1
|
Do DT, Yang MR, Vo TNS, Le NQK, Wu YW. Unitig-centered pan-genome machine learning approach for predicting antibiotic resistance and discovering novel resistance genes in bacterial strains. Comput Struct Biotechnol J 2024; 23:1864-1876. [PMID: 38707536 PMCID: PMC11067008 DOI: 10.1016/j.csbj.2024.04.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 04/13/2024] [Accepted: 04/13/2024] [Indexed: 05/07/2024] Open
Abstract
In current genomic research, the widely used methods for predicting antimicrobial resistance (AMR) often rely on prior knowledge of known AMR genes or reference genomes. However, these methods have limitations, potentially resulting in imprecise predictions owing to incomplete coverage of AMR mechanisms and genetic variations. To overcome these limitations, we propose a pan-genome-based machine learning approach to advance our understanding of AMR gene repertoires and uncover possible feature sets for precise AMR classification. By building compacted de Brujin graphs (cDBGs) from thousands of genomes and collecting the presence/absence patterns of unique sequences (unitigs) for Pseudomonas aeruginosa, we determined that using machine learning models on unitig-centered pan-genomes showed significant promise for accurately predicting the antibiotic resistance or susceptibility of microbial strains. Applying a feature-selection-based machine learning algorithm led to satisfactory predictive performance for the training dataset (with an area under the receiver operating characteristic curve (AUC) of > 0.929) and an independent validation dataset (AUC, approximately 0.77). Furthermore, the selected unitigs revealed previously unidentified resistance genes, allowing for the expansion of the resistance gene repertoire to those that have not previously been described in the literature on antibiotic resistance. These results demonstrate that our proposed unitig-based pan-genome feature set was effective in constructing machine learning predictors that could accurately identify AMR pathogens. Gene sets extracted using this approach may offer valuable insights into expanding known AMR genes and forming new hypotheses to uncover the underlying mechanisms of bacterial AMR.
Collapse
Affiliation(s)
- Duyen Thi Do
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Ming-Ren Yang
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Department of Electrical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Tran Nam Son Vo
- Department of Business Administration, College of Management, Lunghwa University of Science and Technology, Taoyuan City, Taiwan
| | - Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yu-Wei Wu
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei, Taiwan
- TMU Research Center for Digestive Medicine, Taipei Medical University, Taipei, Taiwan
| |
Collapse
|
2
|
Quiñonero-Coronel MDM, Devos DP, Garcillán-Barcia MP. Specificities and commonalities of the Planctomycetes plasmidome. Environ Microbiol 2024; 26:e16638. [PMID: 38733104 DOI: 10.1111/1462-2920.16638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
Plasmids, despite their critical role in antibiotic resistance and modern biotechnology, are understood in only a few bacterial groups in terms of their natural ecological dynamics. The bacterial phylum Planctomycetes, known for its unique molecular and cellular biology, has a largely unexplored plasmidome. This study offers a thorough exploration of the diversity of natural plasmids within Planctomycetes, which could serve as a foundation for developing various genetic research tools for this phylum. Planctomycetes plasmids encode a broad range of biological functions and appear to have coevolved significantly with their host chromosomes, sharing many homologues. Recent transfer events of insertion sequences between cohabiting chromosomes and plasmids were also observed. Interestingly, 64% of plasmid genes are distantly related to either chromosomally encoded genes or have homologues in plasmids from other bacterial groups. The planctomycetal plasmidome is composed of 36% exclusive proteins. Most planctomycetal plasmids encode a replication initiation protein from the Replication Protein A family near a putative iteron-containing replication origin, as well as active type I partition systems. The identification of one conjugative and three mobilizable plasmids suggests the occurrence of horizontal gene transfer via conjugation within this phylum. This comprehensive description enhances our understanding of the plasmidome of Planctomycetes and its potential implications in antibiotic resistance and biotechnology.
Collapse
Affiliation(s)
| | - Damien Paul Devos
- Centro Andaluz de Biología del Desarrollo (CABD, CSIC-Universidad Pablo de Olavide), Sevilla, Spain
| | - M Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC, CSIC-Universidad de Cantabria), Cantabria, Spain
| |
Collapse
|
3
|
Haudiquet M, Le Bris J, Nucci A, Bonnin RA, Domingo-Calap P, Rocha EPC, Rendueles O. Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency. Nat Commun 2024; 15:2032. [PMID: 38448399 PMCID: PMC10918111 DOI: 10.1038/s41467-024-46147-5] [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: 05/31/2023] [Accepted: 02/14/2024] [Indexed: 03/08/2024] Open
Abstract
Bacterial evolution is affected by mobile genetic elements like phages and conjugative plasmids, offering new adaptive traits while incurring fitness costs. Their infection is affected by the bacterial capsule. Yet, its importance has been difficult to quantify because of the high diversity of confounding mechanisms in bacterial genomes such as anti-viral systems and surface receptor modifications. Swapping capsule loci between Klebsiella pneumoniae strains allowed us to quantify their impact on plasmid and phage infection independently of genetic background. Capsule swaps systematically invert phage susceptibility, revealing serotypes as key determinants of phage infection. Capsule types also influence conjugation efficiency in both donor and recipient cells, a mechanism shaped by capsule volume and conjugative pilus structure. Comparative genomics confirmed that more permissive serotypes in the lab correspond to the strains acquiring more conjugative plasmids in nature. The least capsule-sensitive pili (F-like) are the most frequent in the species' plasmids, and are the only ones associated with both antibiotic resistance and virulence factors, driving the convergence between virulence and antibiotics resistance in the population. These results show how traits of cellular envelopes define slow and fast lanes of infection by mobile genetic elements, with implications for population dynamics and horizontal gene transfer.
Collapse
Affiliation(s)
- Matthieu Haudiquet
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France.
- Ecole Doctoral FIRE-Programme Bettencourt, CRI, Paris, France.
| | - Julie Le Bris
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France
- Sorbonne Université, Collège Doctoral, Ecole Doctorale Complexité du Vivant, 75005, Paris, France
| | - Amandine Nucci
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France
| | - Rémy A Bonnin
- Team Resist UMR1184 Université Paris Saclay, CEA, Inserm, Le Kremlin-Bicêtre, Paris, France
- Service de bactériologie, Hôpital Bicêtre, Université Paris Saclay, AP-HP, Le Kremlin-Bicêtre, Paris, France
- Centre National de Référence Associé de la Résistance aux Antibiotiques, Le Kremlin-Bicêtre, Paris, France
| | - Pilar Domingo-Calap
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, 46980, Paterna, Spain
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France.
| | - Olaya Rendueles
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France.
| |
Collapse
|
4
|
Yakubu B, Appiah EM, Adu AF. Pangenome Analysis of Helicobacter pylori Isolates from Selected Areas of Africa Indicated Diverse Antibiotic Resistance and Virulence Genes. Int J Genomics 2024; 2024:5536117. [PMID: 38469580 PMCID: PMC10927345 DOI: 10.1155/2024/5536117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/20/2023] [Accepted: 02/06/2024] [Indexed: 03/13/2024] Open
Abstract
The challenge facing Helicobacter pylori (H. pylori) infection management in some parts of Africa is the evolution of drug-resistant species, the lack of gold standard in diagnostic methods, and the ineffectiveness of current vaccines against the bacteria. It is being established that even though clinical consequences linked to the bacteria vary geographically, there is rather a generic approach to treatment. This situation has remained problematic in the successful fight against the bacteria in parts of Africa. As a result, this study compared the genomes of selected H. pylori isolates from selected areas of Africa and evaluated their virulence and antibiotic drug resistance, those that are highly pathogenic and are associated with specific clinical outcomes and those that are less virulent and rarely associated with clinical outcomes. 146 genomes of H. pylori isolated from selected locations of Africa were sampled, and bioinformatic tools such as Abricate, CARD RGI, MLST, Prokka, Roary, Phandango, Google Sheets, and iTOLS were used to compare the isolates and their antibiotic resistance or susceptibility. Over 20 k virulence and AMR genes were observed. About 95% of the isolates were genetically diverse, 90% of the isolates harbored shell genes, and 50% harbored cloud and core genes. Some isolates did not retain the cagA and vacA genes. Clarithromycin, metronidazole, amoxicillin, and tinidazole were resistant to most AMR genes (vacA, cagA, oip, and bab). Conclusion. This study found both virulence and AMR genes in all H. pylori strains in all the selected geographies around Africa with differing quantities. MLST, Pangenome, and ORF analyses showed disparities among the isolates. This in general could imply diversities in terms of genetics, evolution, and protein production. Therefore, generic administration of antibiotics such as clarithromycin, amoxicillin, and erythromycin as treatment methods in the African subregion could be contributing to the spread of the bacterium's antibiotic resistance.
Collapse
Affiliation(s)
- Biigba Yakubu
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Edwin Moses Appiah
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Andrews Frimpong Adu
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| |
Collapse
|
5
|
Boyer C, Lefeuvre P, Richard D, Lobin KK, Pruvost O. Complete Genome Sequence of a Copper-Resistant Xanthomonas campestris pv . campestris Strain Isolated from Broccoli in Mauritius Suggests Adaptive Gene Gain Through Horizontal Gene Transfer. PHYTOPATHOLOGY 2024; 114:328-333. [PMID: 37584505 DOI: 10.1094/phyto-05-23-0177-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
Bacterial adaptation is facilitated by the presence of mobile genetic elements and horizontal gene transfer of genes, such as those coding for virulence factors or resistance to antimicrobial compounds. A hybrid assembly of Nanopore MinIon long-read and Illumina short-read data was produced from a copper-resistant Xanthomonas campestris pv. campestris strain isolated from symptomatic broccoli leaves in Mauritius. We obtained a 5.2-Mb high-quality chromosome and no plasmid. We found four genomic islands, three of which were characterized as integrative conjugative elements or integrative mobilizable elements. These genomic islands carried type III effectors and the copper resistance copLABMGF system involved in pathogenicity and environmental adaptation, respectively.
Collapse
Affiliation(s)
- Claudine Boyer
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France
| | | | - Damien Richard
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France
| | | | | |
Collapse
|
6
|
Algarni S, Foley SL, Tang H, Zhao S, Gudeta DD, Khajanchi BK, Ricke SC, Han J. Development of an antimicrobial resistance plasmid transfer gene database for enteric bacteria. FRONTIERS IN BIOINFORMATICS 2023; 3:1279359. [PMID: 38033626 PMCID: PMC10682676 DOI: 10.3389/fbinf.2023.1279359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction: Type IV secretion systems (T4SSs) are integral parts of the conjugation process in enteric bacteria. These secretion systems are encoded within the transfer (tra) regions of plasmids, including those that harbor antimicrobial resistance (AMR) genes. The conjugal transfer of resistance plasmids can lead to the dissemination of AMR among bacterial populations. Methods: To facilitate the analyses of the conjugation-associated genes, transfer related genes associated with key groups of AMR plasmids were identified, extracted from GenBank and used to generate a plasmid transfer gene dataset that is part of the Virulence and Plasmid Transfer Factor Database at FDA, serving as the foundation for computational tools for the comparison of the conjugal transfer genes. To assess the genetic feature of the transfer gene database, genes/proteins of the same name (e.g., traI/TraI) or predicted function (VirD4 ATPase homologs) were compared across the different plasmid types to assess sequence diversity. Two analyses tools, the Plasmid Transfer Factor Profile Assessment and Plasmid Transfer Factor Comparison tools, were developed to evaluate the transfer genes located on plasmids and to facilitate the comparison of plasmids from multiple sequence files. To assess the database and associated tools, plasmid, and whole genome sequencing (WGS) data were extracted from GenBank and previous WGS experiments in our lab and assessed using the analysis tools. Results: Overall, the plasmid transfer database and associated tools proved to be very useful for evaluating the different plasmid types, their association with T4SSs, and increased our understanding how conjugative plasmids contribute to the dissemination of AMR genes.
Collapse
Affiliation(s)
- Suad Algarni
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, United States
- Cellular and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, AR, United States
| | - Steven L. Foley
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, United States
| | - Hailin Tang
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, United States
| | - Shaohua Zhao
- Office of Applied Science, Center for Veterinary Medicine, Food and Drug Administration, Laurel, MD, United States
| | - Dereje D. Gudeta
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, United States
| | - Bijay K. Khajanchi
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, United States
| | - Steven C. Ricke
- Meat Science and Animal Biologics Discovery Program, Animal and Dairy Sciences Department, University of Wisconsin, Madison, WI, United States
| | - Jing Han
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, United States
| |
Collapse
|
7
|
Beard S, Moya-Beltrán A, Silva-García D, Valenzuela C, Pérez-Acle T, Loyola A, Quatrini R. Pangenome-level analysis of nucleoid-associated proteins in the Acidithiobacillia class: insights into their functional roles in mobile genetic elements biology. Front Microbiol 2023; 14:1271138. [PMID: 37817747 PMCID: PMC10561277 DOI: 10.3389/fmicb.2023.1271138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/01/2023] [Indexed: 10/12/2023] Open
Abstract
Mobile genetic elements (MGEs) are relevant agents in bacterial adaptation and evolutionary diversification. Stable appropriation of these DNA elements depends on host factors, among which are the nucleoid-associated proteins (NAPs). NAPs are highly abundant proteins that bind and bend DNA, altering its topology and folding, thus affecting all known cellular DNA processes from replication to expression. Even though NAP coding genes are found in most prokaryotic genomes, their functions in host chromosome biology and xenogeneic silencing are only known for a few NAP families. Less is known about the occurrence, abundance, and roles of MGE-encoded NAPs in foreign elements establishment and mobility. In this study, we used a combination of comparative genomics and phylogenetic strategies to gain insights into the diversity, distribution, and functional roles of NAPs within the class Acidithiobacillia with a special focus on their role in MGE biology. Acidithiobacillia class members are aerobic, chemolithoautotrophic, acidophilic sulfur-oxidizers, encompassing substantial genotypic diversity attributable to MGEs. Our search for NAP protein families (PFs) in more than 90 genomes of the different species that conform the class, revealed the presence of 1,197 proteins pertaining to 12 different NAP families, with differential occurrence and conservation across species. Pangenome-level analysis revealed 6 core NAP PFs that were highly conserved across the class, some of which also existed as variant forms of scattered occurrence, in addition to NAPs of taxa-restricted distribution. Core NAPs identified are reckoned as essential based on the conservation of genomic context and phylogenetic signals. In turn, various highly diversified NAPs pertaining to the flexible gene complement of the class, were found to be encoded in known plasmids or, larger integrated MGEs or, present in genomic loci associated with MGE-hallmark genes, pointing to their role in the stabilization/maintenance of these elements in strains and species with larger genomes. Both core and flexible NAPs identified proved valuable as markers, the former accurately recapitulating the phylogeny of the class, and the later, as seed in the bioinformatic identification of novel episomal and integrated mobile elements.
