect producing organisms from toxic ART intermediates. Further analyses revealed a wide distribution of this initiation strategy for polyketide biosynthesis in various bacteria. Aurantinins are polyketides with unusual connectivities and broad antibacterial activity. Here the authors show the biosynthesis of aurantinins, which proceeds via an on-line methyl esterification at the terminus that enables the iterative chain elongations prior to condensation and cyclization.
Collapse
Affiliation(s)
- Pengwei Li
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Meng Chen
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wei Tang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhengyan Guo
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuwei Zhang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Min Wang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, Guangdong, China
| | - Geoff P Horsman
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Jin Zhong
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agriculture University, Nanjing, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
36
|
Sadecki PW, Balboa SJ, Lopez LR, Kedziora KM, Arthur JC, Hicks LM. Evolution of Polymyxin Resistance Regulates Colibactin Production in Escherichia coli. ACS Chem Biol 2021; 16:1243-1254. [PMID: 34232632 PMCID: PMC8601121 DOI: 10.1021/acschembio.1c00322] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The complex reservoir of metabolite-producing bacteria in the gastrointestinal tract contributes tremendously to human health and disease. Bacterial composition, and by extension gut metabolomic composition, is undoubtably influenced by the use of modern antibiotics. Herein, we demonstrate that polymyxin B, a last resort antibiotic, influences the production of the genotoxic metabolite colibactin from adherent-invasive Escherichia coli (AIEC) NC101. Colibactin can promote colorectal cancer through DNA double stranded breaks and interstrand cross-links. While the structure and biosynthesis of colibactin have been elucidated, chemical-induced regulation of its biosynthetic gene cluster and subsequent production of the genotoxin by E. coli are largely unexplored. Using a multiomic approach, we identified that polymyxin B stress enhances the abundance of colibactin biosynthesis proteins (Clb's) in multiple pks+ E. coli strains, including pro-carcinogenic AIEC, NC101; the probiotic strain, Nissle 1917; and the antibiotic testing strain, ATCC 25922. Expression analysis via qPCR revealed that increased transcription of clb genes likely contributes to elevated Clb protein levels in NC101. Enhanced production of Clb's by NC101 under polymyxin stress matched an increased production of the colibactin prodrug motif, a proxy for the mature genotoxic metabolite. Furthermore, E. coli with a heightened tolerance for polymyxin induced greater mammalian DNA damage, assessed by quantification of γH2AX staining in cultured intestinal epithelial cells. This study establishes a key link between the polymyxin B stress response and colibactin production in pks+ E. coli. Ultimately, our findings will inform future studies investigating colibactin regulation and the ability of seemingly innocuous commensal microbes to induce host disease.
Collapse
Affiliation(s)
- Patric W. Sadecki
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Samantha J. Balboa
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Lacey R. Lopez
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Katarzyna M. Kedziora
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Bioinformatics and Analytics Research Collaborative (BARC), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Janelle C. Arthur
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Leslie M. Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| |
Collapse
|
37
|
Abstract
![]()
The genomic era has dramatically changed how we discover and investigate
microbial biochemistry. In particular, the exponential expansion in
the number of sequenced microbial genomes provides investigators with
a vast wealth of sequence data to exploit for the discovery of biochemical
functions and mechanisms, as well as novel enzymes and metabolites.
In contrast to early biochemical work, which was largely characterized
by “forward” approaches that proceed from biomass to
enzyme to gene, the availability of genome sequences enables the discovery
of new microbial metabolic activities, enzymes, and metabolites by
“reverse” approaches that originate with genetic information
or by approaches that incorporate features of both forward and reverse
methodologies. In the genomic era, the canonical organization of microbial
genomes into gene clusters presents a singular opportunity for the
utilization of genomic data. Specifically, genomic context (information
gleaned from the genes surrounding a gene of interest in the chromosome)
is a powerful tool for chemical discovery in microbial systems because
of the functional and/or physiological relationship that usually exists
between genes found within a gene cluster. This means that the investigator
can use this inferred link to generate hypotheses about the functions
of individual genes in the cluster or even the function of the entire
cluster itself. Here, we discuss how analysis of genomic context in
combination with a mechanistic understanding of enzymes can facilitate
numerous facets of microbial biochemical research including the identification
of biosynthetic gene clusters, the discovery of important and novel
enzymes, the elucidation of natural product structures, and the identification
of new metabolic pathways. We highlight work from our laboratory using
genomic context to discover and study biosynthetic pathways that produce
natural products, including the cylindrocyclophanes, nitrogen–nitrogen
bond-containing metabolites, and the gut microbial genotoxin colibactin.
