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Shi C, Patel VA, Mitchell DA, Zhao H. Enterolyin S, a Polythiazole-containing Hemolytic Peptide from Enterococcus caccae. Chembiochem 2024; 25:e202400212. [PMID: 38648232 PMCID: PMC11186716 DOI: 10.1002/cbic.202400212] [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: 04/01/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 04/25/2024]
Abstract
The β-hemolytic factor streptolysin S (SLS) is an important linear azol(in)e-containing peptide (LAP) that contributes significantly to the virulence of Streptococcus pyogenes. Despite its discovery 85 years ago, SLS has evaded structural characterizing owing to its notoriously problematic physicochemical properties. Here, we report the discovery and characterization of a structurally analogous hemolytic peptide from Enterococcus caccae, termed enterolysin S (ELS). Through heterologous expression, site-directed mutagenesis, chemoselective modification, and high-resolution mass spectrometry, we found that ELS contains an intriguing contiguous octathiazole moiety. The discovery of ELS expands our knowledge of hemolytic LAPs by adding a new member to this virulence-promoting family of modified peptides.
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Affiliation(s)
- Chengyou Shi
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana Champaign, Urbana, IL, 61801, USA
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana Champaign, Urbana, IL, 61801, USA
| | - Varshal A Patel
- Department of Biochemistry, University of Illinois, Urbana Champaign, Urbana, IL, 61801, USA
| | - Douglas A Mitchell
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana Champaign, Urbana, IL, 61801, USA
- Department of Chemistry, University of Illinois, Urbana Champaign, Urbana, IL, 61801, USA
| | - Huimin Zhao
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana Champaign, Urbana, IL, 61801, USA
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana Champaign, Urbana, IL, 61801, USA
- Department of Biochemistry, University of Illinois, Urbana Champaign, Urbana, IL, 61801, USA
- Department of Chemistry, University of Illinois, Urbana Champaign, Urbana, IL, 61801, USA
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2
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Sengupta S, Pabbaraja S, Mehta G. Natural products from the human microbiome: an emergent frontier in organic synthesis and drug discovery. Org Biomol Chem 2024; 22:4006-4030. [PMID: 38669195 DOI: 10.1039/d4ob00236a] [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: 04/28/2024]
Abstract
Often referred to as the "second genome", the human microbiome is at the epicenter of complex inter-habitat biochemical networks like the "gut-brain axis", which has emerged as a significant determinant of cognition, overall health and well-being, as well as resistance to antibiotics and susceptibility to diseases. As part of a broader understanding of the nexus between the human microbiome, diseases and microbial interactions, whether encoded secondary metabolites (natural products) play crucial signalling roles has been the subject of intense scrutiny in the recent past. A major focus of these activities involves harvesting the genomic potential of the human microbiome via bioinformatics guided genome mining and culturomics. Through these efforts, an impressive number of structurally intriguing antibiotics, with enhanced chemical diversity vis-à-vis conventional antibiotics have been isolated from human commensal bacteria, thereby generating considerable interest in their total synthesis and expanding their therapeutic space for drug discovery. These developments augur well for the discovery of new drugs and antibiotics, particularly in the context of challenges posed by mycobacterial resistance and emerging new diseases. The current landscape of various synthetic campaigns and drug discovery initiatives on antibacterial natural products from the human microbiome is captured in this review with an intent to stimulate further activities in this interdisciplinary arena among the new generation.
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Affiliation(s)
- Saumitra Sengupta
- School of Chemistry, University of Hyderabad, Hyderabad-500046, India.
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad-500007, India
| | - Srihari Pabbaraja
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad-500007, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Goverdhan Mehta
- School of Chemistry, University of Hyderabad, Hyderabad-500046, India.
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3
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Ajeigbe M, Childs S, Paget TA, Bingle LEH. Complete nucleotide sequence and comparative genomic analysis of microcin B17 plasmid pMccB17. Microbiologyopen 2024; 13:e1402. [PMID: 38440924 PMCID: PMC10912980 DOI: 10.1002/mbo3.1402] [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] [Revised: 02/11/2024] [Accepted: 02/16/2024] [Indexed: 03/06/2024] Open
Abstract
We present a comprehensive sequence and bioinformatic analysis of the prototypical microcin plasmid, pMccb17, which includes a definitive sequence for the microcin operon, mcb. Microcin B17 (MccB17) is a ribosomally synthesized and posttranslationally modified peptide produced by Escherichia coli. It inhibits bacterial DNA gyrase similarly to quinolone antibiotics. The mcb operon, which consists of seven genes encoding biosynthetic and immunity/export functions, was originally located on the low copy number IncFII plasmid pMccB17 in the Escherichia coli strain LP17. It was later transferred to E. coli K-12 through conjugation. In this study, the plasmid was extracted from the E. coli K-12 strain RYC1000 [pMccB17] and sequenced twice using an Illumina short-read method. The first sequencing was conducted with the host bacterial chromosome, and the plasmid DNA was then purified and sequenced separately. After assembly into a single contig, polymerase chain reaction primers were designed to close the single remaining gap via Sanger sequencing. The resulting complete circular DNA sequence is 69,190 bp long and includes 81 predicted genes. These genes were initially identified by Prokka and subsequently manually reannotated using BLAST. The plasmid was assigned to the F2:A-:B- replicon type with a MOBF12 group conjugation system. A comparison with other IncFII plasmids revealed a large proportion of shared genes, particularly in the conjugative plasmid backbone. However, unlike many contemporary IncFII plasmids, pMccB17 lacks transposable elements and antibiotic resistance genes. In addition to the mcb operon, this plasmid carries 25 genes of unknown function.
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Affiliation(s)
- Mayokun Ajeigbe
- School of Nursing and Health Sciences, Faculty of Health Sciences and WellbeingUniversity of SunderlandSunderlandUK
| | - Stephen Childs
- School of Pharmacy & Pharmaceutical Sciences, Faculty of Health Sciences and WellbeingUniversity of SunderlandSunderlandUK
| | - Timothy A. Paget
- School of Medicine, Faculty of Health Sciences and WellbeingUniversity of SunderlandSunderlandUK
| | - Lewis E. H. Bingle
- School of Nursing and Health Sciences, Faculty of Health Sciences and WellbeingUniversity of SunderlandSunderlandUK
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4
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Telhig S, Pham NP, Ben Said L, Rebuffat S, Ouellette M, Zirah S, Fliss I. Exploring the genetic basis of natural resistance to microcins. Microb Genom 2024; 10:001156. [PMID: 38407259 PMCID: PMC10926693 DOI: 10.1099/mgen.0.001156] [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: 03/29/2023] [Accepted: 11/28/2023] [Indexed: 02/27/2024] Open
Abstract
Enterobacteriaceae produce an arsenal of antimicrobial compounds including microcins, ribosomally produced antimicrobial peptides showing diverse structures and mechanisms of action. Microcins target close relatives of the producing strain to promote its survival. Their narrow spectrum of antibacterial activity makes them a promising alternative to conventional antibiotics, as it should decrease the probability of resistance dissemination and collateral damage to the host's microbiota. To assess the therapeutic potential of microcins, there is a need to understand the mechanisms of resistance to these molecules. In this study, we performed genomic analyses of the resistance to four microcins [microcin C, a nucleotide peptide; microcin J25, a lasso peptide; microcin B17, a linear azol(in)e-containing peptide; and microcin E492, a siderophore peptide] on a collection of 54 Enterobacteriaceae from three species: Escherichia coli, Salmonella enterica and Klebsiella pneumoniae. A gene-targeted analysis revealed that about half of the microcin-resistant strains presented mutations of genes involved in the microcin mechanism of action, especially those involved in their uptake (fhuA, fepA, cirA and ompF). A genome-wide association study did not reveal any significant correlations, yet relevant genetic elements were associated with microcin resistance. These were involved in stress responses, biofilm formation, transport systems and acquisition of immunity genes. Additionally, microcin-resistant strains exhibited several mutations within genes involved in specific metabolic pathways, especially for S. enterica and K. pneumoniae.