Collapse
Affiliation(s)
- Simón Beard
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Ana Moya-Beltrán
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Danitza Silva-García
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Cesar Valenzuela
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Tomás Pérez-Acle
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Alejandra Loyola
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Raquel Quatrini
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| |
Collapse
|
8
|
Yang M, Zhou X, Bao Y, Zhang Y, Liu B, Gan L, Tao W, Tuo J, Gong H. Comprehensive Genomic Analysis Reveals Extensive Diversity of Type I and Type IV Secretion Systems in Klebsiella pneumoniae. Curr Microbiol 2023; 80:270. [PMID: 37402963 DOI: 10.1007/s00284-023-03362-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 06/02/2023] [Indexed: 07/06/2023]
Abstract
The diversity and distribution of secretion systems in Klebsiella pneumoniae are unclear. In this study, the six common secretion systems (T1SS-T6SS) were comprehensively investigated in the genomes of 952 K. pneumoniae strains. T1SS, T2SS, type T subtype of T4SS, T5SS, and subtype T6SSi of T6SS were found. The findings indicated fewer types of secretion systems in K. pneumoniae than reported in Enterobacteriaceae, such as Escherichia coli. One conserved T2SS, one conserved T5SS, and two conserved T6SS were detected in more than 90% of the strains. In contrast, the strains displayed extensive diversity of T1SS and T4SS. Notably, T1SS and T4SS were enriched in the hypervirulent and classical multidrug resistance pathotypes of K. pneumoniae, respectively. The results expand the epidemiological knowledge of the virulence and transmissibility of pathogenic K. pneumoniae and contribute to identify the potential strains for safe applications.
Collapse
Affiliation(s)
- Menglei Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Xiaoqin Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Yangyang Bao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Yang Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Boya Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Luxi Gan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Weihua Tao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Jinyou Tuo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Heng Gong
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China.
| |
Collapse
|
9
|
Moya-Beltrán A, Gajdosik M, Rojas-Villalobos C, Beard S, Mandl M, Silva-García D, Johnson DB, Ramirez P, Quatrini R, Kucera J. Influence of mobile genetic elements and insertion sequences in long- and short-term adaptive processes of Acidithiobacillus ferrooxidans strains. Sci Rep 2023; 13:10876. [PMID: 37407610 DOI: 10.1038/s41598-023-37341-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 06/20/2023] [Indexed: 07/07/2023] Open
Abstract
The recent revision of the Acidithiobacillia class using genomic taxonomy methods has shown that, in addition to the existence of previously unrecognized genera and species, some species of the class harbor levels of divergence that are congruent with ongoing differentiation processes. In this study, we have performed a subspecies-level analysis of sequenced strains of Acidithiobacillus ferrooxidans to prove the existence of distinct sublineages and identify the discriminant genomic/genetic characteristics linked to these sublineages, and to shed light on the processes driving such differentiation. Differences in the genomic relatedness metrics, levels of synteny, gene content, and both integrated and episomal mobile genetic elements (MGE) repertoires support the existence of two subspecies-level taxa within A. ferrooxidans. While sublineage 2A harbors a small plasmid related to pTF5, this episomal MGE is absent in sublineage 2B strains. Likewise, clear differences in the occurrence, coverage and conservation of integrated MGEs are apparent between sublineages. Differential MGE-associated gene cargo pertained to the functional categories of energy metabolism, ion transport, cell surface modification, and defense mechanisms. Inferred functional differences have the potential to impact long-term adaptive processes and may underpin the basis of the subspecies-level differentiation uncovered within A. ferrooxidans. Genome resequencing of iron- and sulfur-adapted cultures of a selected 2A sublineage strain (CCM 4253) showed that both episomal and large integrated MGEs are conserved over twenty generations in either growth condition. In turn, active insertion sequences profoundly impact short-term adaptive processes. The ISAfe1 element was found to be highly active in sublineage 2A strain CCM 4253. Phenotypic mutations caused by the transposition of ISAfe1 into the pstC2 encoding phosphate-transport system permease protein were detected in sulfur-adapted cultures and shown to impair growth on ferrous iron upon the switch of electron donor. The phenotypic manifestation of the △pstC2 mutation, such as a loss of the ability to oxidize ferrous iron, is likely related to the inability of the mutant to secure the phosphorous availability for electron transport-linked phosphorylation coupled to iron oxidation. Depletion of the transpositional △pstC2 mutation occurred concomitantly with a shortening of the iron-oxidation lag phase at later transfers on a ferrous iron-containing medium. Therefore, the pstII operon appears to play an essential role in A. ferrooxidans when cells oxidize ferrous iron. Results highlight the influence of insertion sequences and both integrated and episomal mobile genetic elements in the short- and long-term adaptive processes of A. ferrooxidans strains under changing growth conditions.
Collapse
Affiliation(s)
- Ana Moya-Beltrán
- Fundación Ciencia & Vida, Avenida Del Valle Norte 725, 8580702, Huechuraba, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Martin Gajdosik
- Department of Biochemistry, Faculty of Science, Masaryk University, 61137, Brno, Czech Republic
| | - Camila Rojas-Villalobos
- Fundación Ciencia & Vida, Avenida Del Valle Norte 725, 8580702, Huechuraba, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Simón Beard
- Fundación Ciencia & Vida, Avenida Del Valle Norte 725, 8580702, Huechuraba, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, 7510157, Providencia, Santiago, Chile
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Santiago, Chile
| | - Martin Mandl
- Department of Biochemistry, Faculty of Science, Masaryk University, 61137, Brno, Czech Republic
| | - Danitza Silva-García
- Fundación Ciencia & Vida, Avenida Del Valle Norte 725, 8580702, Huechuraba, Santiago, Chile
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Camino La Piramide 5750, 8580000, Huechuraba, Santiago, Chile
| | - D Barrie Johnson
- College of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
- Faculty of Health and Life Sciences, Coventry University, Coventry, CV1 5FB, UK
- Natural History Museum, London, UK
| | - Pablo Ramirez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Raquel Quatrini
- Fundación Ciencia & Vida, Avenida Del Valle Norte 725, 8580702, Huechuraba, Santiago, Chile.
- Facultad de Medicina y Ciencia, Universidad San Sebastián, 7510157, Providencia, Santiago, Chile.
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Santiago, Chile.
| | - Jiri Kucera
- Department of Biochemistry, Faculty of Science, Masaryk University, 61137, Brno, Czech Republic.
| |
Collapse
|
10
|
Catchpole RJ, Barbe V, Magdelenat G, Marguet E, Terns M, Oberto J, Forterre P, Da Cunha V. A self-transmissible plasmid from a hyperthermophile that facilitates genetic modification of diverse Archaea. Nat Microbiol 2023; 8:1339-1347. [PMID: 37277532 PMCID: PMC10788138 DOI: 10.1038/s41564-023-01387-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 04/19/2023] [Indexed: 06/07/2023]
Abstract
Conjugative plasmids are self-transmissible mobile genetic elements that transfer DNA between host cells via type IV secretion systems (T4SS). While T4SS-mediated conjugation has been well-studied in bacteria, information is sparse in Archaea and known representatives exist only in the Sulfolobales order of Crenarchaeota. Here we present the first self-transmissible plasmid identified in a Euryarchaeon, Thermococcus sp. 33-3. The 103 kbp plasmid, pT33-3, is seen in CRISPR spacers throughout the Thermococcales order. We demonstrate that pT33-3 is a bona fide conjugative plasmid that requires cell-to-cell contact and is dependent on canonical, plasmid-encoded T4SS-like genes. Under laboratory conditions, pT33-3 transfers to various Thermococcales and transconjugants propagate at 100 °C. Using pT33-3, we developed a genetic toolkit that allows modification of phylogenetically diverse Archaeal genomes. We demonstrate pT33-3-mediated plasmid mobilization and subsequent targeted genome modification in previously untransformable Thermococcales species, and extend this process to interphylum transfer to a Crenarchaeon.
Collapse
Affiliation(s)
- Ryan J Catchpole
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Département de Microbiologie, Institut Pasteur, Paris, France.
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay, Gif-sur-Yvette, Cedex, France.
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
| | - Valérie Barbe
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Ghislaine Magdelenat
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Evelyne Marguet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay, Gif-sur-Yvette, Cedex, France
| | - Michael Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Jacques Oberto
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay, Gif-sur-Yvette, Cedex, France
| | - Patrick Forterre
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Département de Microbiologie, Institut Pasteur, Paris, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay, Gif-sur-Yvette, Cedex, France
| | - Violette Da Cunha
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Département de Microbiologie, Institut Pasteur, Paris, France.
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay, Gif-sur-Yvette, Cedex, France.
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.
| |
Collapse
|
11
|
Murthy AC, Aleksanyan N, Morton GM, Toyoda HC, Kalashyan M, Chen S, Ragucci AE, Broulidakis MP, Swerdlow KJ, Bui MNN, Muccioli M, Berkmen MB. Characterization of ConE, the VirB4 Homolog of the Integrative and Conjugative Element ICE Bs1 of Bacillus subtilis. J Bacteriol 2023; 205:e0003323. [PMID: 37219457 PMCID: PMC10294652 DOI: 10.1128/jb.00033-23] [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: 02/03/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
Conjugation is a major form of horizontal gene transfer, contributing to bacterial evolution and the acquisition of new traits. During conjugation, a donor cell transfers DNA to a recipient through a specialized DNA translocation channel classified as a type IV secretion system (T4SS). Here, we focused on the T4SS of ICEBs1, an integrative and conjugative element in Bacillus subtilis. ConE, encoded by ICEBs1, is a member of the VirB4 family of ATPases, the most conserved component of T4SSs. ConE is required for conjugation and localizes to the cell membrane, predominantly at the cell poles. In addition to Walker A and B boxes, VirB4 homologs have conserved ATPase motifs C, D, and E. Here, we created alanine substitutions in five conserved residues within or near ATPase motifs in ConE. Mutations in all five residues drastically decreased conjugation frequency but did not affect ConE protein levels or localization, indicating that an intact ATPase domain is critical for DNA transfer. Purified ConE is largely monomeric with some oligomers and lacks enzymatic activity, suggesting that ATP hydrolysis may be regulated or require special solution conditions. Finally, we investigated which ICEBs1 T4SS components interact with ConE using a bacterial two-hybrid assay. ConE interacts with itself, ConB, and ConQ, but these interactions are not required to stabilize ConE protein levels and largely do not depend on conserved residues within the ATPase motifs of ConE. The structure-function characterization of ConE provides more insight into this conserved component shared by all T4SSs. IMPORTANCE Conjugation is a major form of horizontal gene transfer and involves the transfer of DNA from one bacterium to another through the conjugation machinery. Conjugation contributes to bacterial evolution by disseminating genes involved in antibiotic resistance, metabolism, and virulence. Here, we characterized ConE, a protein component of the conjugation machinery of the conjugative element ICEBs1 of the bacterium Bacillus subtilis. We found that mutations in the conserved ATPase motifs of ConE disrupt mating but do not alter ConE localization, self-interaction, or levels. We also explored which conjugation proteins ConE interacts with and whether these interactions contribute to stabilizing ConE. Our work contributes to the understanding of the conjugative machinery of Gram-positive bacteria.