Although use of genomic context is most commonly associated with studies
of natural product biosynthesis, we also show that it can be applied
to the study of primary metabolism. We illustrate this with examples
from our work studying the members of the glycyl radical enzyme superfamily
involved in choline and 4-hydroxyproline degradation in the human
gut. Looking forward, we envision increased opportunities to use such
information, with the combination of biochemical knowledge and computational
tools poised to fuel a new revolution in our ability to connect genes
and their biochemical functions. In particular, we note a need for
methods that computationally formalize the functional association
between genes when such associations are not obvious from manual gene
annotations. Such tools will drastically augment the feasibility and
scope of gene cluster analysis and accelerate the discovery of new
microbial enzymes, metabolites, and metabolic processes.
Collapse
Affiliation(s)
- Duncan J. Kountz
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| |
Collapse
|
38
|
Gut-inhabiting Clostridia build human GPCR ligands by conjugating neurotransmitters with diet- and human-derived fatty acids. Nat Microbiol 2021; 6:792-805. [PMID: 33846627 DOI: 10.1038/s41564-021-00887-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/01/2021] [Indexed: 02/01/2023]
Abstract
Human physiology is regulated by endogenous signalling compounds, including fatty acid amides (FAAs), chemical mimics of which are made by bacteria. The molecules produced by human-associated microbes are difficult to identify because they may only be made in a local niche or they require a substrate sourced from the host, diet or other microbes. We identified a set of uncharacterized gene clusters in metagenomics data from the human gut microbiome. These clusters were discovered to make FAAs by fusing exogenous fatty acids with amines. Using an in vitro assay, we tested their ability to incorporate 25 fatty acids and 53 amines known to be present in the human gut, from which the production of six FAAs was deduced (oleoyl dopamine, oleoyl tyramine, lauroyl tryptamine, oleoyl aminovaleric acid, α-linolenoyl phenylethylamine and caproyl tryptamine). These molecules were screened against panels of human G-protein-coupled receptors to deduce their putative human targets. Lauroyl tryptamine is found to be an antagonist to the immunomodulatory receptor EBI2 against its native oxysterol ligand (0.98 μM half-maximal inhibitory concentration), is produced in culture by Eubacterium rectale and is present in human faecal samples. FAAs produced by Clostridia may serve as a mechanism to modulate their host by mimicking human signalling molecules.
Collapse
|
39
|
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.
Collapse
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
| |
Collapse
|
40
|
Tripathi P, Bruner SD. Structural Basis for the Interactions of the Colibactin Resistance Gene Product ClbS with DNA. Biochemistry 2021; 60:1619-1625. [PMID: 33945270 DOI: 10.1021/acs.biochem.1c00201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The natural product colibactin, along with its associated biosynthetic gene cluster, is an example system for the role microbially derived small molecules play in the human microbiome. This is particularly relevant in the human gut, where host microbiota is involved in various disorders, including colorectal cancer pathogenesis. Bacteria harboring the colibactin gene cluster induce alkylation of nucleobases in host DNA, forming interstrand cross-links both in vivo and in vitro. These lesions can lead to deleterious double-strand breaks and have been identified as the primary mechanism of colibactin-induced cytotoxicity. The gene product ClbS is one of several mechanisms utilized by the producing bacteria to maintain genome integrity. ClbS catalyzes hydrolytic inactivation of colibactin and has been shown to bind DNA, incurring self-resistance. Presented is the molecular basis for ClbS bound to a DNA oligonucleotide. The structure shows the interaction of the protein with the ends of a DNA duplex with terminal nucleotides flipped to the enzyme active site. The structure suggests an additional function for ClbS, the binding to damaged DNA followed by repair. Additionally, our study provides general insight into the function of the widely distributed and largely uncharacterized DUF1706 protein family.