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Affiliation(s)
- Soufiane Telhig
- Food Science Department, Food and Agriculture Faculty, Laval University, Quebec, Canada
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum national d’Histoire naturelle, Centre national de la Recherche scientifique, Paris, France
| | - Nguyen Phuong Pham
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Laila Ben Said
- Food Science Department, Food and Agriculture Faculty, Laval University, Quebec, Canada
- Institute of Nutrition and Functional Foods, Laval University, Quebec, Canada
| | - Sylvie Rebuffat
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum national d’Histoire naturelle, Centre national de la Recherche scientifique, Paris, France
| | - Marc Ouellette
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Séverine Zirah
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum national d’Histoire naturelle, Centre national de la Recherche scientifique, Paris, France
| | - Ismaïl Fliss
- Food Science Department, Food and Agriculture Faculty, Laval University, Quebec, Canada
- Institute of Nutrition and Functional Foods, Laval University, Quebec, Canada
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5
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Ruan S, Tu CH, Bourne CR. Friend or Foe: Protein Inhibitors of DNA Gyrase. BIOLOGY 2024; 13:84. [PMID: 38392303 PMCID: PMC10886550 DOI: 10.3390/biology13020084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/20/2024] [Accepted: 01/26/2024] [Indexed: 02/24/2024]
Abstract
DNA gyrase is essential for the successful replication of circular chromosomes, such as those found in most bacterial species, by relieving topological stressors associated with unwinding the double-stranded genetic material. This critical central role makes gyrase a valued target for antibacterial approaches, as exemplified by the highly successful fluoroquinolone class of antibiotics. It is reasonable that the activity of gyrase could be intrinsically regulated within cells, thereby helping to coordinate DNA replication with doubling times. Numerous proteins have been identified to exert inhibitory effects on DNA gyrase, although at lower doses, it can appear readily reversible and therefore may have regulatory value. Some of these, such as the small protein toxins found in plasmid-borne addiction modules, can promote cell death by inducing damage to DNA, resulting in an analogous outcome as quinolone antibiotics. Others, however, appear to transiently impact gyrase in a readily reversible and non-damaging mechanism, such as the plasmid-derived Qnr family of DNA-mimetic proteins. The current review examines the origins and known activities of protein inhibitors of gyrase and highlights opportunities to further exert control over bacterial growth by targeting this validated antibacterial target with novel molecular mechanisms. Furthermore, we are gaining new insights into fundamental regulatory strategies of gyrase that may prove important for understanding diverse growth strategies among different bacteria.
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Affiliation(s)
- Shengfeng Ruan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Chih-Han Tu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Christina R Bourne
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
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Gu Q, Yan J, Lou Y, Zhang Z, Li Y, Zhu Z, Liu M, Wu D, Liang Y, Pu J, Zhao X, Xiao H, Li P. Bacteriocins: Curial guardians of gastrointestinal tract. Compr Rev Food Sci Food Saf 2024; 23:e13292. [PMID: 38284593 DOI: 10.1111/1541-4337.13292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/05/2023] [Accepted: 12/14/2023] [Indexed: 01/30/2024]
Abstract
The human gastrointestinal (GI) tract microbiome secretes various metabolites that play pivotal roles in maintaining host physiological balance and influencing disease progression. Among these metabolites, bacteriocins-small, heat-stable peptides synthesized by ribosomes-are notably prevalent in the GI region. Their multifaceted benefits have garnered significant interest in the scientific community. This review comprehensively explores the methods for mining bacteriocins (traditional separation and purification, bioinformatics, and artificial intelligence), their effects on the stomach and intestines, and their complex bioactive mechanisms. These mechanisms include flora regulation, biological barrier restoration, and intervention in epithelial cell pathways. By detailing each well-documented bacteriocin, we reveal the diverse ways in which bacteriocins interact with the GI environment. Moreover, the future research direction is prospected. By further studying the function and interaction of intestinal bacteriocins, we can discover new pharmacological targets and develop drugs targeting intestinal bacteriocins to regulate and improve human health. It provides innovative ideas and infinite possibilities for further exploration, development, and utilization of bacteriocins. The inevitable fact is that the continuously exploration of bacteriocins is sure to bring the promising future for demic GI health understanding and interference strategy.
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Affiliation(s)
- Qing Gu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Jiaqian Yan
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Yeqing Lou
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Zihao Zhang
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Yonglu Li
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Zichun Zhu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Manman Liu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Danli Wu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Ying Liang
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Jiaqian Pu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Xiaodan Zhao
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Hang Xiao
- Department of Food Science, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Ping Li
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
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Biswas P, Sengupta S, Nagaraja V. Evolution of YacG to safeguard DNA gyrase from external perturbation. Res Microbiol 2023; 174:104093. [PMID: 37343614 DOI: 10.1016/j.resmic.2023.104093] [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: 03/20/2023] [Revised: 06/10/2023] [Accepted: 06/14/2023] [Indexed: 06/23/2023]
Abstract
Cells have evolved strategies to safeguard their genome integrity. We describe a mechanism to counter double strand breaks in the chromosome that involves the protection of an essential housekeeping enzyme from external agents. YacG is a DNA gyrase inhibitory protein from Escherichia coli that protects the bacterium from the cytotoxic effects of catalytic inhibitors as well as cleavage-complex stabilizers of DNA gyrase. By virtue of blocking the primary DNA binding site of the enzyme, YacG prevents the accumulation of double strand breaks induced by gyrase poisons. It also enables the bacterium to resist the growth-inhibitory property of novobiocin. Gyrase poison-induced oxidative stress upregulates YacG production, probably as a cellular response to counter DNA damage. YacG-mediated protection of the genome is specific for gyrase targeting agents as the protection is not observed from the action of general DNA damaging agents. YacG also intensifies the transcription stress induced by rifampicin substantiating the importance of gyrase activity during transcription. Although essential for bacterial survival, DNA gyrase often gets entrapped by external inhibitors and poisons, resulting in cell death. The existence of YacG to specifically protect an essential housekeeping enzyme might be a strategy adopted by bacteria for competitive fitness advantage.
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Affiliation(s)
- Priti Biswas
- Department of Life Sciences, Presidency University Kolkata, 86/1 College Street, Kolkata-700073, India.
| | - Sugopa Sengupta
- Department of Life Sciences, Presidency University Kolkata, 86/1 College Street, Kolkata-700073, India.
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore-560064, India.
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8
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Le MNT, Nguyen THH, Trinh VM, Nguyen TPB, Kawada-Matsuo M, Kayama S, Sugai M, Komatsuzawa H. Comprehensive Analysis of Bacteriocins Produced by the Hypermucoviscous Klebsiella pneumoniae Species Complex. Microbiol Spectr 2023; 11:e0086323. [PMID: 37154746 PMCID: PMC10269471 DOI: 10.1128/spectrum.00863-23] [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: 03/06/2023] [Accepted: 04/11/2023] [Indexed: 05/10/2023] Open
Abstract
Klebsiella pneumoniae produces several kinds of bacteriocins that have antimicrobial effects against closely related species, but few studies have comprehensively reported bacteriocin distribution among the Klebsiella population. In this study, we identified bacteriocin genes in 180 K. pneumoniae species complex genomes, including 170 hypermucoviscous isolates, and investigated the antibacterial activity against 50 strains, including antimicrobial-resistant organisms, belonging to multiple species, namely, Klebsiella spp., Escherichia coli, Pseudomonas spp., Acinetobacter spp., Enterobacter cloacae, Stenotrophomonas maltophilia, Chryseobacterium indologenes, Staphylococcus aureus, Staphylococcus epidermidis, and Streptococcus mutans. Our study determined that 32.8% (59/180) of isolates carried at least one bacteriocin type. Different types of bacteriocin were usually present in different specific sequence types (STs); meanwhile, bacteriocins were not detected in certain STs. Microcin E492 was the most prevalent bacteriocin (14.4%), mostly in ST23 isolates, and displayed a wide spectrum of activity, including against Klebsiella spp., E. coli, Pseudomonas spp., and Acinetobacter spp. Cloacin-like bacteriocin was detected in 7.2% of strains, all of which were non-ST23 isolates, and exhibited inhibitory activity against closely related species, mainly Klebsiella spp. Klebicin B-like bacteriocin was detected at a rate of 9.4%, although 82.4% of these strains carried a disrupted bacteriocin gene, and an inhibitory effect could not be observed from the intact-gene-carrying isolates. Other bacteriocins, such as microcin S-like, microcin B17, and klebicin C-like, were detected at lower rates and had limited inhibitory activity. Our findings suggested that Klebsiella strains that carry different bacteriocin types may affect the composition of the surrounding bacterial community. IMPORTANCE Klebsiella pneumoniae is a Gram-negative commensal bacterium that asymptomatically colonizes human mucosal membranes, such as the intestinal tract, but it is also a leading cause of health care- and community-associated infections. Additionally, multidrug-resistant K. pneumoniae has been continuously evolving, which significantly challenges the available chemotherapeutic treatment for its infections. K. pneumoniae produces several kinds of antimicrobial peptides known as bacteriocins, which have antibacterial activity against closely related species. This work was the first comprehensive report of bacteriocin distribution among the hypermucoviscous K. pneumoniae species complex population and the inhibitory activity of each bacteriocin type against various species, including multidrug-resistant strains. Our findings provide a foundation for future studies on the K. pneumoniae species complex, including studies on the competition within the microflora and the potential applications of bacteriocins in treating multidrug-resistant bacteria.