Collapse
Affiliation(s)
- Anastasia C. Murthy
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Naira Aleksanyan
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Georgeanna M. Morton
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Hunter C. Toyoda
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Meri Kalashyan
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Sirui Chen
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Adelyn E. Ragucci
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
- Cancer Immunology and Virology Department, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Matthew P. Broulidakis
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Kyle J. Swerdlow
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Minh N. N. Bui
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Maria Muccioli
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Melanie B. Berkmen
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| |
Collapse
|
12
|
Zhang H, Song J, Zheng Z, Li T, Shi N, Han Y, Zhang L, Yu Y, Fang H. Fungicide exposure accelerated horizontal transfer of antibiotic resistance genes via plasmid-mediated conjugation. WATER RESEARCH 2023; 233:119789. [PMID: 36863279 DOI: 10.1016/j.watres.2023.119789] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Co-pollution of soil with pesticide residues and antibiotic resistance genes (ARGs) is increasing due to the substantial usage of pesticides and organic fertilizers in greenhouse-based agricultural production. Non-antibiotic stresses, including those from agricultural fungicides, are potential co-selectors for the horizontal transfer of ARGs, but the underlying mechanism remains unclear. Intragenus and intergenus conjugative transfer systems of the antibiotic resistant plasmid RP4 were established to examine conjugative transfer frequency under stress from four widely used fungicides: triadimefon, chlorothalonil, azoxystrobin, and carbendazim. The mechanisms were elucidated at the cellular and molecular levels using transmission electron microscopy, flow cytometry, RT-qPCR, and RNA-seq techniques. The conjugative transfer frequency of plasmid RP4 between Escherichia coli strains increased with the rising exposure concentrations of chlorothalonil, azoxystrobin, and carbendazim, but was suppressed between E. coli and Pseudomonas putida by a high fungicide concentration (10 µg/mL). Triadimefon did not significantly affect conjugative transfer frequency. Exploration of the underlying mechanisms revealed that: (i) chlorothalonil exposure mainly promoted generation of intracellular reactive oxygen species, stimulated the SOS response, and increased cell membrane permeability, while (ii) azoxystrobin and carbendazim primarily enhanced expression of conjugation-related genes on the plasmid. These findings reveal the fungicide-triggered mechanisms associated with plasmid conjugation and highlight the potential role of non-bactericidal pesticides on the dissemination of ARGs.
Collapse
Affiliation(s)
- Houpu Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR. China; College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, PR. China
| | - Jiajin Song
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR. China
| | - Zhiruo Zheng
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR. China
| | - Tongxin Li
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR. China
| | - Nan Shi
- Department of Developmental and Cell Biology, University of California, Irvine CA 92697, United States
| | - Yuling Han
- Institute of Environmental Health and Pollution Control, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Luqing Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR. China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture and Rural Affairs, PR. China
| | - Yunlong Yu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR. China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture and Rural Affairs, PR. China
| | - Hua Fang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR. China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture and Rural Affairs, PR. China.
| |
Collapse
|
13
|
Byadgi OV, Rahmawaty A, Wang PC, Chen SC. Comparative genomics of Edwardsiella anguillarum and Edwardsiella piscicida isolated in Taiwan enables the identification of distinctive features and potential virulence factors using Oxford-Nanopore MinION® sequencing. JOURNAL OF FISH DISEASES 2023; 46:287-297. [PMID: 36571326 DOI: 10.1111/jfd.13743] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Edwardsiella tarda (ET) and Edwardsiella anguillarum (EA) are the most harmful bacterial fish pathogens in Taiwan. However, there is confusion regarding the genotypic identification of E. tarda and E. piscicida (EP). Therefore, we used a novel Nanopore MinION MK1C platform to sequence and compare the complete genomes of E. piscicida and E. anguillarum. The number of coding genes, rRNA, and tRNA recorded for E. anguillarum and E. piscicida were 8322, 25, and 98, and 5458, 25, and 98, respectively. Ribosomal multilocus sequence typing (rMLST) for E. piscicida indicated 35 rps. The shared clusters between E. anguillarum and E. piscicida indicated several unique clusters for the individual genomes. The phylogenetic tree analysis for all complete genomes indicated that E. anguillarum and E. piscicida were placed into two species-specific genotypes. Distribution of subsystems for annotated genomes found that genes related to virulence, defence, and disease for E. anguillarum were 103 and those for E. piscicida were 60 and pathogenic islands (PI) were 498 and 225, respectively. Vaccine candidates were identified in silico from the core genes using high antigenic, solubility, and secretion probabilities. Altogether, the genome data revealed distinctive features between E. anguillarum and E. piscicida, which suggest different pathogenicity and thus the need for separate preventive strategies.
Collapse
Affiliation(s)
- Omkar Vijay Byadgi
- International College, International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Atiek Rahmawaty
- International College, International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Pei-Chi Wang
- International College, International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Research Centre for Fish Vaccine and Diseases, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Southern Taiwan Fish Diseases Research Centre, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Shih-Chu Chen
- International College, International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Research Centre for Fish Vaccine and Diseases, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Southern Taiwan Fish Diseases Research Centre, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Research Centre for Animal Biologics, National Pingtung University of Science and Technology, Pingtung, Taiwan
| |
Collapse
|
14
|
Daveri A, Benigno V, van der Meer JR. Characterization of an atypical but widespread type IV secretion system for transfer of the integrative and conjugative element (ICEclc) in Pseudomonas putida. Nucleic Acids Res 2023; 51:2345-2362. [PMID: 36727472 PMCID: PMC10018362 DOI: 10.1093/nar/gkad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/23/2022] [Accepted: 01/26/2023] [Indexed: 02/03/2023] Open
Abstract
Conjugation of DNA relies on multicomponent protein complexes bridging two bacterial cytoplasmic compartments. Whereas plasmid conjugation systems have been well documented, those of integrative and conjugative elements (ICEs) have remained poorly studied. We characterize here the conjugation system of the ICEclc element in Pseudomonas putida UWC1 that is a model for a widely distributed family of ICEs. By in frame deletion and complementation, we show the importance on ICE transfer of 22 genes in a 20-kb conserved ICE region. Protein comparisons recognized seven homologs to plasmid type IV secretion system components, another six homologs to frequent accessory proteins, and the rest without detectable counterparts. Stationary phase imaging of P. putida ICEclc with in-frame fluorescent protein fusions to predicted type IV components showed transfer-competent cell subpopulations with multiple fluorescent foci, largely overlapping in dual-labeled subcomponents, which is suggestive for multiple conjugation complexes per cell. Cross-dependencies between subcomponents in ICE-type IV secretion system assembly were revealed by quantitative foci image analysis in a variety of ICEclc mutant backgrounds. In conclusion, the ICEclc family presents an evolutionary distinct type IV conjugative system with transfer competent cells specialized in efficient transfer.
Collapse
Affiliation(s)
- Andrea Daveri
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Valentina Benigno
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | | |
Collapse
|
15
|
Ortiz Charneco G, Kelleher P, Buivydas A, Dashko S, de Waal PP, van Peij NNME, Roberts RJ, Mahony J, van Sinderen D. Delineation of a lactococcal conjugation system reveals a restriction-modification evasion system. Microb Biotechnol 2023; 16:1250-1263. [PMID: 36942662 DOI: 10.1111/1751-7915.14221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/06/2023] [Accepted: 01/08/2023] [Indexed: 03/23/2023] Open
Abstract
Plasmid pUC11B is a 49.3-kb plasmid harboured by the fermented meat isolate Lactococcus lactis subsp. lactis UC11. Among other features, pUC11B encodes a pMRC01-like conjugation system and tetracycline-resistance. In this study, we demonstrate that this plasmid can be conjugated at high frequencies to recipient strains. Mutational analysis of the 22 genes encompassing the presumed pUC11B conjugation cluster revealed the presence of several genes with essential conjugation functions, as well as a gene, trsR, encoding a putative transcriptional repressor of this conjugation cluster. Furthermore, plasmid pUC11B encodes an anti-restriction protein, TrsAR, which facilitates higher conjugation frequencies when pUC11B is transferred into recipient strains containing Type II or Type III RM systems. These findings demonstrate how RM mechanisms can be circumvented when they act as a biological barrier for conjugation events.
Collapse
Affiliation(s)
| | - Philip Kelleher
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Andrius Buivydas
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Sofia Dashko
- DSM Food and Beverage, Center for Food Innovation, Delft, The Netherlands
| | - Paul P de Waal
- DSM Food and Beverage, Center for Food Innovation, Delft, The Netherlands
| | | | | | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| |
Collapse
|
16
|
Liu W, Xu Y, Slaveykova VI. Oxidative stress induced by sub-lethal exposure to copper as a mediator in development of bacterial resistance to antibiotics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 860:160516. [PMID: 36470380 DOI: 10.1016/j.scitotenv.2022.160516] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Limited information exists on how bacterial resistance to antibiotics is acquired and altered in response to short-term metal stress, and what the prevailing pathways are. Here the precursor mechanisms of development of bacterial antibiotic resistance mediated by oxidative stress induce under sub-lethal Cu2+ exposure were explored. The results showed that the overall level of antibiotic resistance in wild-type Escherichia coli and antibiotic-resistant E. coli was enhanced under 4 and 20 mg/L Cu2+ exposure, as demonstrated by the 2- to 8-fold increase in minimum inhibitory concentration (MIC). The MIC correlated with the increase of the cellular ROS generation and the enhancement of the antioxidant enzyme activity (p < 0.05), suggesting that changes in antibiotic resistance under sub-lethal Cu2+ exposure could be associated with oxidative stress. Likewise, enhanced cell membrane permeability and an increase in the number of bacteria entering the viable but non culturable (VBNC) state contributed to bacterial resistance to antibiotics. Moreover, the variance partitioning analysis demonstrated that the alterations of the antibiotic resistance phenotype of wild-type E. coli was mainly caused by oxidative stress-mediated increase in cell membrane permeability and entry into the VBNC state. The development of antibiotic resistance in resistant E. coli was primarily attributed to changes in the abundance and horizontal transfer ability of its antibiotic resistance genes, both of which contributed up to 20 %. Taken together the results allowed to propose a conseptual scheme on developing bacterial antibiotic resistance mediated by oxidative stress under sub-lethal Cu2+ exposure. This result provided a strong basis for reduction of early bacterial resistance.
Collapse
Affiliation(s)
- Wei Liu
- Environmental Biogeochemistry and Ecotoxicology, Department F.A. Forel for Environmental and Aquatic Sciences, Faculty of Sciences, University of Geneva, Bvd. Carl-Vogt 66, 1211 Geneva, Switzerland
| | - Yan Xu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, 300191, Fukang Road 31, Tianjin, China.
| | - Vera I Slaveykova
- Environmental Biogeochemistry and Ecotoxicology, Department F.A. Forel for Environmental and Aquatic Sciences, Faculty of Sciences, University of Geneva, Bvd. Carl-Vogt 66, 1211 Geneva, Switzerland.
| |
Collapse
|
17
|
Sciallano C, Auguy F, Boulard G, Szurek B, Cunnac S. The Complete Genome Resource of Xanthomonas oryzae pv. oryzae CIX2779 Includes the First Sequence of a Plasmid for an African Representative of This Rice Pathogen. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:73-77. [PMID: 36537805 DOI: 10.1094/mpmi-09-22-0191-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The bacterial plant pathogen Xanthomonas oryzae pv. oryzae is responsible for the foliar rice bacterial blight disease. Genetically contrasted, continent-specific, sublineages of this species can cause important damages to rice production both in Asia and Africa. We report on the genome of the CIX2779 strain of this pathogen, previously named NAI1 and originating from Niger. Oxford Nanopore long reads assembly and Illumina short reads polishing produced a genome sequence composed of a 4,725,792-bp circular chromosome and a 39,798-bp-long circular plasmid designated pCIX2779_1. The chromosome structure and base-level sequence are highly related to reference strains of African X. oryzae pv. oryzae and encode identical transcription activator-like effectors for virulence. Importantly, our in silico analysis strongly indicates that pCIX2779_1 is a genuine conjugative plasmid, the first indigenous one sequenced from an African strain of the X. oryzae species. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Collapse
Affiliation(s)
- Coline Sciallano
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Florence Auguy
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Gabriel Boulard
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Boris Szurek
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Sébastien Cunnac
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| |
Collapse
|
18
|
Tang B, Wang C, Sun D, Lin H, Ma J, Guo H, Yang H, Li X. In Silico Characterization of blaNDM-Harboring Conjugative Plasmids in Acinetobacter Species. Microbiol Spectr 2022; 10:e0210222. [PMID: 36301090 PMCID: PMC9769834 DOI: 10.1128/spectrum.02102-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 09/28/2022] [Indexed: 01/06/2023] Open
Abstract
New Delhi metallo-β-lactamase (NDM)-producing clinical strains in Acinetobacter spp. have been recently reported in many countries and have received considerable attention. The vast majority of blaNDM cases occur on conjugative plasmids, which play a vital role in disseminating blaNDM. To characterize the conjugative plasmids bearing blaNDM genes in Acinetobacter spp., we analyzed the variants of blaNDM, conjugative transfer regions, genetic contexts of blaNDM, and the phylogenetic pattern of the 62 predicted blaNDM-positive plasmids, which were selected from 1,191 plasmids of Acinetobacter species from GenBank. We identified 30 conjugative plasmids from the 62 blaNDM-harboring plasmids in Acinetobacter species, with the oriT sites similar to plasmid pNDM-YR7 in our study, genes coding for relaxases of the MOBQ family, genes encoding type IV coupling proteins (T4CPs) of the TrwB/TraD subfamily, and VirB-like type IV secretion system (T4SS) gene clusters. The genome sizes of all 30 pNDM-YR7-like plasmids ranged from 39.36 kb to 49.65 kb, with a median size of 44.56 kb. The most common species of Acinetobacter containing the blaNDM-positive conjugative plasmids was A. baumannii, followed by Acinetobacter lwoffii and Acinetobacter indicus. Notably, pNDM-YR7 is the first report on a blaNDM-positive conjugative plasmid in Acinetobacter junii. Moreover, all 30 blaNDM-positive conjugative plasmids in Acinetobacter species were found to contain genetic contexts with the structure ISAba14-aph(3')-VI-ISAba125-blaNDM-ble. Our findings provide important insights into the phylogeny and evolution of blaNDM-positive plasmids of Acinetobacter species and further address their role in acquiring and spreading blaNDM genes in Acinetobacter species. IMPORTANCE Conjugative plasmids harboring the blaNDM gene play a vital role in disseminating carbapenem resistance. In this study, we first report a conjugative plasmid, pNDM-YR7, in Acinetobacter junii. Based on the genomic characteristics of the blaNDM-positive pNDM-YR7, we performed in silico typing and comparative analysis of blaNDM-positive plasmids using the 1,191 plasmids of Acinetobacter species available in the NCBI RefSeq database. We analyzed the characteristics of blaNDM-positive plasmids, including the variants of blaNDM, genetic features associated with blaNDM, conjugative transfer regions, and the phylogenetic pattern of the blaNDM-positive plasmids. All 30 blaNDM-positive conjugative plasmids were found to contain an ISAba14-aph(3')-VI-ISAba125-blaNDM-ble region. This study provides novel insights into the phylogeny and evolution of blaNDM-harboring conjugative plasmids and contributes to the repertoire of knowledge surrounding blaNDM-positive plasmids in the genus Acinetobacter.