Collapse
Affiliation(s)
- Prabhanshu Tripathi
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Steven D Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| |
Collapse
|
41
|
Auvray F, Perrat A, Arimizu Y, Chagneau CV, Bossuet-Greif N, Massip C, Brugère H, Nougayrède JP, Hayashi T, Branchu P, Ogura Y, Oswald E. Insights into the acquisition of the pks island and production of colibactin in the Escherichia coli population. Microb Genom 2021; 7:000579. [PMID: 33961542 PMCID: PMC8209727 DOI: 10.1099/mgen.0.000579] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/11/2021] [Indexed: 01/19/2023] Open
Abstract
The pks island codes for the enzymes necessary for synthesis of the genotoxin colibactin, which contributes to the virulence of Escherichia coli strains and is suspected of promoting colorectal cancer. From a collection of 785 human and bovine E. coli isolates, we identified 109 strains carrying a highly conserved pks island, mostly from phylogroup B2, but also from phylogroups A, B1 and D. Different scenarios of pks acquisition were deduced from whole genome sequence and phylogenetic analysis. In the main scenario, pks was introduced and stabilized into certain sequence types (STs) of the B2 phylogroup, such as ST73 and ST95, at the asnW tRNA locus located in the vicinity of the yersiniabactin-encoding High Pathogenicity Island (HPI). In a few B2 strains, pks inserted at the asnU or asnV tRNA loci close to the HPI and occasionally was located next to the remnant of an integrative and conjugative element. In a last scenario specific to B1/A strains, pks was acquired, independently of the HPI, at a non-tRNA locus. All the pks-positive strains except 18 produced colibactin. Sixteen strains contained mutations in clbB or clbD, or a fusion of clbJ and clbK and were no longer genotoxic but most of them still produced low amounts of potentially active metabolites associated with the pks island. One strain was fully metabolically inactive without pks alteration, but colibactin production was restored by overexpressing the ClbR regulator. In conclusion, the pks island is not restricted to human pathogenic B2 strains and is more widely distributed in the E. coli population, while preserving its functionality.
Collapse
Affiliation(s)
- Frédéric Auvray
- IRSD, INSERM, Université de Toulouse, INRAE, ENVT, UPS, Toulouse, France
| | - Alexandre Perrat
- IRSD, INSERM, Université de Toulouse, INRAE, ENVT, UPS, Toulouse, France
| | - Yoko Arimizu
- Department of Bacteriology, Kyushu University, Fukuoka, Japan
| | | | | | - Clémence Massip
- IRSD, INSERM, Université de Toulouse, INRAE, ENVT, UPS, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse, France
| | - Hubert Brugère
- IRSD, INSERM, Université de Toulouse, INRAE, ENVT, UPS, Toulouse, France
| | | | - Tetsuya Hayashi
- Department of Bacteriology, Kyushu University, Fukuoka, Japan
| | - Priscilla Branchu
- IRSD, INSERM, Université de Toulouse, INRAE, ENVT, UPS, Toulouse, France
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Eric Oswald
- IRSD, INSERM, Université de Toulouse, INRAE, ENVT, UPS, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse, France
| |
Collapse
|
42
|
Figueiredo SAC, Preto M, Moreira G, Martins TP, Abt K, Melo A, Vasconcelos VM, Leão PN. Discovery of Cyanobacterial Natural Products Containing Fatty Acid Residues**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sandra A. C. Figueiredo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR) University of Porto Avenida General Norton de Matos, s/n 4450-208 Matosinhos Portugal
| | - Marco Preto
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR) University of Porto Avenida General Norton de Matos, s/n 4450-208 Matosinhos Portugal
| | - Gabriela Moreira
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR) University of Porto Avenida General Norton de Matos, s/n 4450-208 Matosinhos Portugal
| | - Teresa P. Martins
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR) University of Porto Avenida General Norton de Matos, s/n 4450-208 Matosinhos Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS) University of Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| | - Kathleen Abt