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Affiliation(s)
- Mi Nguyen-Tra Le
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
| | - Thao Huu-Huong Nguyen
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Van Minh Trinh
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Tam Phuc-Bao Nguyen
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Miki Kawada-Matsuo
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
| | - Shizuo Kayama
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Motoyuki Sugai
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hitoshi Komatsuzawa
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
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9
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Vagstad AL. Engineering ribosomally synthesized and posttranslationally modified peptides as new antibiotics. Curr Opin Biotechnol 2023; 80:102891. [PMID: 36702077 DOI: 10.1016/j.copbio.2023.102891] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/22/2022] [Accepted: 12/19/2022] [Indexed: 01/25/2023]
Abstract
The rise of antimicrobial resistance is an urgent public health threat demanding the invention of new drugs to combat infections. Naturally sourced nonribosomal peptides (NRPs) have a long history as antimicrobial drugs. Through recent advances in genome mining and engineering technologies, their ribosomally synthesized and posttranslationally modified peptide (RiPP) counterparts are poised to further contribute to the arsenal of anti-infectives. As natural products from diverse organisms involved in interspecies competition, many RiPPs already possess antimicrobial activities that can be further optimized as drug candidates. Owing to the mutability of precursor protein genes that encode their core structures and the availability of diverse posttranslational modification (PTM) enzymes with broad substrate tolerances, RiPP systems are well suited to engineer complex peptides with desired functions.
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Affiliation(s)
- Anna L Vagstad
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland.
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10
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Karthik Y, Kalyani MI. Occurrence of Streptomyces tauricus in mangrove soil of Mangalore region in Dakshina Kannada as a source for antimicrobial peptide. J Basic Microbiol 2023; 63:389-403. [PMID: 35876342 DOI: 10.1002/jobm.202200108] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 06/09/2022] [Accepted: 07/10/2022] [Indexed: 11/09/2022]
Abstract
Microbial resistance and deprivation of the effective drugs have become the foremost problem that propels to seek out for advanced approach. This concept initiated a need to search for more effective antimicrobial compounds from reliable sources. The Streptomyces is grouped under phylum Actinobacteria and are considered prolific producers of antibiotics, around 70% of presently available antibiotics are contributed by Streptomyces alone. In this study, Mangroves of the Mangalore Coast offered a unique source for screening Actinomyces group of microorganisms. We investigated on the four soil samples collected from Mangrove swamps of Mangalore, Karnataka, India. Based on their culture traits, the 18 distinct Actinomyces isolates were analyzed through a series of morphological and biochemical tests on starch casein nitrate (SCN) media. Culture biomasses were subjected for intracellular protein extraction through acetone precipitation method; the extracted proteins from each Actinomyces isolate were examined for antimicrobial activity against test organisms. The isolate ANTB-YKMU4 showed potential antimicrobial activity against significant number of test organisms; Bacillus cereus, Proteus vulgaris, Staphylococcus aureus, Salmonella typhimurium, and Pseudomonas aeruginosa. The isolate ANTB-YKMU4 through 16 s rRNA gene sequence analysis was identified as Streptomyces tauricus strain with GenBank accession no. MW785875.1. The S. tauricus further cultivated for efficient biomass growth on SCN media for subsequent protein extraction and purification by a series of Electrophoretic and chromatographic techniques. Thus, by intracellular extractions from S. tauricus resulted in the identification of peptide with a molecular weight of 266 Da that was characterized by LC-MS.
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Affiliation(s)
- Yalpi Karthik
- Department of Studies and Research in Microbiology, Mangalore University, Jnana Kaveri Campus, Chikka Aluvara, Kodagu, Karnataka, India
| | - Manjula Ishwara Kalyani
- Department of Studies and Research in Microbiology, Mangalore University, Jnana Kaveri Campus, Chikka Aluvara, Kodagu, Karnataka, India
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11
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Karthik Y, Ishwara Kalyani M, Krishnappa S, Devappa R, Anjali Goud C, Ramakrishna K, Wani MA, Alkafafy M, Hussen Abduljabbar M, Alswat AS, Sayed SM, Mushtaq M. Antiproliferative activity of antimicrobial peptides and bioactive compounds from the mangrove Glutamicibacter mysorens. Front Microbiol 2023; 14:1096826. [PMID: 36876075 PMCID: PMC9982118 DOI: 10.3389/fmicb.2023.1096826] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 01/26/2023] [Indexed: 02/19/2023] Open
Abstract
The Glutamicibacter group of microbes is known for antibiotic and enzyme production. Antibiotics and enzymes produced by them are important in the control, protection, and treatment of chronic human diseases. In this study, the Glutamicibacter mysorens (G. mysorens) strain MW647910.1 was isolated from mangrove soil in the Mangalore region of India. After optimization of growth conditions for G. mysorens on starch casein agar media, the micromorphology of G. mysorens was found to be spirally coiled spore chain, each spore visualized as an elongated cylindrical hairy appearance with curved edges visualized through Field Emission Scanning Electron Microscopy (FESEM) analysis. The culture phenotype with filamentous mycelia, brown pigmentation, and ash-colored spore production was observed. The intracellular extract of G. mysorens characterized through GCMS analysis detected bioactive compounds reported for pharmacological applications. The majority of bioactive compounds identified in intracellular extract when compared to the NIST library revealed molecular weight ranging below 1kgmole-1. The Sephadex G-10 could result in 10.66 fold purification and eluted peak protein fraction showed significant anticancer activity on the prostate cancer cell line. Liquid Chromatography-Mass Spectrometry (LC-MS) analysis revealed Kinetin-9-ribose and Embinin with a molecular weight below 1 kDa. This study showed small molecular weight bioactive compounds produced from microbial origin possess dual roles, acting as antimicrobial peptides (AMPs) and anticancer peptides (ACPs). Hence, the bioactive compounds produced from microbial origin are a promising source of future therapeutics.