Collapse
Affiliation(s)
- Biao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Chenyu Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Dongchang Sun
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Hui Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Jiangang Ma
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Hengzhao Guo
- Department of Radiation Oncology, Zhuhai People’s Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, Guangdong, China
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Xiaobin Li
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, Guangdong, China
| |
Collapse
|
19
|
Giannotti D, Boscaro V, Husnik F, Vannini C, Keeling PJ. At the threshold of symbiosis: the genome of obligately endosymbiotic ' Candidatus Nebulobacter yamunensis' is almost indistinguishable from that of a cultivable strain. Microb Genom 2022; 8:mgen000909. [PMID: 36748607 PMCID: PMC9837558 DOI: 10.1099/mgen.0.000909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Comparing obligate endosymbionts with their free-living relatives is a powerful approach to investigate the evolution of symbioses, and it has led to the identification of several genomic traits consistently associated with the establishment of symbiosis. 'Candidatus Nebulobacter yamunensis' is an obligate bacterial endosymbiont of the ciliate Euplotes that seemingly depends on its host for survival. A subsequently characterized bacterial strain with an identical 16S rRNA gene sequence, named Fastidiosibacter lacustris, can instead be maintained in pure culture. We analysed the genomes of 'Candidatus Nebulobacter' and Fastidiosibacter seeking to identify key differences between their functional traits and genomic structure that might shed light on a recent transition to obligate endosymbiosis. Surprisingly, we found almost no such differences: the two genomes share a high level of sequence identity, the same overall structure, and largely overlapping sets of genes. The similarities between the genomes of the two strains are at odds with their different ecological niches, confirmed here with a parallel growth experiment. Although other pairs of closely related symbiotic/free-living bacteria have been compared in the past, 'Candidatus Nebulobacter' and Fastidiosibacter represent an extreme example proving that a small number of (unknown) factors might play a pivotal role in the earliest stages of obligate endosymbiosis establishment.
Collapse
Affiliation(s)
- Daniele Giannotti
- Department of Biology, University of Pisa, Pisa, Italy,Department of Botany, University of British Columbia, Vancouver, Canada
| | - Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, Canada,*Correspondence: Vittorio Boscaro,
| | - Filip Husnik
- Department of Botany, University of British Columbia, Vancouver, Canada,Okinawa Institute of Science and Technology, Okinawa, Japan
| | | | | |
Collapse
|
20
|
Añorga M, Urriza M, Ramos C, Murillo J. Multiple relaxases contribute to the horizontal transfer of the virulence plasmids from the tumorigenic bacterium Pseudomonas syringae pv. savastanoi NCPPB 3335. Front Microbiol 2022; 13:1076710. [PMID: 36578579 PMCID: PMC9791958 DOI: 10.3389/fmicb.2022.1076710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022] Open
Abstract
Pseudomonas syringae pv. savastanoi NCPPB 3335 is the causal agent of olive knot disease and contains three virulence plasmids: pPsv48A (pA), 80 kb; pPsv48B (pB), 45 kb, and pPsv48C (pC), 42 kb. Here we show that pB contains a complete MPFT (previously type IVA secretion system) and a functional origin of conjugational transfer adjacent to a relaxase of the MOBP family; pC also contains a functional oriT-MOBP array, whereas pA contains an incomplete MPFI (previously type IVB secretion system), but not a recognizable oriT. Plasmid transfer occurred on solid and in liquid media, and on leaf surfaces of a non-host plant (Phaseolus vulgaris) with high (pB) or moderate frequency (pC); pA was transferred only occasionally after cointegration with pB. We found three plasmid-borne and three chromosomal relaxase genes, although the chromosomal relaxases did not contribute to plasmid dissemination. The MOBP relaxase genes of pB and pC were functionally interchangeable, although with differing efficiencies. We also identified a functional MOBQ mobilization region in pC, which could only mobilize this plasmid. Plasmid pB could be efficiently transferred to strains of six phylogroups of P. syringae sensu lato, whereas pC could only be mobilized to two strains of phylogroup 3 (genomospecies 2). In two of the recipient strains, pB was stably maintained after 21 subcultures in liquid medium. The carriage of several relaxases by the native plasmids of P. syringae impacts their transfer frequency and, by providing functional diversity and redundancy, adds robustness to the conjugation system.
Collapse
Affiliation(s)
- Maite Añorga
- Institute for Multidisciplinary Research in Applied Biology, Universidad Pública de Navarra (UPNA), Edificio de Agrobiotecnología, Mutilva Baja, Spain
| | - Miriam Urriza
- Institute for Multidisciplinary Research in Applied Biology, Universidad Pública de Navarra (UPNA), Edificio de Agrobiotecnología, Mutilva Baja, Spain
| | - Cayo Ramos
- Área de Genética, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain,Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
| | - Jesús Murillo
- Institute for Multidisciplinary Research in Applied Biology, Universidad Pública de Navarra (UPNA), Edificio de Agrobiotecnología, Mutilva Baja, Spain,*Correspondence: Jesús Murillo
| |
Collapse
|
21
|
Zeng Z, Lei L, Li L, Hua S, Li W, Zhang L, Lin Q, Zheng Z, Yang J, Dou X, Li L, Li X. In silico characterization of bla NDM-harboring plasmids in Klebsiella pneumoniae. Front Microbiol 2022; 13:1008905. [PMID: 36504778 PMCID: PMC9727287 DOI: 10.3389/fmicb.2022.1008905] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/07/2022] [Indexed: 11/24/2022] Open
Abstract
Klebsiella pneumoniae is a primary culprit of antibiotic-resistant nosocomial infections worldwide, and infections caused by NDM-producing strains are a major threat due to limited therapeutic options. The majority of bla NDM cases occur on plasmids; therefore, we explored the relationships between plasmids and bla NDM genes in K. pneumoniae by analyzing the variants of bla NDM, replicon types, conjugative transfer regions of 171 bla NDM-harboring plasmids from 4,451 K. pneumoniae plasmids. Of the nine identified bla NDM variants, bla NDM-1 (73.68%) and bla NDM-5 (16.37%) were the most dominant. Over half of the bla NDM-harboring plasmids of K. pneumoniae were classified into IncF plasmids. IncX3 single-replicon plasmids (46-57 kb) carried genes encoding relaxases of the MOBP family, T4CP genes of the VirD4/TraG subfamily, and VirB-like T4SS gene clusters, which were mainly geographically distributed in China. We found 10 bla NDM-harboring IncN plasmids (38.38-63.05 kb) carrying the NW-type origin of transfer (oriT) regions, genes coding for relaxases of MOBF family, genes encoding T4CPs of the TrwB/TraD subfamily, and Trw-like T4SS gene clusters, which were also mainly geographically distributed in China. Moreover, we identified 21 IncC plasmids carrying bla NDM-1 (140.1-329.2 kb), containing the A/C-type oriTs, genes encoding relaxases of MOBH family, genes encoding T4CPs belonging to TrwB/TraD subfamily, and Tra_F-like T4SS gene clusters. The bla NDM-harboring IncC plasmids were widely geographically distributed all over the world, mainly in the United States, China and Viet Nam. These findings enhance our understanding of the diversity of bla NDM-harboring plasmids in K. pneumoniae.
Collapse
Affiliation(s)
- Zhu Zeng
- Department of Respiratory Diseases, The First Affiliated Hospital of College of Medicine, Zhejiang University, Hangzhou, China
| | - Lei Lei
- Department of Cadre Health Care, Guizhou Provincial People's Hospital, Guiyang, China
| | - Linman Li
- Health Management Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shengni Hua
- Department of Radiation Oncology, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China
| | - Wenting Li
- Zhuhai Precision Medical Center, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China
| | - Limei Zhang
- Zhuhai Precision Medical Center, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China
| | - Qiuping Lin
- Zhuhai Precision Medical Center, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China
| | - Zhixiong Zheng
- Zhuhai Precision Medical Center, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China
| | - Jing Yang
- Department of Pulmonary and Critical Care Medicine, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China
| | - Xiaohui Dou
- Health Management Center, Zhuhai People’s Hospital (Zhuhai Hospital affiliated With Jinan University), Zhuhai, China,*Correspondence: Luan Li, ; Xiaobin Li, ; Xiaohui Dou,
| | - Luan Li
- Department of Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China,*Correspondence: Luan Li, ; Xiaobin Li, ; Xiaohui Dou,
| | - Xiaobin Li
- Zhuhai Precision Medical Center, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China,*Correspondence: Luan Li, ; Xiaobin Li, ; Xiaohui Dou,
| |
Collapse
|
22
|
Lopes AR, Bunin E, Viana AT, Froufe H, Muñoz-Merida A, Pinho D, Figueiredo J, Barroso C, Vaz-Moreira I, Bellanger X, Egas C, Nunes OC. In silico prediction of the enzymes involved in the degradation of the herbicide molinate by Gulosibacter molinativorax ON4T. Sci Rep 2022; 12:15502. [PMID: 36109598 PMCID: PMC9477822 DOI: 10.1038/s41598-022-18732-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 08/18/2022] [Indexed: 12/01/2022] Open
Abstract
Gulosibacter molinativorax ON4T is the only known organism to produce molinate hydrolase (MolA), which catalyses the breakdown of the thiocarbamate herbicide into azepane-1-carboxylic acid (ACA) and ethanethiol. A combined genomic and transcriptomic strategy was used to fully characterize the strain ON4T genome, particularly the molA genetic environment, to identify the potential genes encoding ACA degradation enzymes. Genomic data revealed that molA is the only catabolic gene of a novel composite transposon (Tn6311), located in a novel low copy number plasmid (pARLON1) harbouring a putative T4SS of the class FATA. pARLON1 had an ANI value of 88.2% with contig 18 from Agrococcus casei LMG 22410T draft genome. Such results suggest that pARLON1 is related to genomic elements of other Actinobacteria, although Tn6311 was observed only in strain ON4T. Furthermore, genomic and transcriptomic data demonstrated that the genes involved in ACA degradation are chromosomal. Based on their overexpression when growing in the presence of molinate, the enzymes potentially involved in the heterocyclic ring breakdown were predicted. Among these, the activity of a protein related to caprolactone hydrolase was demonstrated using heterologous expression. However, further studies are needed to confirm the role of the other putative enzymes.
Collapse
|
23
|
Yu Z, Zhang Z, Shi L, Hua S, Luan T, Lin Q, Zheng Z, Feng X, Liu M, Li X. In silico characterization of IncX3 plasmids carrying blaOXA-181 in Enterobacterales. Front Cell Infect Microbiol 2022; 12:988236. [PMID: 36159637 PMCID: PMC9492964 DOI: 10.3389/fcimb.2022.988236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/23/2022] [Indexed: 12/03/2022] Open
Abstract
Carbapenem-resistant Enterobacterales poses a global urgent antibiotic resistance threat because of its ability to transfer carbapenemase genes to other bacteria via horizontal gene transfer mediated by mobile genetic elements such as plasmids. Oxacillinase-181 (OXA-181) is one of the most common OXA-48-like carbapenemases, and OXA-181-producing Enterobacterales has been reported in many countries worldwide. However, systematic research concerning the overall picture of plasmids harboring blaOXA-181 in Enterobacterales is currently scarce. In this study, we aimed to determine the phylogeny and evolution of blaOXA-181-positive (gene encoding OXA-181) plasmids. To characterize the plasmids harboring blaOXA-181 in Enterobacterales, we identified 81 blaOXA-181-positive plasmids from 35,150 bacterial plasmids downloaded from the NCBI RefSeq database. Our results indicated that diverse plasmid types harbored blaOXA-181 but was predominantly carried by IncX3-type plasmids. We systematically compared the host strains, plasmid types, conjugative transfer regions, and genetic contexts of blaOXA-181 among the 66 blaOXA-181-positive IncX3 plasmids. We found that IncX3 plasmids harboring blaOXA-181 were mostly ColKP3-IncX3 hybrid plasmids with a length of 51 kb each and were mainly distributed in Escherichia coli and Klebsiella pneumoniae. Most of the IncX3 plasmids harboring blaOXA-181 were human origin. Almost all the blaOXA-181-positive IncX3 plasmids were found to carry genes coding for relaxases of the MOBP family and VirB-like type IV secretion system (T4SS) gene clusters, and all the 66 IncX3 plasmids were found to carry the genes encoding type IV coupling proteins (T4CPs) of the VirD4/TraG subfamily. Most IncX3 plasmids harbored both blaOXA-181 and qnrS1 in their genomes, and the two antibiotic resistance genes were found to a composite transposon bracketed by two copies of insertion sequence IS26 in the same orientation. Our findings provide important insights into the phylogeny and evolution of blaOXA-181-positive IncX3 plasmids and further address their role in acquiring and spreading blaOXA-181 genes in Enterobacterales.
