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Wang S, Zhan Y, Jiang X, Lai Y. Engineering Microbial Consortia as Living Materials: Advances and Prospectives. ACS Synth Biol 2024. [PMID: 39174016 DOI: 10.1021/acssynbio.4c00313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
The field of Engineered Living Materials (ELMs) integrates engineered living organisms into natural biomaterials to achieve diverse objectives. Multiorganism consortia, prevalent in both naturally occurring and synthetic microbial cultures, exhibit complex functionalities and interrelationships, extending the scope of what can be achieved with individual engineered bacterial strains. However, the ELMs comprising microbial consortia are still in the developmental stage. In this Review, we introduce two strategies for designing ELMs constituted of microbial consortia: a top-down strategy, which involves characterizing microbial interactions and mimicking and reconstructing natural ecosystems, and a bottom-up strategy, which entails the rational design of synthetic consortia and their assembly with material substrates to achieve user-defined functions. Next, we summarize technologies from synthetic biology that facilitate the efficient engineering of microbial consortia for performing tasks more complex than those that can be done with single bacterial strains. Finally, we discuss essential challenges and future perspectives for microbial consortia-based ELMs.
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Affiliation(s)
- Shuchen Wang
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Yuewei Zhan
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Xue Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong SAR, China
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yong Lai
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
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2
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McDonald JB, Wade B, Andrews DM, Van TTH, Moore RJ. Development of tools for the genetic manipulation of Campylobacter and their application to the N-glycosylation system of Campylobacter hepaticus, an emerging pathogen of poultry. mBio 2024:e0110124. [PMID: 39072641 DOI: 10.1128/mbio.01101-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 06/19/2024] [Indexed: 07/30/2024] Open
Abstract
Various species of campylobacters cause significant disease problems in both humans and animals. The continuing development of tools and methods for genetic and molecular manipulation of campylobacters enables the detailed study of bacterial virulence and disease pathogenesis. Campylobacter hepaticus is an emerging pathogen that causes spotty liver disease (SLD) in poultry. SLD has a significant economic and animal welfare impact as the disease results in elevated mortalities and significant decreases in egg production. Although potential virulence genes of C. hepaticus have been identified, they have not been further studied and characterized, as appropriate genetic tools and methods to transform and perform mutagenesis studies in C. hepaticus have not been available. In this study, the genetic manipulation of C. hepaticus is reported, with the development of novel plasmid vectors, methods for transformation, site-specific mutagenesis, and mutant complementation. These tools were used to delete the pglB gene, an oligosaccharyltransferase, a central enzyme of the N-glycosylation pathway, by allelic exchange. In the mutant strain, N-glycosylation was completely abolished. The tools and methods developed in this study represent innovative approaches that can be applied to further explore important virulence factors of C. hepaticus and other closely related Campylobacter species. IMPORTANCE Spotty liver disease (SLD) of layer chickens, caused by infection with Campylobacter hepaticus, is a significant economic and animal welfare burden on an important food production industry. Currently, SLD is controlled using antibiotics; however, alternative intervention methods are needed due to increased concerns associated with environmental contamination with antibiotics, and the development of antimicrobial resistance in many bacterial pathogens of humans and animals. This study has developed methods that have enabled the genetic manipulation of C. hepaticus. To validate the methods, the pglB gene was inactivated by allelic exchange to produce a C. hepaticus strain that could no longer N-glycosylate proteins. Subsequently, the mutation was complemented by reintroduction of the gene in trans, on a plasmid vector, to demonstrate that the phenotypic changes noted were caused by the mutation of the targeted gene. The tools developed enable ongoing studies to understand other virulence mechanisms of this important emerging pathogen.