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Affiliation(s)
- Yalpi Karthik
- Department of Studies and Research in Microbiology, Mangalore University, Mangalore, Karnataka, India
| | - Manjula Ishwara Kalyani
- Department of Studies and Research in Microbiology, Mangalore University, Mangalore, Karnataka, India
| | - Srinivasa Krishnappa
- Department of Studies and Research in Biochemistry, Mangalore University, Mangalore, Karnataka, India
| | - Ramakrishna Devappa
- Dr. C.D Sagar Centre for Life Sciences, Biotechnology Department, Dayananda Sagar College of Engineering, Dayananda Sagar Institutions, Bengaluru, India
| | - Chengeshpur Anjali Goud
- Department of Plant Biotechnology, School of Agricultural Sciences, Malla Reddy University, Hyderabad, India
| | - Krishnaveni Ramakrishna
- Department of Studies and Research in Microbiology, Vijayanagara Sri Krishnadevaraya University, Ballari, Karnataka, India
| | - Muneeb Ahmad Wani
- Division of Floriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, Jammu and Kashmir, India
| | - Mohamed Alkafafy
- Department of Cytology and Histology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Maram Hussen Abduljabbar
- Department of Pharmacology and Toxicology, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Amal S Alswat
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Samy M Sayed
- Department of Economic Entomology and Pesticides, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Muntazir Mushtaq
- ICAR-National Bureau of Plant Genetic Resources, Division of Germplasm Evaluation, New Delhi, India.,MS Swaminathan School of Agriculture, Shoolini University of Biotechnology and Management, Bajhol, Himachal Pradesh, India
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12
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Vobruba S, Kadlcik S, Janata J, Kamenik Z. TldD/TldE peptidases and N-deacetylases: A structurally unique yet ubiquitous protein family in the microbial metabolism. Microbiol Res 2022; 265:127186. [PMID: 36155963 DOI: 10.1016/j.micres.2022.127186] [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: 07/03/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 10/14/2022]
Abstract
Here we provide a review on TldD/TldE family proteins, summarizing current knowledge and outlining further research perspectives. Despite being widely distributed in bacteria and archaea, TldD/TldE proteins have been escaping attention for a long time until several recent reports pointed to their unique features. Specifically, TldD/TldE generally act as peptidases, though some of them turned out to be N-deacetylases. Biological function of TldD/TldE has been extensively described in bacterial specialized metabolism, in which they participate in the biosynthesis of lincosamide antibiotics (as N-deacetylases), and in the biosynthesis of ribosomally synthesized and post-translationally modified bioactive peptides (as peptidases). These enzymes possess special position in the relevant biosynthesis since they convert non-bioactive intermediates into bioactive metabolites. Further, based on a recent study of Escherichia coli TldD/TldE, these heterodimeric metallopeptidases possess a new protein fold exhibiting several structural features with no precedent in the Protein Data Bank. The most interesting ones are structural elements forming metal-containing active site on the inner surface of the catalytically active subunit TldD, in which substrates bind through β sheet interactions in the sequence-independent manner. It results in relaxed substrate specificity of TldD/TldE, which is counterbalanced by enclosing the active centre within the hollow core of the heterodimer and only appropriate substrates can entry through a narrow channel. Based on the published data, we hypothesize a yet unrecognized central metabolic function of TldD/TldE in the degradation of (partially) unfolded proteins, i.e., in protein quality control.
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Affiliation(s)
- Simon Vobruba
- Czech Academy of Sciences, Institute of Microbiology, Prague, Czech Republic
| | - Stanislav Kadlcik
- Czech Academy of Sciences, Institute of Microbiology, Prague, Czech Republic
| | - Jiri Janata
- Czech Academy of Sciences, Institute of Microbiology, Prague, Czech Republic
| | - Zdenek Kamenik
- Czech Academy of Sciences, Institute of Microbiology, Prague, Czech Republic.
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13
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Comparative Metagenomic Analysis of Biosynthetic Diversity across Sponge Microbiomes Highlights Metabolic Novelty, Conservation, and Diversification. mSystems 2022; 7:e0035722. [PMID: 35862823 PMCID: PMC9426513 DOI: 10.1128/msystems.00357-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine sponges and their microbial symbiotic communities are rich sources of diverse natural products (NPs) that often display biological activity, yet little is known about the global distribution of NPs and the symbionts that produce them. Since the majority of sponge symbionts remain uncultured, it is a challenge to characterize their NP biosynthetic pathways, assess their prevalence within the holobiont, and measure the diversity of NP biosynthetic gene clusters (BGCs) across sponge taxa and environments. Here, we explore the microbial biosynthetic landscapes of three high-microbial-abundance (HMA) sponges from the Atlantic Ocean and the Mediterranean Sea. This data set reveals striking novelty, with <1% of the recovered gene cluster families (GCFs) showing similarity to any characterized BGC. When zooming in on the microbial communities of each sponge, we observed higher variability of specialized metabolic and taxonomic profiles between sponge species than within species. Nonetheless, we identified conservation of GCFs, with 20% of sponge GCFs being shared between at least two sponge species and a GCF core comprised of 6% of GCFs shared across all species. Within this functional core, we identified a set of widespread and diverse GCFs encoding nonribosomal peptide synthetases that are potentially involved in the production of diversified ether lipids, as well as GCFs putatively encoding the production of highly modified proteusins. The present work contributes to the small, yet growing body of data characterizing NP landscapes of marine sponge symbionts and to the cryptic biosynthetic potential contained in this environmental niche. IMPORTANCE Marine sponges and their microbial symbiotic communities are a rich source of diverse natural products (NPs). However, little is known about the sponge NP global distribution landscape and the symbionts that produce them. Here, we make use of recently developed tools to perform untargeted mining and comparative analysis of sponge microbiome metagenomes of three sponge species in the first study considering replicate metagenomes of multiple sponge species. We present an overview of the biosynthetic diversity across these sponge holobionts, which displays extreme biosynthetic novelty. We report not only the conservation of biosynthetic and taxonomic diversity but also a core of conserved specialized metabolic pathways. Finally, we highlight several novel GCFs with unknown ecological function, and observe particularly high biosynthetic potential in Acidobacteriota and Latescibacteria symbionts. This study paves the way toward a better understanding of the marine sponge holobionts' biosynthetic potential and the functional and ecological role of sponge microbiomes.
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14
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Teng K, Huang F, Liu Y, Wang Y, Xia T, Yun F, Zhong J. Food and gut originated bacteriocins involved in gut microbe-host interactions. Crit Rev Microbiol 2022:1-13. [PMID: 35713699 DOI: 10.1080/1040841x.2022.2082860] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The gut microbes interact with each other as well as host, influencing human health and some diseases. Many gut commensals and food originated bacteria produce bacteriocins which can inhibit pathogens and modulate gut microbiota. Bacteriocins have comparable narrow antimicrobial spectrum and are attractive potentials for precision therapy of gut disorders. In this review, the bacteriocins from food and gut microbiomes and their involvement in the interaction between producers and gut ecosystem, along with their characteristics, types, biosynthesis, and functions are described and discussed. Bacteriocins are produced by many intestinal commensals and food microbes among which lactic acid bacteria (many are probiotics) has been paid more attention. Bacteriocin production has been generally regarded as a probiotic trait. They give a competitive advantage to bacteria, enabling their colonization in human gut, and mediating the interaction between the producers and host ecosystem. They fight against unwanted bacteria and pathogens without significant impact on the composition of commensal microbiota. Bacteriocins assist the producers to survive and colonize in the gut microbial populations. There is a great need to evaluate and utilize the potential of bacteriocins for improved therapeutic implications for intestinal health.
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Affiliation(s)
- Kunling Teng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Fuqing Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yayong Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yudong Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Tianqi Xia
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Fangfei Yun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Jin Zhong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
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15
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Johnston CW, Badran AH. Natural and engineered precision antibiotics in the context of resistance. Curr Opin Chem Biol 2022; 69:102160. [PMID: 35660248 DOI: 10.1016/j.cbpa.2022.102160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 04/18/2022] [Accepted: 04/22/2022] [Indexed: 12/14/2022]
Abstract
Antibiotics are essential weapons in our fight against infectious disease, yet the consequences of broad-spectrum antibiotic use on microbiome stability and pathogen resistance are prompting investigations into more selective alternatives. Echoing the advent of precision medicine in oncology, precision antibiotics with focused activities are emerging as a means of addressing infections without damaging microbiomes or incentivizing resistance. Historically, antibiotic design principles have been gleaned from Nature, and reinvestigation of overlooked antibacterials is now providing scaffolds and targets for the design of pathogen-specific drugs. In this perspective, we summarize the biosynthetic and antibacterial mechanisms used to access these activities, and discuss how such strategies may be co-opted through engineering approaches to afford precision antibiotics.
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Affiliation(s)
- Chad W Johnston
- Department of Pharmacology & Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Ahmed H Badran
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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16
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Li X, Zuo S, Wang B, Zhang K, Wang Y. Antimicrobial Mechanisms and Clinical Application Prospects of Antimicrobial Peptides. Molecules 2022; 27:2675. [PMID: 35566025 PMCID: PMC9104849 DOI: 10.3390/molecules27092675] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 12/16/2022] Open
Abstract
Antimicrobial peptides are a type of small-molecule peptide that widely exist in nature and are components of the innate immunity of almost all living things. They play an important role in resisting foreign invading microorganisms. Antimicrobial peptides have a wide range of antibacterial activities against bacteria, fungi, viruses and other microorganisms. They are active against traditional antibiotic-resistant strains and do not easily induce the development of drug resistance. Therefore, they have become a hot spot of medical research and are expected to become a new substitute for fighting microbial infection and represent a new method for treating drug-resistant bacteria. This review briefly introduces the source and structural characteristics of antimicrobial peptides and describes those that have been used against common clinical microorganisms (bacteria, fungi, viruses, and especially coronaviruses), focusing on their antimicrobial mechanism of action and clinical application prospects.