Collapse
Affiliation(s)
- Zhijian Yu
- Department of Otolaryngology, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, China
| | - Zhengrong Zhang
- Department of Urology, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, China
| | - Lile Shi
- Department of Cardiology, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, China
| | - Shengni Hua
- Department of Radiation Oncology, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, China
| | - Ting Luan
- Community Health Service Center of Xinkou Town, Tianjin, China
| | - Qiuping Lin
- Zhuhai Precision Medical Center, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, China
| | - Zhixiong Zheng
- Zhuhai Precision Medical Center, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, China
| | - Xiaosan Feng
- Department of Neonatology, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, China
- *Correspondence: Xiaobin Li, ; Mubiao Liu, ; Xiaosan Feng,
| | - Mubiao Liu
- Department of Obstetrics and Gynecology, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, China
- *Correspondence: Xiaobin Li, ; Mubiao Liu, ; Xiaosan Feng,
| | - Xiaobin Li
- Zhuhai Precision Medical Center, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, China
- *Correspondence: Xiaobin Li, ; Mubiao Liu, ; Xiaosan Feng,
| |
Collapse
|
24
|
Gurinovich AS, Titok MA. Molecular Genetic and Functional Analysis of the Conjugation System of the pBS72 Plasmid from Bacillus subtilis Environmental Isolates. Microbiology (Reading) 2022. [DOI: 10.1134/s002626172230018x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
25
|
Coluzzi C, Garcillán-Barcia MP, de la Cruz F, Rocha EPC. Evolution of plasmid mobility: origin and fate of conjugative and non-conjugative plasmids. Mol Biol Evol 2022; 39:6593704. [PMID: 35639760 PMCID: PMC9185392 DOI: 10.1093/molbev/msac115] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Conjugation drives the horizontal transfer of adaptive traits across prokaryotes. One-fourth of the plasmids encode the functions necessary to conjugate autonomously, the others being eventually mobilizable by conjugation. To understand the evolution of plasmid mobility, we studied plasmid size, gene repertoires, and conjugation-related genes. Plasmid gene repertoires were found to vary rapidly in relation to the evolutionary rate of relaxases, for example, most pairs of plasmids with 95% identical relaxases have fewer than 50% of homologs. Among 249 recent transitions of mobility type, we observed a clear excess of plasmids losing the capacity to conjugate. These transitions are associated with even greater changes in gene repertoires, possibly mediated by transposable elements, including pseudogenization of the conjugation locus, exchange of replicases reducing the problem of incompatibility, and extensive loss of other genes. At the microevolutionary scale of plasmid taxonomy, transitions of mobility type sometimes result in the creation of novel taxonomic units. Interestingly, most transitions from conjugative to mobilizable plasmids seem to be lost in the long term. This suggests a source-sink dynamic, where conjugative plasmids generate nonconjugative plasmids that tend to be poorly adapted and are frequently lost. Still, in some cases, these relaxases seem to have evolved to become efficient at plasmid mobilization in trans, possibly by hijacking multiple conjugative systems. This resulted in specialized relaxases of mobilizable plasmids. In conclusion, the evolution of plasmid mobility is frequent, shapes the patterns of gene flow in bacteria, the dynamics of gene repertoires, and the ecology of plasmids.
Collapse
Affiliation(s)
- Charles Coluzzi
- Institut Pasteur, Université de Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France
| | - M Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, C/Albert Einstein 22, 39011, Santander, Spain
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, C/Albert Einstein 22, 39011, Santander, Spain
| | - Eduardo P C Rocha
- Institut Pasteur, Université de Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France
| |
Collapse
|
26
|
Dia NC, Morinière L, Cottyn B, Bernal E, Jacobs J, Koebnik R, Osdaghi E, Potnis N, Pothier J. Xanthomonas hortorum - beyond gardens: Current taxonomy, genomics, and virulence repertoires. MOLECULAR PLANT PATHOLOGY 2022; 23:597-621. [PMID: 35068051 PMCID: PMC8995068 DOI: 10.1111/mpp.13185] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 05/02/2023]
Abstract
TAXONOMY Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Lysobacterales (earlier synonym of Xanthomonadales); Family Lysobacteraceae (earlier synonym of Xanthomonadaceae); Genus Xanthomonas; Species X. hortorum; Pathovars: pv. carotae, pv. vitians, pv. hederae, pv. pelargonii, pv. taraxaci, pv. cynarae, and pv. gardneri. HOST RANGE Xanthomonas hortorum affects agricultural crops, and horticultural and wild plants. Tomato, carrot, artichoke, lettuce, pelargonium, ivy, and dandelion were originally described as the main natural hosts of the seven separate pathovars. Artificial inoculation experiments also revealed other hosts. The natural and experimental host ranges are expected to be broader than initially assumed. Additionally, several strains, yet to be assigned to a pathovar within X. hortorum, cause diseases on several other plant species such as peony, sweet wormwood, lavender, and oak-leaf hydrangea. EPIDEMIOLOGY AND CONTROL X. hortorum pathovars are mainly disseminated by infected seeds (e.g., X. hortorum pvs carotae and vitians) or cuttings (e.g., X. hortorum pv. pelargonii) and can be further dispersed by wind and rain, or mechanically transferred during planting and cultivation. Global trade of plants, seeds, and other propagating material constitutes a major pathway for their introduction and spread into new geographical areas. The propagules of some pathovars (e.g., X. horturum pv. pelargonii) are spread by insect vectors, while those of others can survive in crop residues and soils, and overwinter until the following growing season (e.g., X. hortorum pvs vitians and carotae). Control measures against X. hortorum pathovars are varied and include exclusion strategies (i.e., by using certification programmes and quarantine regulations) to multiple agricultural practices such as the application of phytosanitary products. Copper-based compounds against X. hortorum are used, but the emergence of copper-tolerant strains represents a major threat for their effective management. With the current lack of efficient chemical or biological disease management strategies, host resistance appears promising, but is not without challenges. The intrastrain genetic variability within the same pathovar poses a challenge for breeding cultivars with durable resistance. USEFUL WEBSITES https://gd.eppo.int/taxon/XANTGA, https://gd.eppo.int/taxon/XANTCR, https://gd.eppo.int/taxon/XANTPE, https://www.euroxanth.eu, http://www.xanthomonas.org, http://www.xanthomonas.org/dokuwiki.
Collapse
Affiliation(s)
- Nay C. Dia
- Environmental Genomics and Systems Biology Research GroupInstitute for Natural Resource SciencesZurich University of Applied SciencesWädenswilSwitzerland
- Molecular Plant BreedingInstitute of Agricultural SciencesETH ZurichZurichSwitzerland
| | - Lucas Morinière
- University of LyonUniversité Claude Bernard Lyon 1CNRSINRAEUMR Ecologie MicrobienneVilleurbanneFrance
| | - Bart Cottyn
- Plant Sciences UnitFlanders Research Institute for Agriculture, Fisheries and FoodMerelbekeBelgium
| | - Eduardo Bernal
- Department of Plant PathologyThe Ohio State UniversityColumbusOhioUSA
| | - Jonathan M. Jacobs
- Department of Plant PathologyThe Ohio State UniversityColumbusOhioUSA
- Infectious Diseases InstituteThe Ohio State UniversityColumbusOhioUSA
| | - Ralf Koebnik
- Plant Health Institute of MontpellierUniversity of Montpellier, CIRAD, INRAe, Institut Agro, IRDMontpellierFrance
| | - Ebrahim Osdaghi
- Department of Plant ProtectionCollege of AgricultureUniversity of TehranKarajIran
| | - Neha Potnis
- Department of Entomology and Plant PathologyAuburn UniversityAlabamaUSA
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research GroupInstitute for Natural Resource SciencesZurich University of Applied SciencesWädenswilSwitzerland
| |
Collapse
|
27
|
Kishida K, Bosserman RE, Harb L, Khara P, Song L, Hu B, Zeng L, Christie PJ. Contributions of F‐specific Subunits to the F
Plasmid‐Encoded
Type
IV
Secretion System and F pilus. Mol Microbiol 2022; 117:1275-1290. [DOI: 10.1111/mmi.14908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/26/2022] [Accepted: 04/12/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Kouhei Kishida
- Department of Microbiology and Molecular Genetics McGovern Medical School 6431 Fannin St, Houston, Texas 77030
| | - Rachel E. Bosserman
- Department of Microbiology and Molecular Genetics McGovern Medical School 6431 Fannin St, Houston, Texas 77030
- Current address: Department of Medicine, Division of Infectious Diseases Washington School of Medicine St. Louis, MO, 63110
| | - Laith Harb
- Department of Biochemistry and Biophysics, Texas A&M University College Station TX, 77843 USA
- Center for Phage Technology, Texas A&M University College Station TX, 77843 USA
| | - Pratick Khara
- Department of Microbiology and Molecular Genetics McGovern Medical School 6431 Fannin St, Houston, Texas 77030
| | - Liqiang Song
- Department of Microbiology and Molecular Genetics McGovern Medical School 6431 Fannin St, Houston, Texas 77030
| | - Bo Hu
- Department of Microbiology and Molecular Genetics McGovern Medical School 6431 Fannin St, Houston, Texas 77030
| | - Lanying Zeng
- Department of Biochemistry and Biophysics, Texas A&M University College Station TX, 77843 USA
- Center for Phage Technology, Texas A&M University College Station TX, 77843 USA
| | - Peter J. Christie
- Department of Microbiology and Molecular Genetics McGovern Medical School 6431 Fannin St, Houston, Texas 77030
| |
Collapse
|
28
|
Zhang Q, Liu Y, Zhang C, Zhou D. Easily biodegradable substrates are crucial for enhancing antibiotic risk reduction: Low-carbon discharging policies need to be more specified. WATER RESEARCH 2022; 210:117972. [PMID: 34952454 DOI: 10.1016/j.watres.2021.117972] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Governments have formulated stricter wastewater treatment plant (WWTP) discharge standards to address water pollution; however, with the cost of aggravating the refractory of the discharges. These policies are not in line with the classic co-metabolism theory; thus, we evaluated the effects of an easily biodegradable substrate on the removal efficiency of antibiotics and antibiotic resistance genes (ARGs) in the receiving water. In this study, reactor with 8 d of hydraulic retention time (HRT) was constructed to simulate a receiving river, and several antibiotics (0.30 mg/L each) were continuously discharged to the reactor (tetracycline, ciprofloxacin, amoxicillin, chloramphenicol, and sulfamethoxazole). Sodium acetate (NaAc) was used as a representative easily biodegradable substrate, and treatment protocols with and without a co-substrate were compared. The attenuation of the antibiotics in the simulated river and the production and dissemination of ARGs were analyzed. The results showed that 50 mg/L NaAc activated non-specific enzymes (a log2-fold change of 3.1-8.8 compared with 0 mg/L NaAc). The removal rate of the antibiotics was increased by 4-32%, and the toxicity of the downstream water was reduced by 35%. The upregulation of antioxidant enzymes caused the intracellular reactive oxygen species (ROSs) decreased by up to 47%, inhibiting horizontal gene transfer and reducing mobile genetic element-mediated ARGs (mARGs) by 18-56%. Furthermore, NaAc also increased the alpha diversity of the microbial community by 5-15% (Shannon-Wiener Index) and reduced the abundance of human bacterial pathogens by 22-36%. In summary, easily biodegradable substrates in the receiving water are crucial for reducing antibiotic risk.
Collapse
Affiliation(s)
- Qifeng Zhang
- Engineering Lab for Water Pollution Control and Resources Recovery of Jilin Province, School of Environment, Northeast Normal University, Changchun 130117, China
| | - Yang Liu
- Engineering Lab for Water Pollution Control and Resources Recovery of Jilin Province, School of Environment, Northeast Normal University, Changchun 130117, China
| | - Chongjun Zhang
- Engineering Lab for Water Pollution Control and Resources Recovery of Jilin Province, School of Environment, Northeast Normal University, Changchun 130117, China.
| | - Dandan Zhou
- Engineering Lab for Water Pollution Control and Resources Recovery of Jilin Province, School of Environment, Northeast Normal University, Changchun 130117, China.
| |
Collapse
|
29
|
Ramnarine SDBJ, Jayaraman J, Ramsubhag A. Comparative genomics of the black rot pathogen Xanthomonas campestris pv. campestris and non-pathogenic co-inhabitant Xanthomonas melonis from Trinidad reveal unique pathogenicity determinants and secretion system profiles. PeerJ 2022; 9:e12632. [PMID: 35036136 PMCID: PMC8734464 DOI: 10.7717/peerj.12632] [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] [Received: 07/27/2021] [Accepted: 11/22/2021] [Indexed: 11/20/2022] Open
Abstract
Black-rot disease caused by the phytopathogen Xanthomonas campestris pv. campestris (Xcc) continues to have considerable impacts on the productivity of cruciferous crops in Trinidad and Tobago and the wider Caribbean region. While the widespread occurrence of resistance of Xcc against bactericidal agrochemicals can contribute to the high disease burdens, the role of virulence and pathogenicity features of local strains on disease prevalence and severity has not been investigated yet. In the present study, a comparative genomic analysis was performed on 6 pathogenic Xcc and 4 co-isolated non-pathogenic Xanthomonas melonis (Xmel) strains from diseased crucifer plants grown in fields with heavy chemical use in Trinidad. Native isolates were grouped into two known and four newly assigned ribosomal sequence types (rST). Mobile genetic elements were identified which belonged to the IS3, IS5 family, Tn3 transposon, resolvases, and tra T4SS gene clusters. Additionally, exogenous plasmid derived sequences with origins from other bacterial species were characterised. Although several instances of genomic rearrangements were observed, native Xcc and Xmel isolates shared a significant level of structural homology with reference genomes, Xcc ATCC 33913 and Xmel CFBP4644, respectively. Complete T1SS hlyDB, T2SS, T4SS vir and T5SS xadA, yapH and estA gene clusters were identified in both species. Only Xmel strains contained a complete T6SS but no T3SS. Both species contained a complex repertoire of extracellular cell wall degrading enzymes. Native Xcc strains contained 37 T3SS and effector genes but a variable and unique profile of 8 avr, 4 xop and 1 hpa genes. Interestingly, Xmel strains contained several T3SS effectors with low similarity to references including avrXccA1 (~89%), hrpG (~73%), hrpX (~90%) and xopAZ (~87%). Furthermore, only Xmel genomes contained a CRISPR-Cas I-F array, but no lipopolysaccharide wxc gene cluster. Xmel strains were confirmed to be non-pathogenic by pathogenicity assays. The results of this study will be useful to guide future research into virulence mechanisms, agrochemical resistance, pathogenomics and the potential role of the co-isolated non-pathogenic Xanthomonas strains on Xcc infections.