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR) University of Porto Avenida General Norton de Matos, s/n 4450-208 Matosinhos Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS) University of Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| | - André Melo
- LAQV@REQUIMTE/Department of Chemistry and Biochemistry Faculty of Sciences University of Porto Rua do Campo Alegre 4169-007 Porto Portugal
| | - Vitor M. Vasconcelos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR) University of Porto Avenida General Norton de Matos, s/n 4450-208 Matosinhos Portugal
- Department of Biology Faculty of Sciences University of Porto Rua do Campo Alegre 4169-007 Porto Portugal
| | - Pedro N. Leão
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR) University of Porto Avenida General Norton de Matos, s/n 4450-208 Matosinhos Portugal
| |
Collapse
|
43
|
Figueiredo SAC, Preto M, Moreira G, Martins TP, Abt K, Melo A, Vasconcelos VM, Leão PN. Discovery of Cyanobacterial Natural Products Containing Fatty Acid Residues*. Angew Chem Int Ed Engl 2021; 60:10064-10072. [PMID: 33599093 PMCID: PMC8252387 DOI: 10.1002/anie.202015105] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Indexed: 12/16/2022]
Abstract
In recent years, extensive sequencing and annotation of bacterial genomes has revealed an unexpectedly large number of secondary metabolite biosynthetic gene clusters whose products are yet to be discovered. For example, cyanobacterial genomes contain a variety of gene clusters that likely incorporate fatty acid derived moieties, but for most cases we lack the knowledge and tools to effectively predict or detect the encoded natural products. Here, we exploit the apparent absence of a functional β-oxidation pathway in cyanobacteria to achieve efficient stable-isotope-labeling of their fatty acid derived lipidome. We show that supplementation of cyanobacterial cultures with deuterated fatty acids can be used to easily detect natural product signatures in individual strains. The utility of this strategy is demonstrated in two cultured cyanobacteria by uncovering analogues of the multidrug-resistance reverting hapalosin, and novel, cytotoxic, lactylate-nocuolin A hybrids-the nocuolactylates.
Collapse
Affiliation(s)
- Sandra A. C. Figueiredo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR)University of PortoAvenida General Norton de Matos, s/n4450-208MatosinhosPortugal
| | - Marco Preto
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR)University of PortoAvenida General Norton de Matos, s/n4450-208MatosinhosPortugal
| | - Gabriela Moreira
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR)University of PortoAvenida General Norton de Matos, s/n4450-208MatosinhosPortugal
| | - Teresa P. Martins
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR)University of PortoAvenida General Norton de Matos, s/n4450-208MatosinhosPortugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS)University of PortoRua de Jorge Viterbo Ferreira, 2284050-313PortoPortugal
| | - Kathleen Abt
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR)University of PortoAvenida General Norton de Matos, s/n4450-208MatosinhosPortugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS)University of PortoRua de Jorge Viterbo Ferreira, 2284050-313PortoPortugal
| | - André Melo
- LAQV@REQUIMTE/Department of Chemistry and BiochemistryFaculty of SciencesUniversity of PortoRua do Campo Alegre4169-007PortoPortugal
| | - Vitor M. Vasconcelos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR)University of PortoAvenida General Norton de Matos, s/n4450-208MatosinhosPortugal
- Department of BiologyFaculty of SciencesUniversity of PortoRua do Campo Alegre4169-007PortoPortugal
| | - Pedro N. Leão
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR)University of PortoAvenida General Norton de Matos, s/n4450-208MatosinhosPortugal
| |
Collapse
|
44
|
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.
Collapse
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
| |
Collapse
|
45
|
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.