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Affiliation(s)
- Xin Li
- Department of Infectious Diseases, First Hospital of Jilin University, Changchun 130021, China; (X.L.); (B.W.)
| | - Siyao Zuo
- Department of Dermatology and Venereology, First Hospital of Jilin University, Changchun 130021, China;
| | - Bin Wang
- Department of Infectious Diseases, First Hospital of Jilin University, Changchun 130021, China; (X.L.); (B.W.)
| | - Kaiyu Zhang
- Department of Infectious Diseases, First Hospital of Jilin University, Changchun 130021, China; (X.L.); (B.W.)
| | - Yang Wang
- Department of Infectious Diseases, First Hospital of Jilin University, Changchun 130021, China; (X.L.); (B.W.)
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17
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Parker JK, Davies BW. Microcins reveal natural mechanisms of bacterial manipulation to inform therapeutic development. MICROBIOLOGY (READING, ENGLAND) 2022; 168:001175. [PMID: 35438625 PMCID: PMC10233263 DOI: 10.1099/mic.0.001175] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/17/2022] [Indexed: 12/20/2022]
Abstract
Microcins are an understudied and poorly characterized class of antimicrobial peptides. Despite the existence of only 15 examples, all identified from the Enterobacteriaceae, microcins display diversity in sequence, structure, target cell uptake, cytotoxic mechanism of action and target specificity. Collectively, these features describe some of the unique means nature has contrived for molecules to cross the 'impermeable' barrier of the Gram-negative bacterial outer membrane and inflict cytotoxic effects. Microcins appear to be widely dispersed among different species and in different environments, where they function in regulating microbial communities in diverse ways, including through competition. Growing evidence suggests that microcins may be adapted for therapeutic uses such as antimicrobial drugs, microbiome modulators or facilitators of peptide uptake into cells. Advancing our biological, ecological and biochemical understanding of the roles of microcins in bacterial interactions, and learning how to regulate and modify microcin activity, is essential to enable such therapeutic applications.
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Affiliation(s)
| | - Bryan William Davies
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- John Ring LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, Texas, USA
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18
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Baquero F, del Campo R, Martínez JL. Interventions in Nicotinamide Adenine Dinucleotide Metabolism, the Intestinal Microbiota and Microcin Peptide Antimicrobials. Front Mol Biosci 2022; 9:861603. [PMID: 35372517 PMCID: PMC8967132 DOI: 10.3389/fmolb.2022.861603] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/22/2022] [Indexed: 11/23/2022] Open
Abstract
A proper NADH/NAD + balance allows for the flow of metabolic and catabolic activities determining cellular growth. In Escherichia coli, more than 80 NAD + dependent enzymes are involved in all major metabolic pathways, including the post-transcriptional build-up of thiazole and oxazole rings from small linear peptides, which is a critical step for the antibiotic activity of some microcins. In recent years, NAD metabolism boosting drugs have been explored, mostly precursors of NAD + synthesis in human cells, with beneficial effects on the aging process and in preventing oncological and neurological diseases. These compounds also enhance NAD + metabolism in the human microbiota, which contributes to these beneficial effects. On the other hand, inhibition of NAD + metabolism has been proposed as a therapeutic approach to reduce the growth and propagation of tumor cells and mitigating inflammatory bowel diseases; in this case, the activity of the microbiota might mitigate therapeutic efficacy. Antibiotics, which reduce the effect of microbiota, should synergize with NAD + metabolism inhibitors, but these drugs might increase the proportion of antibiotic persistent populations. Conversely, antibiotics might have a stronger killing effect on bacteria with active NAD + production and reduce the cooperation of NAD + producing bacteria with tumoral cells. The use of NADH/NAD + modulators should take into consideration the use of antibiotics and the population structure of the microbiota.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
- Network Center for Research in Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
- *Correspondence: Fernando Baquero,
| | - Rosa del Campo
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
- Network Center for Research in Infectious Diseases (CIBER-INFEC), Madrid, Spain
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19
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Suissa R, Oved R, Jankelowitz G, Turjeman S, Koren O, Kolodkin-Gal I. Molecular genetics for probiotic engineering: dissecting lactic acid bacteria. Trends Microbiol 2022; 30:293-306. [PMID: 34446338 DOI: 10.1016/j.tim.2021.07.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 02/08/2023]
Abstract
The composition of the gut microbiome is greatly influenced by nutrition and dietary alterations which can also induce large temporary microbial shifts. However, the molecular mechanisms that promote these changes remain to be determined. Species of the family Lactobacillaceae and Bacillus species are genetically manipulatable bacteria that are naturally found in the human gastrointestinal (GI) tract and are often considered models of beneficial microbiota. Here, we identify specific conserved molecular pathways that play a key role in host colonization by beneficial members of the microbiota. In particular, we highlight three pathways important to the success of lactic acid bacteria (LAB) in the GI tract: glycolysis and fermentation, microbial communication via membrane vesicles, and condition-dependent antibiotic production. We elaborate on how the understanding of these circuits can lead to the development of novel therapeutic approaches to combat GI tract infections.
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Affiliation(s)
- Ronit Suissa
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rela Oved
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | | | - Sondra Turjeman
- Azrieli Faculty of Medicine, Bar-Ilan University, Zefad, Israel
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Zefad, Israel.
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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20
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Lacey HJ, Rutledge PJ. Recently Discovered Secondary Metabolites from Streptomyces Species. Molecules 2022; 27:molecules27030887. [PMID: 35164153 PMCID: PMC8838263 DOI: 10.3390/molecules27030887] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 12/13/2022] Open
Abstract
The Streptomyces genus has been a rich source of bioactive natural products, medicinal chemicals, and novel drug leads for three-quarters of a century. Yet studies suggest that the genus is capable of making some 150,000 more bioactive compounds than all Streptomyces secondary metabolites reported to date. Researchers around the world continue to explore this enormous potential using a range of strategies including modification of culture conditions, bioinformatics and genome mining, heterologous expression, and other approaches to cryptic biosynthetic gene cluster activation. Our survey of the recent literature, with a particular focus on the year 2020, brings together more than 70 novel secondary metabolites from Streptomyces species, which are discussed in this review. This diverse array includes cyclic and linear peptides, peptide derivatives, polyketides, terpenoids, polyaromatics, macrocycles, and furans, the isolation, chemical structures, and bioactivity of which are appraised. The discovery of these many different compounds demonstrates the continued potential of Streptomyces as a source of new and interesting natural products and contributes further important pieces to the mostly unfinished puzzle of Earth’s myriad microbes and their multifaceted chemical output.