Collapse
Affiliation(s)
- Stephen D B Jr Ramnarine
- Department of Life Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Jayaraj Jayaraman
- Department of Life Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Adesh Ramsubhag
- Department of Life Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| |
Collapse
|
30
|
Abstract
Naturally occurring plasmids come in different sizes. The smallest are less than a kilobase of DNA, while the largest can be over three orders of magnitude larger. Historically, research has tended to focus on smaller plasmids that are usually easier to isolate, manipulate and sequence, but with improved genome assemblies made possible by long-read sequencing, there is increased appreciation that very large plasmids—known as megaplasmids—are widespread, diverse, complex, and often encode key traits in the biology of their host microorganisms. Why are megaplasmids so big? What other features come with large plasmid size that could affect bacterial ecology and evolution? Are megaplasmids 'just' big plasmids, or do they have distinct characteristics? In this perspective, we reflect on the distribution, diversity, biology, and gene content of megaplasmids, providing an overview to these large, yet often overlooked, mobile genetic elements. This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.
Collapse
Affiliation(s)
- James P J Hall
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - João Botelho
- Antibiotic Resistance Evolution Group, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian Albrechts University, Kiel, Germany
| | - Adrian Cazares
- EMBL's European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - David A Baltrus
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| |
Collapse
|
31
|
Shen Z, Tang CM, Liu GY. Towards a better understanding of antimicrobial resistance dissemination: what can be learnt from studying model conjugative plasmids? Mil Med Res 2022; 9:3. [PMID: 35012680 PMCID: PMC8744291 DOI: 10.1186/s40779-021-00362-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/26/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteria can evolve rapidly by acquiring new traits such as virulence, metabolic properties, and most importantly, antimicrobial resistance, through horizontal gene transfer (HGT). Multidrug resistance in bacteria, especially in Gram-negative organisms, has become a global public health threat often through the spread of mobile genetic elements. Conjugation represents a major form of HGT and involves the transfer of DNA from a donor bacterium to a recipient by direct contact. Conjugative plasmids, a major vehicle for the dissemination of antimicrobial resistance, are selfish elements capable of mediating their own transmission through conjugation. To spread to and survive in a new bacterial host, conjugative plasmids have evolved mechanisms to circumvent both host defense systems and compete with co-resident plasmids. Such mechanisms have mostly been studied in model plasmids such as the F plasmid, rather than in conjugative plasmids that confer antimicrobial resistance (AMR) in important human pathogens. A better understanding of these mechanisms is crucial for predicting the flow of antimicrobial resistance-conferring conjugative plasmids among bacterial populations and guiding the rational design of strategies to halt the spread of antimicrobial resistance. Here, we review mechanisms employed by conjugative plasmids that promote their transmission and establishment in Gram-negative bacteria, by following the life cycle of conjugative plasmids.
Collapse
Affiliation(s)
- Zhen Shen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.,Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Guang-Yu Liu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.
| |
Collapse
|
32
|
Crespo I, Bernardo N, Cuppari A, Malfois M, Boer DR. Structural and biochemical characterization of the relaxosome auxiliary proteins encoded on the Bacillus subtilis plasmid pLS20. Comput Struct Biotechnol J 2022; 20:757-765. [PMID: 35198129 PMCID: PMC8829557 DOI: 10.1016/j.csbj.2021.12.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 12/22/2021] [Accepted: 12/30/2021] [Indexed: 12/03/2022] Open
Abstract
Bacterial conjugation is an important route for horizontal gene transfer. The initial step in this process involves a macromolecular protein-DNA complex called the relaxosome, which in plasmids consists of the origin of transfer (oriT) and several proteins that prepare the transfer. The relaxosome protein named relaxase introduces a nick in one of the strands of the oriT to initiate the process. Additional relaxosome proteins can exist. Recently, several relaxosome proteins encoded on the Bacillus subtilis plasmid pLS20 were identified, including the relaxase, named RelpLS20, and two auxiliary DNA-binding factors, named Aux1pLS20 and Aux2pLS20. Here, we extend this characterization in order to define their function. We present the low-resolution SAXS envelope of the Aux1pLS20 and the atomic X-ray structure of the C-terminal domain of Aux2pLS20. We also study the interactions between the auxiliary proteins and the full-length RelpLS20, as well as its separate domains. The results show that the quaternary structure of the auxiliary protein Aux1pLS20 involves a tetramer, as previously determined. The crystal structure of the C-terminal domain of Aux2pLS20 shows that it forms a tetramer and suggests that it is an analog of TraMpF of plasmid F. This is the first evidence of the existence of a TraMpF analog in gram positive conjugative systems, although, unlike other TraMpF analogs, Aux2pLS20 does not interact with the relaxase. Aux1pLS20 interacts with the C-terminal domain, but not the N-terminal domain, of the relaxase RelpLS20. Thus, the pLS20 relaxosome exhibits some unique features despite the apparent similarity to some well-studied G- conjugation systems.
Collapse
|
33
|
The Facts and Family Secrets of Plasmids That Replicate via the Rolling-Circle Mechanism. Microbiol Mol Biol Rev 2021; 86:e0022220. [PMID: 34878299 DOI: 10.1128/mmbr.00222-20] [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] [Indexed: 12/11/2022] Open
Abstract
Plasmids are self-replicative DNA elements that are transferred between bacteria. Plasmids encode not only antibiotic resistance genes but also adaptive genes that allow their hosts to colonize new niches. Plasmid transfer is achieved by conjugation (or mobilization), phage-mediated transduction, and natural transformation. Thousands of plasmids use the rolling-circle mechanism for their propagation (RCR plasmids). They are ubiquitous, have a high copy number, exhibit a broad host range, and often can be mobilized among bacterial species. Based upon the replicon, RCR plasmids have been grouped into several families, the best known of them being pC194 and pUB110 (Rep_1 family), pMV158 and pE194 (Rep_2 family), and pT181 and pC221 (Rep_trans family). Genetic traits of RCR plasmids are analyzed concerning (i) replication mediated by a DNA-relaxing initiator protein and its interactions with the cognate DNA origin, (ii) lagging-strand origins of replication, (iii) antibiotic resistance genes, (iv) mobilization functions, (v) replication control, performed by proteins and/or antisense RNAs, and (vi) the participating host-encoded functions. The mobilization functions include a relaxase initiator of transfer (Mob), an origin of transfer, and one or two small auxiliary proteins. There is a family of relaxases, the MOBV family represented by plasmid pMV158, which has been revisited and updated. Family secrets, like a putative open reading frame of unknown function, are reported. We conclude that basic research on RCR plasmids is of importance, and our perspectives contemplate the concept of One Earth because we should incorporate bacteria into our daily life by diminishing their virulence and, at the same time, respecting their genetic diversity.
Collapse
|
34
|
Val-Calvo J, Miguel-Arribas A, Abia D, Wu LJ, Meijer WJJ. pLS20 is the archetype of a new family of conjugative plasmids harboured by Bacillus species. NAR Genom Bioinform 2021; 3:lqab096. [PMID: 34729475 PMCID: PMC8557374 DOI: 10.1093/nargab/lqab096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 09/03/2021] [Accepted: 10/04/2021] [Indexed: 12/12/2022] Open
Abstract
Conjugation plays important roles in genome plasticity, adaptation and evolution but is also the major horizontal gene-transfer route responsible for spreading toxin, virulence and antibiotic resistance genes. A better understanding of the conjugation process is required for developing drugs and strategies to impede the conjugation-mediated spread of these genes. So far, only a limited number of conjugative elements have been studied. For most of them, it is not known whether they represent a group of conjugative elements, nor about their distribution patterns. Here we show that pLS20 from the Gram-positive bacterium Bacillus subtilis is the prototype conjugative plasmid of a family of at least 35 members that can be divided into four clades, and which are harboured by different Bacillus species found in different global locations and environmental niches. Analyses of their phylogenetic relationship and their conjugation operons have expanded our understanding of a family of conjugative plasmids of Gram-positive origin.
Collapse
Affiliation(s)
- Jorge Val-Calvo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049, Madrid, Spain
| | - Andrés Miguel-Arribas
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049, Madrid, Spain
| | - David Abia
- Bioinformatics Facility, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049, Madrid, Spain
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Wilfried J J Meijer
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049, Madrid, Spain
| |
Collapse
|
35
|
Protein Transfer through an F Plasmid-Encoded Type IV Secretion System Suppresses the Mating-Induced SOS Response. mBio 2021; 12:e0162921. [PMID: 34253063 PMCID: PMC8406263 DOI: 10.1128/mbio.01629-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Bacterial type IV secretion systems (T4SSs) mediate the conjugative transfer of mobile genetic elements (MGEs) and their cargoes of antibiotic resistance and virulence genes. Here, we report that the pED208-encoded T4SS (TrapED208) translocates not only this F plasmid but several plasmid-encoded proteins, including ParA, ParB1, single-stranded DNA-binding protein SSB, ParB2, PsiB, and PsiA, to recipient cells. Conjugative protein translocation through the TrapED208 T4SS required engagement of the pED208 relaxosome with the TraD substrate receptor or coupling protein. T4SSs translocate MGEs as single-stranded DNA intermediates (T-strands), which triggers the SOS response in recipient cells. Transfer of pED208 deleted of psiB or ssb, which, respectively, encode the SOS inhibitor protein PsiB and single-stranded DNA-binding protein SSB, elicited a significantly stronger SOS response than pED208 or mutant plasmids deleted of psiA, parA, parB1, or parB2. Conversely, translocation of PsiB or SSB, but not PsiA, through the TrapED208 T4SS suppressed the mating-induced SOS response. Our findings expand the repertoire of known substrates of conjugation systems to include proteins with functions associated with plasmid maintenance. Furthermore, for this and other F-encoded Tra systems, docking of the DNA substrate with the TraD receptor appears to serve as a critical activating signal for protein translocation. Finally, the observed effects of PsiB and SSB on suppression of the mating-induced SOS response establishes a novel biological function for conjugative protein translocation and suggests the potential for interbacterial protein translocation to manifest in diverse outcomes influencing bacterial communication, physiology, and evolution.
Collapse
|
36
|
Fröhlich C, Sørum V, Huber S, Samuelsen Ø, Berglund F, Kristiansson E, Kotsakis SD, Marathe NP, Larsson DGJ, Leiros HKS. Structural and biochemical characterization of the environmental MBLs MYO-1, ECV-1 and SHD-1. J Antimicrob Chemother 2021; 75:2554-2563. [PMID: 32464640 PMCID: PMC7443720 DOI: 10.1093/jac/dkaa175] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/27/2020] [Accepted: 04/06/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND MBLs form a large and heterogeneous group of bacterial enzymes conferring resistance to β-lactam antibiotics, including carbapenems. A large environmental reservoir of MBLs has been identified, which can act as a source for transfer into human pathogens. Therefore, structural investigation of environmental and clinically rare MBLs can give new insights into structure-activity relationships to explore the role of catalytic and second shell residues, which are under selective pressure. OBJECTIVES To investigate the structure and activity of the environmental subclass B1 MBLs MYO-1, SHD-1 and ECV-1. METHODS The respective genes of these MBLs were cloned into vectors and expressed in Escherichia coli. Purified enzymes were characterized with respect to their catalytic efficiency (kcat/Km). The enzymatic activities and MICs were determined for a panel of different β-lactams, including penicillins, cephalosporins and carbapenems. Thermostability was measured and structures were solved using X-ray crystallography (MYO-1 and ECV-1) or generated by homology modelling (SHD-1). RESULTS Expression of the environmental MBLs in E. coli resulted in the characteristic MBL profile, not affecting aztreonam susceptibility and decreasing susceptibility to carbapenems, cephalosporins and penicillins. The purified enzymes showed variable catalytic activity in the order of <5% to ∼70% compared with the clinically widespread NDM-1. The thermostability of ECV-1 and SHD-1 was up to 8°C higher than that of MYO-1 and NDM-1. Using solved structures and molecular modelling, we identified differences in their second shell composition, possibly responsible for their relatively low hydrolytic activity. CONCLUSIONS These results show the importance of environmental species acting as reservoirs for MBL-encoding genes.