Collapse
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
| |
Collapse
|
46
|
Yang J, Zhu Q, Xu F, Yang M, Du H, Bian X, Lu Z, Lu Y, Lu F. Genome Mining, Heterologous Expression, Antibacterial and Antioxidant Activities of Lipoamides and Amicoumacins from Compost-Associated Bacillus subtilis fmb60. Molecules 2021; 26:molecules26071892. [PMID: 33810551 PMCID: PMC8036425 DOI: 10.3390/molecules26071892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 11/25/2022] Open
Abstract
Bacillus subtilis fmb60, which has broad-spectrum antimicrobial activities, was isolated from plant straw compost. A hybrid NRPS/PKS cluster was screened from the genome. Sixteen secondary metabolites produced by the gene cluster were isolated and identified using LC-HRMS and NMR. Three lipoamides D–F (1–3) and two amicoumacin derivatives, amicoumacins D, E (4, 5), were identified, and are reported here for the first time. Lipoamides D–F exhibited strong antibacterial activities against harmful foodborne bacteria, with the MIC ranging from 6.25 to 25 µg/mL. Amicoumacin E scavenged 38.8% of ABTS+ radicals at 1 mg/mL. Direct cloning and heterologous expression of the NRPS/PKS and ace gene cluster identified its importance for the biosynthesis of amicoumacins. This study demonstrated that there is a high potential for biocontrol utilization of B. subtilis fmb60, and genome mining for clusters of secondary metabolites of B. subtilis fmb60 has revealed a greater biosynthetic potential for the production of novel natural products than previously anticipated.
Collapse
Affiliation(s)
- Jie Yang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; (J.Y.); (Q.Z.); (F.X.)
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- Jiangsu Marine Resources Development Research Institute, Lianyungang 222000, China
| | - Qingzheng Zhu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; (J.Y.); (Q.Z.); (F.X.)
| | - Feng Xu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; (J.Y.); (Q.Z.); (F.X.)
| | - Ming Yang
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (M.Y.); (X.B.)
| | - Hechao Du
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China; (H.D.); (Z.L.)
| | - Xiaoying Bian
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (M.Y.); (X.B.)
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China; (H.D.); (Z.L.)
| | - Yingjian Lu
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210003, China
- Correspondence: (Y.L.); (F.L.); Tel./Fax: +86-258-439-5155 (Y.L.); +86-258-439-5963 (F.L.)
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China; (H.D.); (Z.L.)
- Correspondence: (Y.L.); (F.L.); Tel./Fax: +86-258-439-5155 (Y.L.); +86-258-439-5963 (F.L.)
| |
Collapse
|
47
|
Chagneau CV, Massip C, Bossuet-Greif N, Fremez C, Motta JP, Shima A, Besson C, Le Faouder P, Cénac N, Roth MP, Coppin H, Fontanié M, Martin P, Nougayrède JP, Oswald E. Uropathogenic E. coli induces DNA damage in the bladder. PLoS Pathog 2021; 17:e1009310. [PMID: 33630958 PMCID: PMC7906301 DOI: 10.1371/journal.ppat.1009310] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/13/2021] [Indexed: 01/19/2023] Open
Abstract
Urinary tract infections (UTIs) are among the most common outpatient infections, with a lifetime incidence of around 60% in women. We analysed urine samples from 223 patients with community-acquired UTIs and report the presence of the cleavage product released during the synthesis of colibactin, a bacterial genotoxin, in 55 of the samples examined. Uropathogenic Escherichia coli strains isolated from these patients, as well as the archetypal E. coli strain UTI89, were found to produce colibactin. In a murine model of UTI, the machinery producing colibactin was expressed during the early hours of the infection, when intracellular bacterial communities form. We observed extensive DNA damage both in umbrella and bladder progenitor cells. To the best of our knowledge this is the first report of colibactin production in UTIs in humans and its genotoxicity in bladder cells.