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Affiliation(s)
- Heather J. Lacey
- School of Chemistry, The University of Sydney, Camperdown, Sydney, NSW 2006, Australia
- Microbial Screening Technologies, Smithfield, Sydney, NSW 2164, Australia
- Correspondence: (H.J.L.); (P.J.R.); Tel.: +61-2-9351-5020 (P.J.R)
| | - Peter J. Rutledge
- School of Chemistry, The University of Sydney, Camperdown, Sydney, NSW 2006, Australia
- Correspondence: (H.J.L.); (P.J.R.); Tel.: +61-2-9351-5020 (P.J.R)
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21
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Andriūnaitė E, Tamošiūnė I, Aleksandravičiūtė M, Gelvonauskienė D, Vinskienė J, Rugienius R, Baniulis D. Stimulation of Nicotiana tabacum L. In Vitro Shoot Growth by Endophytic Bacillus cereus Group Bacteria. Microorganisms 2021; 9:1893. [PMID: 34576789 PMCID: PMC8470653 DOI: 10.3390/microorganisms9091893] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 11/16/2022] Open
Abstract
In vitro plant tissue cultures face various unfavorable conditions, such as mechanical damage, osmotic shock, and phytohormone imbalance, which can be detrimental to culture viability, growth efficiency, and genetic stability. Recent studies have revealed a presence of diverse endophytic bacteria, suggesting that engineering of the endophytic microbiome of in vitro plant tissues has the potential to improve their acclimatization and growth. Therefore, the aim of this study was to identify cultivated tobacco (Nicotiana tabacum L.) endophytic bacteria isolates that are capable of promoting the biomass accumulation of in vitro tobacco shoots. Forty-five endophytic bacteria isolates were obtained from greenhouse-grown tobacco plant leaves and were assigned to seven Bacillus spp. and one Pseudomonas sp. based on 16S rRNA or genome sequence data. To evaluate the bacterial effect on in vitro plant growth, tobacco shoots were inoculated with 22 isolates selected from distinct taxonomic groups. Four isolates of Bacillus cereus group species B. toyonensis, B. wiedmannii and B. mycoides promoted shoot growth by 11-21%. Furthermore, a contrasting effect on shoot growth was found among several isolates of the same species, suggesting the presence of strain-specific interaction with the plant host. Comparative analysis of genome assemblies was performed on the two closely related B. toyonensis isolates with contrasting plant growth-modulating properties. This revealed distinct structures of the genomic regions, including a putative enzyme cluster involved in the biosynthesis of linear azol(in)e-containing peptides and polysaccharides. However, the function of these clusters and their significance in plant-promoting activity remains elusive, and the observed contrasting effects on shoot growth are more likely to result from genomic sequence variations leading to differences in metabolic or gene expression activity. The Bacillus spp. isolates with shoot-growth-promoting properties have a potential application in improving the growth of plant tissue cultures in vitro.
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Affiliation(s)
| | | | | | | | | | | | - Danas Baniulis
- Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Kaunas str. 30, Babtai, 54333 Kaunas reg., Lithuania; (E.A.); (I.T.); (M.A.); (D.G.); (J.V.); (R.R.)
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22
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De Smet J, Wagemans J, Boon M, Ceyssens PJ, Voet M, Noben JP, Andreeva J, Ghilarov D, Severinov K, Lavigne R. The bacteriophage LUZ24 "Igy" peptide inhibits the Pseudomonas DNA gyrase. Cell Rep 2021; 36:109567. [PMID: 34433028 DOI: 10.1016/j.celrep.2021.109567] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 05/20/2021] [Accepted: 07/29/2021] [Indexed: 01/01/2023] Open
Abstract
The bacterial DNA gyrase complex (GyrA/GyrB) plays a crucial role during DNA replication and serves as a target for multiple antibiotics, including the fluoroquinolones. Despite it being a valuable antibiotics target, resistance emergence by pathogens including Pseudomonas aeruginosa are proving problematic. Here, we describe Igy, a peptide inhibitor of gyrase, encoded by Pseudomonas bacteriophage LUZ24 and other members of the Bruynoghevirus genus. Igy (5.6 kDa) inhibits in vitro gyrase activity and interacts with the P. aeruginosa GyrB subunit, possibly by DNA mimicry, as indicated by a de novo model of the peptide and mutagenesis. In vivo, overproduction of Igy blocks DNA replication and leads to cell death also in fluoroquinolone-resistant bacterial isolates. These data highlight the potential of discovering phage-inspired leads for antibiotics development, supported by co-evolution, as Igy may serve as a scaffold for small molecule mimicry to target the DNA gyrase complex, without cross-resistance to existing molecules.
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Affiliation(s)
- Jeroen De Smet
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
| | - Jeroen Wagemans
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
| | - Maarten Boon
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
| | - Pieter-Jan Ceyssens
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
| | - Marleen Voet
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, School of Life Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Julia Andreeva
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
| | - Dmitry Ghilarov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
| | - Konstantin Severinov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium.
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23
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Romanovska A, Keil J, Tophoven J, Oruc MF, Schmidt M, Breisch M, Sengstock C, Weidlich D, Klostermeier D, Tiller JC. Conjugates of Ciprofloxacin and Amphiphilic Block Copoly(2-alkyl-2-oxazolines)s Overcome Efflux Pumps and Are Active against CIP-Resistant Bacteria. Mol Pharm 2021; 18:3532-3543. [PMID: 34323492 DOI: 10.1021/acs.molpharmaceut.1c00430] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Conjugation of antibiotics with polymers is an emerging strategy to improve the performance of these important drugs. Here, the antibiotic ciprofloxacin (CIP) was conjugated with amphiphilic poly(2-oxazoline) (POx) block copolymers to investigate whether the activity of the antibiotic was enhanced due to additionally induced membrane activity. The resulting polymer-antibiotic conjugates (PACs) are an order of magnitude more active against the bacterial strain Staphylococcus aureus than CIP and show high activities against numerous pathogenic bacterial strains. Their high activity depends on an optimal hydrophobic/hydrophilic balance (HHB) of the POx tail. Mechanistic studies revealed that the derivatization of CIP required for the polymer conjugation lowers the affinity of the antibiotic to its target topoisomerase IV. However, the amphiphilic PACs are most likely concentrated within the bacterial cytoplasm, which overcompensates the loss of affinity and results in high antibacterial activity. In addition, the development of resistance in S. aureus and Escherichia coli is slowed down. More importantly, the amphiphilic PACs are active against CIP-resistant S. aureus and E. coli. The PACs with the highest activity are not cytotoxic toward human stem cells and do not lyse blood cells in saturated solution.
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Affiliation(s)
- Alina Romanovska
- Biomaterials and Polymer Science, Department of Bio- and Chemical Engineering, TU Dortmund, Emil-Figge-Str. 66, 44227 Dortmund, Germany
| | - Johanna Keil
- Biomaterials and Polymer Science, Department of Bio- and Chemical Engineering, TU Dortmund, Emil-Figge-Str. 66, 44227 Dortmund, Germany
| | - Jonas Tophoven
- Biomaterials and Polymer Science, Department of Bio- and Chemical Engineering, TU Dortmund, Emil-Figge-Str. 66, 44227 Dortmund, Germany
| | - Murat Furkan Oruc
- Biomaterials and Polymer Science, Department of Bio- and Chemical Engineering, TU Dortmund, Emil-Figge-Str. 66, 44227 Dortmund, Germany
| | - Martin Schmidt
- Biomaterials and Polymer Science, Department of Bio- and Chemical Engineering, TU Dortmund, Emil-Figge-Str. 66, 44227 Dortmund, Germany
| | - Marina Breisch
- BG University Hospital Bergmannsheil Bochum/Surgical Research, Ruhr University Bochum, Buerkle-de-la-Camp-Platz 1, D-44789 Bochum, Germany
| | - Christina Sengstock
- BG University Hospital Bergmannsheil Bochum/Surgical Research, Ruhr University Bochum, Buerkle-de-la-Camp-Platz 1, D-44789 Bochum, Germany
| | - Daniela Weidlich
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, 48149 Muenster, Germany
| | - Dagmar Klostermeier
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, 48149 Muenster, Germany
| | - Joerg C Tiller
- Biomaterials and Polymer Science, Department of Bio- and Chemical Engineering, TU Dortmund, Emil-Figge-Str. 66, 44227 Dortmund, Germany
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Cao L, Do T, Link AJ. Mechanisms of action of ribosomally synthesized and posttranslationally modified peptides (RiPPs). J Ind Microbiol Biotechnol 2021; 48:6121428. [PMID: 33928382 PMCID: PMC8183687 DOI: 10.1093/jimb/kuab005] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/22/2021] [Indexed: 12/19/2022]
Abstract
Natural products remain a critical source of medicines and drug leads. One of the most rapidly growing superclasses of natural products is RiPPs: ribosomally synthesized and posttranslationally modified peptides. RiPPs have rich and diverse bioactivities. This review highlights examples of the molecular mechanisms of action that underly those bioactivities. Particular emphasis is placed on RiPP/target interactions for which there is structural information. This detailed mechanism of action work is critical toward the development of RiPPs as therapeutics and can also be used to prioritize hits in RiPP genome mining studies.