Collapse
Affiliation(s)
- Christopher Fröhlich
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway, Tromsø, Norway
| | - Vidar Sørum
- Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway
| | - Sandra Huber
- Department of Laboratory Medicine, University Hospital of North Norway, Tromsø, Norway
| | - Ørjan Samuelsen
- Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway.,Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Fanny Berglund
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
| | - Stathis D Kotsakis
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
| | - Nachiket P Marathe
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden.,Institute of Marine Research, Bergen, Norway
| | - D G Joakim Larsson
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
| | - Hanna-Kirsti S Leiros
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway, Tromsø, Norway
| |
Collapse
|
37
|
Smyshlyaev G, Bateman A, Barabas O. Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes. Mol Syst Biol 2021; 17:e9880. [PMID: 34018328 PMCID: PMC8138268 DOI: 10.15252/msb.20209880] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 04/18/2021] [Accepted: 04/20/2021] [Indexed: 11/16/2022] Open
Abstract
Mobile genetic elements (MGEs) sequester and mobilize antibiotic resistance genes across bacterial genomes. Efficient and reliable identification of such elements is necessary to follow resistance spreading. However, automated tools for MGE identification are missing. Tyrosine recombinase (YR) proteins drive MGE mobilization and could provide markers for MGE detection, but they constitute a diverse family also involved in housekeeping functions. Here, we conducted a comprehensive survey of YRs from bacterial, archaeal, and phage genomes and developed a sequence‐based classification system that dissects the characteristics of MGE‐borne YRs. We revealed that MGE‐related YRs evolved from non‐mobile YRs by acquisition of a regulatory arm‐binding domain that is essential for their mobility function. Based on these results, we further identified numerous unknown MGEs. This work provides a resource for comparative analysis and functional annotation of YRs and aids the development of computational tools for MGE annotation. Additionally, we reveal how YRs adapted to drive gene transfer across species and provide a tool to better characterize antibiotic resistance dissemination.
Collapse
Affiliation(s)
- Georgy Smyshlyaev
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK.,European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany.,Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Orsolya Barabas
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany.,Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| |
Collapse
|
38
|
Incompatibility Group I1 (IncI1) Plasmids: Their Genetics, Biology, and Public Health Relevance. Microbiol Mol Biol Rev 2021; 85:85/2/e00031-20. [PMID: 33910982 DOI: 10.1128/mmbr.00031-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Bacterial plasmids are extrachromosomal genetic elements that often carry antimicrobial resistance (AMR) genes and genes encoding increased virulence and can be transmissible among bacteria by conjugation. One key group of plasmids is the incompatibility group I1 (IncI1) plasmids, which have been isolated from multiple Enterobacteriaceae of food animal origin and clinically ill human patients. The IncI group of plasmids were initially characterized due to their sensitivity to the filamentous bacteriophage If1. Two prototypical IncI1 plasmids, R64 and pColIb-P9, have been extensively studied, and the plasmids consist of unique regions associated with plasmid replication, plasmid stability/maintenance, transfer machinery apparatus, single-stranded DNA transfer, and antimicrobial resistance. IncI1 plasmids are somewhat unique in that they encode two types of sex pili, a thick, rigid pilus necessary for mating and a thin, flexible pilus that helps stabilize bacteria for plasmid transfer in liquid environments. A key public health concern with IncI1 plasmids is their ability to carry antimicrobial resistance genes, including those associated with critically important antimicrobials used to treat severe cases of enteric infections, including the third-generation cephalosporins. Because of the potential importance of these plasmids, this review focuses on the distribution of the plasmids, their phenotypic characteristics associated with antimicrobial resistance and virulence, and their replication, maintenance, and transfer.
Collapse
|
39
|
pCTX-M3-Structure, Function, and Evolution of a Multi-Resistance Conjugative Plasmid of a Broad Recipient Range. Int J Mol Sci 2021; 22:ijms22094606. [PMID: 33925677 PMCID: PMC8125031 DOI: 10.3390/ijms22094606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 11/17/2022] Open
Abstract
pCTX-M3 is the archetypic member of the IncM incompatibility group of conjugative plasmids (recently referred to as IncM2). It is responsible for the worldwide dissemination of numerous antibiotic resistance genes, including those coding for extended-spectrum β-lactamases and conferring resistance to aminoglycosides. The IncM plasmids acquired during evolution diverse mobile genetic elements found in one or two multiple resistance regions, MRR(s), grouping antibiotic resistance genes as well as mobile genetic elements or their remnants. The IncM plasmids can be found in bacteria inhabiting various environments. The information on the structure and biology of pCTX-M3 is integrated in this review. It focuses on the functional modules of pCTX-M3 responsible for its replication, stable maintenance, and conjugative transfer, indicating that the host range of the pCTX-M3 replicon is limited to representatives of the family Enterobacteriaceae (Enterobacterales ord. nov.), while the range of recipients of its conjugation system is wide, comprising Alpha-, Beta-, and Gammaproteobacteria, and also Firmicutes.
Collapse
|
40
|
Computational prediction of secreted proteins in gram-negative bacteria. Comput Struct Biotechnol J 2021; 19:1806-1828. [PMID: 33897982 PMCID: PMC8047123 DOI: 10.1016/j.csbj.2021.03.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/18/2021] [Accepted: 03/18/2021] [Indexed: 12/29/2022] Open
Abstract
Gram-negative bacteria harness multiple protein secretion systems and secrete a large proportion of the proteome. Proteins can be exported to periplasmic space, integrated into membrane, transported into extracellular milieu, or translocated into cytoplasm of contacting cells. It is important for accurate, genome-wide annotation of the secreted proteins and their secretion pathways. In this review, we systematically classified the secreted proteins according to the types of secretion systems in Gram-negative bacteria, summarized the known features of these proteins, and reviewed the algorithms and tools for their prediction.
Collapse
|
41
|
Secrete or perish: The role of secretion systems in Xanthomonas biology. Comput Struct Biotechnol J 2020; 19:279-302. [PMID: 33425257 PMCID: PMC7777525 DOI: 10.1016/j.csbj.2020.12.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/13/2020] [Accepted: 12/13/2020] [Indexed: 12/22/2022] Open
Abstract
Bacteria of the Xanthomonas genus are mainly phytopathogens of a large variety of crops of economic importance worldwide. Xanthomonas spp. rely on an arsenal of protein effectors, toxins and adhesins to adapt to the environment, compete with other microorganisms and colonize plant hosts, often causing disease. These protein effectors are mainly delivered to their targets by the action of bacterial secretion systems, dedicated multiprotein complexes that translocate proteins to the extracellular environment or directly into eukaryotic and prokaryotic cells. Type I to type VI secretion systems have been identified in Xanthomonas genomes. Recent studies have unravelled the diverse roles played by the distinct types of secretion systems in adaptation and virulence in xanthomonads, unveiling new aspects of their biology. In addition, genome sequence information from a wide range of Xanthomonas species and pathovars have become available recently, uncovering a heterogeneous distribution of the distinct families of secretion systems within the genus. In this review, we describe the architecture and mode of action of bacterial type I to type VI secretion systems and the distribution and functions associated with these important nanoweapons within the Xanthomonas genus.
Collapse
|
42
|
Aulestia M, Flores A, Mangas EL, Pérez-Pulido AJ, Santero E, Camacho EM. Isolation and genomic characterization of the ibuprofen-degrading bacterium Sphingomonas strain MPO218. Environ Microbiol 2020; 23:267-280. [PMID: 33169907 DOI: 10.1111/1462-2920.15309] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/06/2020] [Indexed: 11/28/2022]
Abstract
The presence of pharmaceutical compounds in waters and soils is of particular concern because these compounds can be biologically active, even at environmental concentrations. Most pharmaceutical contaminants result from inefficient removal of these compounds during wastewater treatment. Although microorganisms able to biodegrade pharmaceuticals compounds have been described, the isolation and characterization of new bacterial strains capable of degrading drugs remain important to improve the removal of this pollutant. In this work, we describe the Sphingomonas wittichii strain MPO218 as able to use ibuprofen as the sole carbon and energy source. The genome of MPO218 consists of a circular chromosome and two circular plasmids. Our analysis shows that the largest plasmid, named pIBU218, is conjugative and can horizontally transfer the capability of growing on ibuprofen after conjugation with another related bacterium, Sphingopyxis granuli TFA. This plasmid appears to be unstable since it undergoes different deletions in absence of selection when growth on ibuprofen is not selected. This is the first described example of a natural and conjugative plasmid that enables growth on ibuprofen and is another example of how horizontal gene transfer plays a crucial role in the evolution of bacteria.
Collapse
Affiliation(s)
- Magaly Aulestia
- Departamento de Biología Molecular e Ingeniería Bioquímica, Centro Andaluz de Biología del Desarrollo/CSIC/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Amando Flores
- Departamento de Biología Molecular e Ingeniería Bioquímica, Centro Andaluz de Biología del Desarrollo/CSIC/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Eugenio L Mangas
- Departamento de Biología Molecular e Ingeniería Bioquímica, Centro Andaluz de Biología del Desarrollo/CSIC/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Antonio J Pérez-Pulido
- Departamento de Biología Molecular e Ingeniería Bioquímica, Centro Andaluz de Biología del Desarrollo/CSIC/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Eduardo Santero
- Departamento de Biología Molecular e Ingeniería Bioquímica, Centro Andaluz de Biología del Desarrollo/CSIC/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Eva M Camacho
- Departamento de Biología Molecular e Ingeniería Bioquímica, Centro Andaluz de Biología del Desarrollo/CSIC/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| |
Collapse
|
43
|
Veith PD, Gorasia DG, Reynolds EC. Towards defining the outer membrane proteome of Porphyromonas gingivalis. Mol Oral Microbiol 2020; 36:25-36. [PMID: 33124778 DOI: 10.1111/omi.12320] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 01/18/2023]
Abstract
Porphyromonas gingivalis is a Gram-negative anaerobic pathogen found in subgingival plaque associated with progressive periodontitis. Proteins associated with the outer membrane (OM) of Gram-negative pathogens are particularly important for understanding virulence and for developing vaccines. The aim of this study was to establish a reliable list of outer membrane associated proteins (Omps) for this organism. Starting with a list of 99 experimentally determined Omps, several bioinformatics tools were used to predict a further 52 proteins, leading to a predicted OM proteome of 151 proteins. The tools used included databases of protein families, prediction of OM β-barrels and structural homology. The list includes 33 T9SS cargo proteins, 43 lipoproteins and 66 OM β-barrel proteins with some overlap between categories. The proteins are discussed both in these structural categories as well as their various functions in OM biogenesis, nutrient acquisition, protein secretion, adhesion and efflux. Proteins that were previously shown to be part of large complexes are highlighted and cross reference is provided to a previous major study of protein localization in P. gingivalis. Finally, proteins were also scored according to their level of conservation within the Bacteroidales taxon. Low scores were shown to correlate with virulence factors and may be predictive of novel virulence factors.
Collapse
Affiliation(s)
- Paul D Veith
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - Dhana G Gorasia
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - Eric C Reynolds
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| |
Collapse
|
44
|
Zhao R, Yu K, Zhang J, Zhang G, Huang J, Ma L, Deng C, Li X, Li B. Deciphering the mobility and bacterial hosts of antibiotic resistance genes under antibiotic selection pressure by metagenomic assembly and binning approaches. WATER RESEARCH 2020; 186:116318. [PMID: 32871290 DOI: 10.1016/j.watres.2020.116318] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/15/2020] [Accepted: 08/18/2020] [Indexed: 05/21/2023]
Abstract
The presence of antibiotics can exert significant selection pressure on the emergence and spread of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB). However, co-selection effects for ARGs, the mobility of ARGs and the identification of ARG hosts under high antibiotic selection pressures are poorly understood. Here, metagenomic assembly and binning approaches were used to comprehensively decipher the prevalence of ARGs and their potential mobility and hosts in activated sludge reactors treating antibiotic production wastewater. We found the abundance of different ARG types in antibiotic treatments varied greatly and certain antibiotic pressure promoted the co-selection for the non-corresponding types of ARGs. Antibiotic selection pressures significantly increased the abundance and proportions of ARGs mediated by plasmids (57.9%), which were more prevalent than those encoded in chromosomes (19.2%). The results indicated that plasmids and chromosomes had a tendency to carry different types of ARGs. Moreover, higher co-occurrence frequency of ARGs and MGEs revealed that antibiotics enhanced the mobility potential of ARGs mediated by both plasmids and integrative and conjugative elements. Among the 689 metagenome-assembled genomes (MAGs) with high estimated quality, 119 MAGs assigning to nine bacterial phyla were identified as the ARG hosts and 33 MAGs exhibited possible multi-resistance to antibiotics. Some ARG types tended to be carried by certain bacteria (e.g. bacitracin resistance genes carried by the family Burkholderiaceae) and thus showed a pronounced host-specific pattern. This study enhances the understanding of the mobility and hosts of ARGs and provides important insights into the risk assessment and management of antibiotic resistance.