Collapse
Affiliation(s)
| | - Clémence Massip
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse, France
| | | | | | - Jean-Paul Motta
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
| | - Ayaka Shima
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
| | - Céline Besson
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
| | | | - Nicolas Cénac
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
| | - Marie-Paule Roth
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
| | - Hélène Coppin
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
| | | | - Patricia Martin
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
- VibioSphen, Prologue Biotech, Labège, France
| | | | - Eric Oswald
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse, France
| |
Collapse
|
48
|
Silpe J, Balskus EP. Deciphering Human Microbiota-Host Chemical Interactions. ACS CENTRAL SCIENCE 2021; 7:20-29. [PMID: 33532566 PMCID: PMC7844856 DOI: 10.1021/acscentsci.0c01030] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Indexed: 05/04/2023]
Abstract
Our gut harbors more microbes than any other body site, and accumulating evidence suggests that these organisms have a sizable impact on human health. Though efforts to classify the metabolic activities that define this microbial community have transformed the way we think about health and disease, our knowledge of gut microbially produced small molecules and their effects on host biology remains in its infancy. This Outlook surveys a range of approaches, hurdles, and advances in defining the chemical repertoire of the gut microbiota, drawing on examples with particularly strong links to human health. Progress toward understanding and manipulating this chemical language is being made with diverse chemical and biological expertise and could hold the key for combatting certain human diseases.
Collapse
Affiliation(s)
- Justin
E. Silpe
- Department of Chemistry and
Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and
Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| |
Collapse
|
49
|
Tang-Fichaux M, Chagneau CV, Bossuet-Greif N, Nougayrède JP, Oswald É, Branchu P. The Polyphosphate Kinase of Escherichia coli Is Required for Full Production of the Genotoxin Colibactin. mSphere 2020; 5:e01195-20. [PMID: 33328353 PMCID: PMC7771237 DOI: 10.1128/msphere.01195-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 12/15/2022] Open
Abstract
Colibactin induces DNA damage in mammalian cells and has been linked to the virulence of Escherichia coli and the promotion of colorectal cancer (CRC). By looking for mutants attenuated in the promoter activity of clbB encoding one of the key enzymes for the production of colibactin, we found that a mutant of the gene coding for the polyphosphate kinase (PPK) produced less colibactin than the parental strain. We observed this phenotype in different strains ranging from pathogens responsible for meningitis, urinary tract infection, or mouse colon carcinogenesis to the probiotic Nissle 1917. We confirmed the role of PPK by using an inhibitor of PPK enzymatic activity, mesalamine (also known as 5-aminosalicylic acid). Interestingly, mesalamine has a local anti-inflammatory effect on the epithelial cells of the colon and is used to treat inflammatory bowel disease (IBD). Upon treatment with mesalamine, a decreased genotoxicity of colibactin-producing E. coli was observed both on epithelial cells and directly on purified DNA. This demonstrates the direct effect of mesalamine on bacteria independently from its anti-inflammatory effect on eukaryotic cells. Our results suggest that the mechanisms of action of mesalamine in treating IBD and preventing CRC could also lie in the inhibition of colibactin production. All in all, we demonstrate that PPK is required for the promoter activity of clbB and the production of colibactin, which suggests that PPK is a promising target for the development of anticolibactin and antivirulence strategies.IMPORTANCE Colibactin-producing E. coli induces DNA damage in eukaryotic cells and promotes tumor formation in mouse models of intestinal inflammation. Recent studies have provided strong evidence supporting the causative role of colibactin in human colorectal cancer (CRC) progression. Therefore, it is important to understand the regulation of the production of this genotoxin. Here, we demonstrate that polyphosphate kinase (PPK) is required for the promoter activity of clbB and the production of colibactin. Interestingly, PPK is a multifunctional player in bacterial virulence and stress responses and has been proposed as a new target for developing antimicrobial medicine. We observed inhibition of colibactin production by using a previously identified PPK inhibitor (i.e., mesalamine, an anti-inflammatory drug commonly prescribed for inflammatory bowel diseases). These data brought us a new perspective on the regulatory network of colibactin production and provided us a clue for the development of anticolibactin strategies for CRC treatment/prophylaxis.
Collapse
Affiliation(s)
- Min Tang-Fichaux
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France
| | - Camille V Chagneau
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France
| | | | | | - Éric Oswald
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France
- CHU Toulouse, Service de Bactériologie-Hygiène, Toulouse, France
| | - Priscilla Branchu
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France
| |
Collapse
|
50
|
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.
Collapse
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
| |
Collapse
|