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Affiliation(s)
- Li Cao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Truc Do
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - A James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.,Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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25
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Nguyen NA, Lin Z, Mohanty I, Garg N, Schmidt EW, Agarwal V. An Obligate Peptidyl Brominase Underlies the Discovery of Highly Distributed Biosynthetic Gene Clusters in Marine Sponge Microbiomes. J Am Chem Soc 2021; 143:10221-10231. [PMID: 34213321 DOI: 10.1021/jacs.1c03474] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Marine sponges are prolific sources of bioactive natural products, several of which are produced by bacteria symbiotically associated with the sponge host. Bacteria-derived natural products, and the specialized bacterial symbionts that synthesize them, are not shared among phylogenetically distant sponge hosts. This is in contrast to nonsymbiotic culturable bacteria in which the conservation of natural products and natural product biosynthetic gene clusters (BGCs) is well established. Here, we demonstrate the widespread conservation of a BGC encoding a cryptic ribosomally synthesized and post-translationally modified peptide (RiPP) in microbiomes of phylogenetically and geographically dispersed sponges from the Pacific and Atlantic oceans. Detection of this BGC was enabled by mining for halogenating enzymes in sponge metagenomes, which, in turn, allowed for the description of a broad-spectrum regiospecific peptidyl tryptophan-6-brominase which possessed no chlorination activity. In addition, we demonstrate the cyclodehydrative installation of azoline heterocycles in proteusin RiPPs. This is the first demonstration of halogenation and cyclodehydration for proteusin RiPPs and the enzymes catalyzing these transformations were found to competently interact with other previously described proteusin substrate peptides. Within a sponge microbiome, many different generalized bacterial taxa harbored this BGC with often more than 50 copies of the BGC detected in individual sponge metagenomes. Moreover, the BGC was found in all sponges queried that possess high diversity microbiomes but it was not detected in other marine invertebrate microbiomes. These data shed light on conservation of cryptic natural product biosynthetic potential in marine sponges that was not detected by traditional natural product-to-BGC (meta)genome mining.
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Affiliation(s)
- Nguyet A Nguyen
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Ipsita Mohanty
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Eric W Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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26
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Yang B, Fang D, Lv Q, Wang Z, Liu Y. Targeted Therapeutic Strategies in the Battle Against Pathogenic Bacteria. Front Pharmacol 2021; 12:673239. [PMID: 34054548 PMCID: PMC8149751 DOI: 10.3389/fphar.2021.673239] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/23/2021] [Indexed: 12/14/2022] Open
Abstract
The emergence and rapid spread of antibiotic resistance in pathogenic bacteria constitute a global threat for public health. Despite ongoing efforts to confront this crisis, the pace of finding new potent antimicrobials is far slower than the evolution of drug resistance. The abuse of broad-spectrum antibiotics not only accelerates the formation of resistance but also imposes a burden on the intestinal microbiota, which acts a critical role in human homeostasis. As such, innovative therapeutic strategies with precision are pressingly warranted and highly anticipated. Recently, target therapies have achieved some breakthroughs by the aid of modern technology. In this review, we provide an insightful illustration of current and future medical targeted strategies, including narrow-spectrum agents, engineered probiotics, nanotechnology, phage therapy, and CRISPR-Cas9 technology. We discuss the recent advances and potential hurdles of these strategies. Meanwhile, the possibilities to mitigate the spread of resistance in these approaches are also mentioned. Altogether, a better understanding of the advantages, disadvantages, and mechanisms of action of these targeted therapies will be conducive to broadening our horizons and optimizing the existing antibacterial approaches.
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Affiliation(s)
- Bingqing Yang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Dan Fang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Qingyan Lv
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yuan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China.,Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
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The pentapeptide-repeat protein, MfpA, interacts with mycobacterial DNA gyrase as a DNA T-segment mimic. Proc Natl Acad Sci U S A 2021; 118:2016705118. [PMID: 33836580 PMCID: PMC7980463 DOI: 10.1073/pnas.2016705118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA gyrase, a type II topoisomerase, introduces negative supercoils into DNA using ATP hydrolysis. The highly effective gyrase-targeted drugs, fluoroquinolones (FQs), interrupt gyrase by stabilizing a DNA-cleavage complex, a transient intermediate in the supercoiling cycle, leading to double-stranded DNA breaks. MfpA, a pentapeptide-repeat protein in mycobacteria, protects gyrase from FQs, but its molecular mechanism remains unknown. Here, we show that Mycobacterium smegmatis MfpA (MsMfpA) inhibits negative supercoiling by M. smegmatis gyrase (Msgyrase) in the absence of FQs, while in their presence, MsMfpA decreases FQ-induced DNA cleavage, protecting the enzyme from these drugs. MsMfpA stimulates the ATPase activity of Msgyrase by directly interacting with the ATPase domain (MsGyrB47), which was confirmed through X-ray crystallography of the MsMfpA-MsGyrB47 complex, and mutational analysis, demonstrating that MsMfpA mimics a T (transported) DNA segment. These data reveal the molecular mechanism whereby MfpA modulates the activity of gyrase and may provide a general molecular basis for the action of other pentapeptide-repeat proteins.
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28
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Bush NG, Diez-Santos I, Abbott LR, Maxwell A. Quinolones: Mechanism, Lethality and Their Contributions to Antibiotic Resistance. Molecules 2020; 25:E5662. [PMID: 33271787 PMCID: PMC7730664 DOI: 10.3390/molecules25235662] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/27/2020] [Accepted: 11/28/2020] [Indexed: 12/05/2022] Open
Abstract
Fluoroquinolones (FQs) are arguably among the most successful antibiotics of recent times. They have enjoyed over 30 years of clinical usage and become essential tools in the armoury of clinical treatments. FQs target the bacterial enzymes DNA gyrase and DNA topoisomerase IV, where they stabilise a covalent enzyme-DNA complex in which the DNA is cleaved in both strands. This leads to cell death and turns out to be a very effective way of killing bacteria. However, resistance to FQs is increasingly problematic, and alternative compounds are urgently needed. Here, we review the mechanisms of action of FQs and discuss the potential pathways leading to cell death. We also discuss quinolone resistance and how quinolone treatment can lead to resistance to non-quinolone antibiotics.
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Affiliation(s)
| | | | | | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; (N.G.B.); (I.D.-S.); (L.R.A.)
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29
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Isolation and structure determination of new linear azole-containing peptides spongiicolazolicins A and B from Streptomyces sp. CWH03. Appl Microbiol Biotechnol 2020; 105:93-104. [PMID: 33215256 DOI: 10.1007/s00253-020-11016-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/02/2020] [Accepted: 11/09/2020] [Indexed: 10/23/2022]
Abstract
Linear azole-containing peptides are a class of ribosomally synthesized and post-translationally modified peptides. We performed a chemical investigation on marine actinomycetes, and new linear azole-containing peptides named spongiicolazolicins A and B were found in the MeOH extracts of a newly isolated strain Streptomyces sp. CWH03 (NBRC 114659) and two strains of S. spongiicola (strain HNM0071T: DSM 103383T and strain 531S: NBRC 113560). The strain Streptomyces sp. CWH03 was indicated to be a new species closely related to S. spongiicola by phylogenetic analysis using the genome sequence. The new peptides named spongiicolazolicins A and B were isolated from the cell of Streptomyces sp. CWH03. The partial structure of spongiicolazolicin A was determined by 2D NMR experiments. Based on data of MS/MS experiments, the chemical structures of spongiicolazolicins A and B were proposed using the amino acid sequence deduced from the precursor-encoding gene, which was found from whole-genome sequence data of Streptomyces sp. CWH03. The biosynthetic gene cluster of spongiicolazolicins was proposed based on comparative analysis with that of a known linear azole peptide goadsporin. KEY POINTS: • Streptomyces sp. CWH03 was a new species isolated from marine sediment. • New linear azole-containing peptides named spongiicolazolicins A and B were isolated. • Biosynthetic pathway of spongiicolazolicins was proposed.