Collapse
Affiliation(s)
- Renxin Zhao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen 518055, China
| | - Jiayu Zhang
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Guijuan Zhang
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Jin Huang
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Liping Ma
- Shanghai Key Laboratory for Urban Ecological Process and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Chunfang Deng
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen 518055, China
| | - Xiaoyan Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Shenzhen Environmental Science and New Energy Laboratory, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen 518055, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.
| |
Collapse
|
45
|
Russo DA, Zedler JAZ. Genomic insights into cyanobacterial protein translocation systems. Biol Chem 2020; 402:39-54. [PMID: 33544489 DOI: 10.1515/hsz-2020-0247] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/25/2020] [Indexed: 02/07/2023]
Abstract
Cyanobacteria are ubiquitous oxygenic photosynthetic bacteria with a versatile metabolism that is highly dependent on effective protein targeting. Protein sorting in diderm bacteria is not trivial and, in cyanobacteria, even less so due to the presence of a complex membrane system: the outer membrane, the plasma membrane and the thylakoid membrane. In cyanobacteria, protein import into the thylakoids is essential for photosynthesis, export to the periplasm fulfills a multifunctional role in maintaining cell homeostasis, and secretion mediates motility, DNA uptake and environmental interactions. Intriguingly, only one set of genes for the general secretory and the twin-arginine translocation pathways seem to be present. However, these systems have to operate in both plasma and thylakoid membranes. This raises the question of how substrates are recognized and targeted to their correct, final destination. Additional complexities arise when a protein has to be secreted across the outer membrane, where very little is known regarding the mechanisms involved. Given their ecological importance and biotechnological interest, a better understanding of protein targeting in cyanobacteria is of great value. This review will provide insights into the known knowns of protein targeting, propose hypotheses based on available genomic sequences and discuss future directions.
Collapse
Affiliation(s)
- David A Russo
- Bioorganic Analytics, Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, D-07743 Jena, Germany
| | - Julie A Z Zedler
- Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Dornburgerstr. 159, D-07743 Jena, Germany
| |
Collapse
|
46
|
Botelho J, Mourão J, Roberts AP, Peixe L. Comprehensive genome data analysis establishes a triple whammy of carbapenemases, ICEs and multiple clinically relevant bacteria. Microb Genom 2020; 6:mgen000424. [PMID: 32841111 PMCID: PMC7660259 DOI: 10.1099/mgen.0.000424] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 08/02/2020] [Indexed: 12/24/2022] Open
Abstract
Carbapenemases inactivate most β-lactam antibiotics, including carbapenems, and have frequently been reported among Enterobacteriaceae, Acinetobacter spp. and Pseudomonas spp. Traditionally, the horizontal gene transfer of carbapenemase-encoding genes (CEGs) has been linked to plasmids. However, given that integrative and conjugative elements (ICEs) are possibly the most abundant conjugative elements among prokaryotes, we conducted an in silico analysis to ascertain the likely role of ICEs in the spread of CEGs among all bacterial genomes (n=182 663). We detected 17 520 CEGs, of which 66 were located within putative ICEs among several bacterial species (including clinically relevant bacteria, such as Pseudomonas aeruginosa, Klebsiella pneumoniae and Escherichia coli). Most CEGs detected within ICEs belong to the IMP, NDM and SPM metallo-beta-lactamase families, and the serine beta-lactamase KPC and GES families. Different mechanisms were likely responsible for acquisition of these genes. The majority of CEG-bearing ICEs belong to the MPFG, MPFT and MPFF classes and often encode resistance to other antibiotics (e.g. aminoglycosides and fluoroquinolones). This study provides a snapshot of the different CEGs associated with ICEs among available bacterial genomes and sheds light on the underappreciated contribution of ICEs to the spread of carbapenem resistance globally.
Collapse
Affiliation(s)
- João Botelho
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Present address: Antibiotic Resistance Evolution Group, Max-Planck-Institute for Evolutionary Biology, 24306 Plön, Germany; Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, 24118 Kiel, Germany
| | - Joana Mourão
- University of Coimbra, Center for Innovative Biomedicine and Biotechnology, Coimbra, Portugal
- University of Coimbra, Center for Neuroscience and Cell Biology, Coimbra, Portugal
- University of Coimbra, Institute for Interdisciplinary Research, Coimbra, Portugal
| | - Adam P. Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| |
Collapse
|
47
|
Kiyokawa K, Ohmine Y, Yunoki K, Yamamoto S, Moriguchi K, Suzuki K. Enhanced Agrobacterium-mediated transformation revealed attenuation of exogenous plasmid DNA installation in recipient bacteria by exonuclease VII and SbcCD. Genes Cells 2020; 25:663-674. [PMID: 32799424 DOI: 10.1111/gtc.12802] [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: 04/15/2020] [Revised: 08/06/2020] [Accepted: 08/06/2020] [Indexed: 11/26/2022]
Abstract
In DNA transfer via type IV secretion system (T4SS), relaxase enzyme releases linear ssDNA in donor cells and recircularizes in recipient cells. Using VirB/D4 T4SS, Agrobacterium cells can transfer an IncQ-type plasmid depending on Mob relaxase and a model T-DNA plasmid depending on VirD2 relaxase. Mobilization to Escherichia coli of the former plasmid is much more efficient than that of the latter, whereas an entirely reverse relationship is observed in transfer to yeast. These data suggest that either plasmid recircularization or conversion of ssDNA to dsDNA in the recipient bacterial cells is a rate-limiting step of the transfer. In this study, we examined involvement of exonuclease genes in the plasmid acceptability. By the VirD2-dependent T-DNA plasmid, E. coli sbcDΔ and sbcCΔ mutant strains produced threefold more exconjugants, and a sbcDΔ xseAΔ mutant strain yielded eightfold more exconjugants than their wild-type strain. In contrast to the enhancing effect on the VirD2-mediated transfer, the mutations exhibited a subtle effect on the Mob-mediated transfer. These results support our working hypothesis that VirD2 can transport its substrate ssDNA efficiently to recipient cells and that recipient nucleases degrade the ssDNA because VirD2 has some defect(s) in the circularization and completion of complementary DNA synthesis.
Collapse
Affiliation(s)
- Kazuya Kiyokawa
- Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan.,Department of Biological Science, Graduate School of Science, Hiroshima University, Hiroshima, Japan
| | - Yuta Ohmine
- Department of Biological Science, Graduate School of Science, Hiroshima University, Hiroshima, Japan
| | - Kazuya Yunoki
- Department of Biological Science, Graduate School of Science, Hiroshima University, Hiroshima, Japan
| | - Shinji Yamamoto
- Department of Biological Science, Graduate School of Science, Hiroshima University, Hiroshima, Japan
| | - Kazuki Moriguchi
- Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan.,Department of Biological Science, Graduate School of Science, Hiroshima University, Hiroshima, Japan
| | - Katsunori Suzuki
- Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan.,Department of Biological Science, Graduate School of Science, Hiroshima University, Hiroshima, Japan
| |
Collapse
|
48
|
Lao J, Guédon G, Lacroix T, Charron-Bourgoin F, Libante V, Loux V, Chiapello H, Payot S, Leblond-Bourget N. Abundance, Diversity and Role of ICEs and IMEs in the Adaptation of Streptococcus salivarius to the Environment. Genes (Basel) 2020; 11:genes11090999. [PMID: 32858915 PMCID: PMC7563491 DOI: 10.3390/genes11090999] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 01/15/2023] Open
Abstract
Streptococcus salivarius is a significant contributor to the human oral, pharyngeal and gut microbiomes that contribute to the maintenance of health. The high genomic diversity observed in this species is mainly caused by horizontal gene transfer. This work aimed to evaluate the contribution of integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs) in S. salivarius genome diversity. For this purpose, we performed an in-depth analysis of 75 genomes of S. salivarius and searched for signature genes of conjugative and mobilizable elements. This analysis led to the retrieval of 69 ICEs, 165 IMEs and many decayed elements showing their high prevalence in S. salivarius genomes. The identification of almost all ICE and IME boundaries allowed the identification of the genes in which these elements are inserted. Furthermore, the exhaustive analysis of the adaptation genes carried by these elements showed that they encode numerous functions such as resistance to stress, to antibiotics or to toxic compounds, and numerous enzymes involved in diverse cellular metabolic pathways. These data support the idea that not only ICEs but also IMEs and decayed elements play an important role in S. salivarius adaptation to the environment.
Collapse
Affiliation(s)
- Julie Lao
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (J.L.); (G.G.); (F.C.-B.); (V.L.); (S.P.)
- Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France; (T.L.); (V.L.); (H.C.)
| | - Gérard Guédon
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (J.L.); (G.G.); (F.C.-B.); (V.L.); (S.P.)
| | - Thomas Lacroix
- Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France; (T.L.); (V.L.); (H.C.)
| | - Florence Charron-Bourgoin
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (J.L.); (G.G.); (F.C.-B.); (V.L.); (S.P.)
| | - Virginie Libante
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (J.L.); (G.G.); (F.C.-B.); (V.L.); (S.P.)
| | - Valentin Loux
- Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France; (T.L.); (V.L.); (H.C.)
| | - Hélène Chiapello
- Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France; (T.L.); (V.L.); (H.C.)
| | - Sophie Payot
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (J.L.); (G.G.); (F.C.-B.); (V.L.); (S.P.)
| | - Nathalie Leblond-Bourget
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (J.L.); (G.G.); (F.C.-B.); (V.L.); (S.P.)
- Correspondence: ; Tel.: +33-3-72-74-51-46
| |
Collapse
|
49
|
Libante V, Sarica N, Mohamad Ali A, Gapp C, Oussalah A, Guédon G, Leblond-Bourget N, Payot S. Mobilization of IMEs Integrated in the oriT of ICEs Involves Their Own Relaxase Belonging to the Rep-Trans Family of Proteins. Genes (Basel) 2020; 11:genes11091004. [PMID: 32859088 PMCID: PMC7563843 DOI: 10.3390/genes11091004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 08/24/2020] [Accepted: 08/24/2020] [Indexed: 01/27/2023] Open
Abstract
Integrative mobilizable elements (IMEs) are widespread but very poorly studied integrated elements that can excise and hijack the transfer apparatus of co-resident conjugative elements to promote their own spreading. Sixty-four putative IMEs, harboring closely related mobilization and recombination modules, were found in 14 Streptococcus species and in Staphylococcus aureus. Fifty-three are integrated into the origin of transfer (oriT) of a host integrative conjugative element (ICE), encoding a MobT relaxase and belonging to three distant families: ICESt3, Tn916, and ICE6013. The others are integrated into an unrelated IME or in chromosomal sites. After labeling by an antibiotic resistance gene, the conjugative transfer of one of these IMEs (named IME_oriTs) and its host ICE was measured. Although the IME is integrated in an ICE, it does not transfer as a part of the host ICE (no cis-mobilization). The IME excises and transfers separately from the ICE (without impacting its transfer rate) using its own relaxase, distantly related to all known MobT relaxases, and integrates in the oriT of the ICE after transfer. Overall, IME_oriTs use MobT-encoding ICEs both as hosts and as helpers for conjugative transfer. As half of them carry lsa(C), they actively participate in the dissemination of lincosamide–streptogramin A–pleuromutilin resistance among Firmicutes.
Collapse
|
50
|
Tekedar HC, Blom J, Kalindamar S, Nho S, Karsi A, Lawrence ML. Comparative genomics of the fish pathogens Edwardsiella ictaluri 93-146 and Edwardsiella piscicida C07-087. Microb Genom 2020; 6. [PMID: 32108566 PMCID: PMC7067208 DOI: 10.1099/mgen.0.000322] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Edwardsiella ictaluri and Edwardsiella piscicida are important fish pathogens affecting cultured and wild fish worldwide. To investigate the genome-level differences and similarities between catfish-adapted strains in these two species, the complete E. ictaluri 93-146 and E. piscicida C07-087 genomes were evaluated by applying comparative genomics analysis. All available complete (10) and non-complete (19) genomes from five Edwardsiella species were also included in a systematic analysis. Average nucleotide identity and core-genome phylogenetic tree analyses indicated that the five Edwardsiella species were separated from each other. Pan-/core-genome analyses for the 29 strains from the five species showed that genus Edwardsiella members have 9474 genes in their pan genome, while the core genome consists of 1421 genes. Orthology cluster analysis showed that E. ictaluri and E. piscicida genomes have the greatest number of shared clusters. However, E. ictaluri and E. piscicida also have unique features; for example, the E. ictaluri genome encodes urease enzymes and cytochrome o ubiquinol oxidase subunits, whereas E. piscicida genomes encode tetrathionate reductase operons, capsular polysaccharide synthesis enzymes and vibrioferrin-related genes. Additionally, we report for what is believed to be the first time that E. ictaluri 93-146 and three other E. ictaluri genomes encode a type IV secretion system (T4SS), whereas none of the E. piscicida genomes encode this system. Additionally, the E. piscicida C07-087 genome encodes two different type VI secretion systems. E. ictaluri genomes tend to encode more insertion elements, phage regions and genomic islands than E. piscicida. We speculate that the T4SS could contribute to the increased number of mobilome elements in E. ictaluri compared to E. piscicida. Two of the E. piscicida genomes encode full CRISPR-Cas regions, whereas none of the E. ictaluri genomes encode Cas proteins. Overall, comparison of the E. ictaluri and E. piscicida genomes reveals unique features and provides new insights on pathogenicity that may reflect the host adaptation of the two species.
Collapse
Affiliation(s)
- Hasan C Tekedar
- College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, 35392 Giessen, Hesse, Germany
| | - Safak Kalindamar
- College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Seongwon Nho
- Division of Microbiology, National Center for Toxicological Research/FDA, Jefferson, AR, USA
| | - Attila Karsi
- College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Mark L Lawrence
- College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| |
Collapse
|