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30
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Telhig S, Ben Said L, Zirah S, Fliss I, Rebuffat S. Bacteriocins to Thwart Bacterial Resistance in Gram Negative Bacteria. Front Microbiol 2020; 11:586433. [PMID: 33240239 PMCID: PMC7680869 DOI: 10.3389/fmicb.2020.586433] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/16/2020] [Indexed: 12/16/2022] Open
Abstract
An overuse of antibiotics both in human and animal health and as growth promoters in farming practices has increased the prevalence of antibiotic resistance in bacteria. Antibiotic resistant and multi-resistant bacteria are now considered a major and increasing threat by national health agencies, making the need for novel strategies to fight bugs and super bugs a first priority. In particular, Gram-negative bacteria are responsible for a high proportion of nosocomial infections attributable for a large part to Enterobacteriaceae, such as pathogenic Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. To cope with their highly competitive environments, bacteria have evolved various adaptive strategies, among which the production of narrow spectrum antimicrobial peptides called bacteriocins and specifically microcins in Gram-negative bacteria. They are produced as precursor peptides that further undergo proteolytic cleavage and in many cases more or less complex posttranslational modifications, which contribute to improve their stability and efficiency. Many have a high stability in the gastrointestinal tract where they can target a single pathogen whilst only slightly perturbing the gut microbiota. Several microcins and antibiotics can bind to similar bacterial receptors and use similar pathways to cross the double-membrane of Gram-negative bacteria and reach their intracellular targets, which they also can share. Consequently, bacteria may use common mechanisms of resistance against microcins and antibiotics. This review describes both unmodified and modified microcins [lasso peptides, siderophore peptides, nucleotide peptides, linear azole(in)e-containing peptides], highlighting their potential as weapons to thwart bacterial resistance in Gram-negative pathogens and discusses the possibility of cross-resistance and co-resistance occurrence between antibiotics and microcins in Gram-negative bacteria.
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Affiliation(s)
- Soufiane Telhig
- Institute of Nutrition and Functional Foods, Université Laval, Québec, QC, Canada
- Laboratory Molecules of Communication and Adaptation of Microorganisms, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Laila Ben Said
- Institute of Nutrition and Functional Foods, Université Laval, Québec, QC, Canada
| | - Séverine Zirah
- Laboratory Molecules of Communication and Adaptation of Microorganisms, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Ismail Fliss
- Institute of Nutrition and Functional Foods, Université Laval, Québec, QC, Canada
| | - Sylvie Rebuffat
- Laboratory Molecules of Communication and Adaptation of Microorganisms, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
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31
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Smits SHJ, Schmitt L, Beis K. Self-immunity to antibacterial peptides by ABC transporters. FEBS Lett 2020; 594:3920-3942. [PMID: 33040342 DOI: 10.1002/1873-3468.13953] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/22/2020] [Accepted: 10/05/2020] [Indexed: 01/17/2023]
Abstract
Bacteria produce under certain stress conditions bacteriocins and microcins that display antibacterial activity against closely related species for survival. Bacteriocins and microcins exert their antibacterial activity by either disrupting the membrane or inhibiting essential intracellular processes of the bacterial target. To this end, they can lyse bacterial membranes and cause subsequent loss of their integrity or nutrients, or hijack membrane receptors for internalisation. Both bacteriocins and microcins are ribosomally synthesised and several are posttranslationally modified, whereas others are not. Such peptides are also toxic to the producer bacteria, which utilise immunity proteins or/and dedicated ATP-binding cassette (ABC) transporters to achieve self-immunity and peptide export. In this review, we discuss the structure and mechanism of self-protection that is conferred by these ABC transporters.
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Affiliation(s)
- Sander H J Smits
- Institute of Biochemistry, Heinrich-Heine-University, Duesseldorf, Germany.,Center for Structural Studies, Heinrich-Heine-University, Duesseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich-Heine-University, Duesseldorf, Germany
| | - Konstantinos Beis
- Department of Life Sciences, Imperial College London, UK.,Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, UK
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32
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Barriot R, Latour J, Castanié-Cornet MP, Fichant G, Genevaux P. J-Domain Proteins in Bacteria and Their Viruses. J Mol Biol 2020; 432:3771-3789. [DOI: 10.1016/j.jmb.2020.04.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/10/2020] [Accepted: 04/14/2020] [Indexed: 02/06/2023]
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33
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Li Y, Rebuffat S. The manifold roles of microbial ribosomal peptide-based natural products in physiology and ecology. J Biol Chem 2020; 295:34-54. [PMID: 31784450 PMCID: PMC6952617 DOI: 10.1074/jbc.rev119.006545] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The ribosomally synthesized and posttranslationally modified peptides (RiPPs), also called ribosomal peptide natural products (RPNPs), form a growing superfamily of natural products that are produced by many different organisms and particularly by bacteria. They are derived from precursor polypeptides whose modification by various dedicated enzymes helps to establish a vast array of chemical motifs. RiPPs have attracted much interest as a source of potential therapeutic agents, and in particular as alternatives to conventional antibiotics to address the bacterial resistance crisis. However, their ecological roles in nature are poorly understood and explored. The present review describes major RiPP actors in competition within microbial communities, the main ecological and physiological functions currently evidenced for RiPPs, and the microbial ecosystems that are the sites for these functions. We envision that the study of RiPPs may lead to discoveries of new biological functions and highlight that a better knowledge of how bacterial RiPPs mediate inter-/intraspecies and interkingdom interactions will hold promise for devising alternative strategies in antibiotic development.
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Affiliation(s)
- Yanyan Li
- Laboratory Molecules of Communication and Adaptation of Microorganisms (MCAM, UMR 7245 CNRS-MNHN), National Museum of Natural History (MNHN), CNRS, CP 54, 57 rue Cuvier 75005, Paris, France.
| | - Sylvie Rebuffat
- Laboratory Molecules of Communication and Adaptation of Microorganisms (MCAM, UMR 7245 CNRS-MNHN), National Museum of Natural History (MNHN), CNRS, CP 54, 57 rue Cuvier 75005, Paris, France.
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Baquero F, Lanza VF, Baquero MR, Del Campo R, Bravo-Vázquez DA. Microcins in Enterobacteriaceae: Peptide Antimicrobials in the Eco-Active Intestinal Chemosphere. Front Microbiol 2019; 10:2261. [PMID: 31649628 PMCID: PMC6795089 DOI: 10.3389/fmicb.2019.02261] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 09/17/2019] [Indexed: 12/31/2022] Open
Abstract
Microcins are low-molecular-weight, ribosomally produced, highly stable, bacterial-inhibitory molecules involved in competitive, and amensalistic interactions between Enterobacteriaceae in the intestine. These interactions take place in a highly complex chemical landscape, the intestinal eco-active chemosphere, composed of chemical substances that positively or negatively influence bacterial growth, including those originated from nutrient uptake, and those produced by the action of the human or animal host and the intestinal microbiome. The contribution of bacteria results from their effect on the host generated molecules, on food and digested food, and organic substances from microbial origin, including from bacterial degradation. Here, we comprehensively review the main chemical substances present in the human intestinal chemosphere, particularly of those having inhibitory effects on microorganisms. With this background, and focusing on Enterobacteriaceae, the most relevant human pathogens from the intestinal microbiota, the microcin’s history and classification, mechanisms of action, and mechanisms involved in microcin’s immunity (in microcin producers) and resistance (non-producers) are reviewed. Products from the chemosphere likely modulate the ecological effects of microcin activity. Several cross-resistance mechanisms are shared by microcins, colicins, bacteriophages, and some conventional antibiotics, which are expected to produce cross-effects. Double-microcin-producing strains (such as microcins MccM and MccH47) have been successfully used for decades in the control of pathogenic gut organisms. Microcins are associated with successful gut colonization, facilitating translocation and invasion, leading to bacteremia, and urinary tract infections. In fact, Escherichia coli strains from the more invasive phylogroups (e.g., B2) are frequently microcinogenic. A publicly accessible APD3 database http://aps.unmc.edu/AP/ shows particular genes encoding microcins in 34.1% of E. coli strains (mostly MccV, MccM, MccH47, and MccI47), and much less in Shigella and Salmonella (<2%). Some 4.65% of Klebsiella pneumoniae are microcinogenic (mostly with MccE492), and even less in Enterobacter or Citrobacter (mostly MccS). The high frequency and variety of microcins in some Enterobacteriaceae indicate key ecological functions, a notion supported by their dominance in the intestinal microbiota of biosynthetic gene clusters involved in the synthesis of post-translationally modified peptide microcins.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Val F Lanza
- Bioinformatics Unit, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Maria-Rosario Baquero
- Department of Microbiology, Alfonso X El Sabio University, Villanueva de la Cañada, Spain
| | - Rosa Del Campo
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Daniel A Bravo-Vázquez
- Department of Microbiology, Alfonso X El Sabio University, Villanueva de la Cañada, Spain
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