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Affiliation(s)
- Jamieson B McDonald
- School of Science, RMIT University, Bundoora West Campus, Bundoora, Victoria, Australia
| | - Ben Wade
- School of Science, RMIT University, Bundoora West Campus, Bundoora, Victoria, Australia
| | - Daniel M Andrews
- Bioproperties Pty Ltd, RMIT University, Bundoora West Campus, Bundoora, Victoria, Australia
| | - Thi Thu Hao Van
- School of Science, RMIT University, Bundoora West Campus, Bundoora, Victoria, Australia
| | - Robert J Moore
- School of Science, RMIT University, Bundoora West Campus, Bundoora, Victoria, Australia
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Christi K, Hudson J, Egan S. Current approaches to genetic modification of marine bacteria and considerations for improved transformation efficiency. Microbiol Res 2024; 284:127729. [PMID: 38663232 DOI: 10.1016/j.micres.2024.127729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/25/2024] [Accepted: 04/15/2024] [Indexed: 05/26/2024]
Abstract
Marine bacteria play vital roles in symbiosis, biogeochemical cycles and produce novel bioactive compounds and enzymes of interest for the pharmaceutical, biofuel and biotechnology industries. At present, investigations into marine bacterial functions and their products are primarily based on phenotypic observations, -omic type approaches and heterologous gene expression. To advance our understanding of marine bacteria and harness their full potential for industry application, it is critical that we have the appropriate tools and resources to genetically manipulate them in situ. However, current genetic tools that are largely designed for model organisms such as E. coli, produce low transformation efficiencies or have no transfer ability in marine bacteria. To improve genetic manipulation applications for marine bacteria, we need to improve transformation methods such as conjugation and electroporation in addition to identifying more marine broad host range plasmids. In this review, we aim to outline the reported methods of transformation for marine bacteria and discuss the considerations for each approach in the context of improving efficiency. In addition, we further discuss marine plasmids and future research areas including CRISPR tools and their potential applications for marine bacteria.
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Affiliation(s)
- Katrina Christi
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, Australia
| | - Jennifer Hudson
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, Australia
| | - Suhelen Egan
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, Australia.
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Bello-López E, Pérez-Oseguera Á, Santos W, Cevallos MÁ. A novel replication initiation region encoded in a widespread Acinetobacter plasmid lineage carrying a blaNDM-1 gene. PLoS One 2024; 19:e0303976. [PMID: 38820537 PMCID: PMC11142715 DOI: 10.1371/journal.pone.0303976] [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: 03/04/2024] [Accepted: 05/05/2024] [Indexed: 06/02/2024] Open
Abstract
The blaNDM-1 gene and its variants encode metallo-beta-lactamases that confer resistance to almost all beta-lactam antibiotics. Genes encoding blaNDM-1 and its variants can be found in several Acinetobacter species, and they are usually linked to two different plasmid clades. The plasmids in one of these clades contain a gene encoding a Rep protein of the Rep_3 superfamily. The other clade consists of medium-sized plasmids in which the gene (s) involved in plasmid replication initiation (rep)have not yet been identified. In the present study, we identified the minimal replication region of a blaNDM-1-carrying plasmid of Acinetobacter haemolyticus AN54 (pAhaeAN54e), a member of this second clade. This region of 834 paired bases encodes three small peptides, all of which have roles in plasmid maintenance. The plasmids containing this minimal replication region are closely related; almost all contain blaNDM genes, and they are found in multiple Acinetobacter species, including A. baumannii. None of these plasmids contain an annotated Rep gene, suggesting that their replication relies on the minimal replication region that they share with the plasmid pAhaeAN54e. These observations suggest that this plasmid lineage plays a crucial role in the dissemination of the blaNDM-1 gene and its variants.
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Affiliation(s)
- Elena Bello-López
- Centro de Ciencias Genómicas, Programa de Genómica Evolutiva, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Ángeles Pérez-Oseguera
- Centro de Ciencias Genómicas, Programa de Genómica Evolutiva, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Walter Santos
- Departamento de Microbiología, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Miguel Ángel Cevallos
- Centro de Ciencias Genómicas, Programa de Genómica Evolutiva, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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5
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Branda F, Scarpa F. Implications of Artificial Intelligence in Addressing Antimicrobial Resistance: Innovations, Global Challenges, and Healthcare's Future. Antibiotics (Basel) 2024; 13:502. [PMID: 38927169 PMCID: PMC11200959 DOI: 10.3390/antibiotics13060502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/25/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Antibiotic resistance poses a significant threat to global public health due to complex interactions between bacterial genetic factors and external influences such as antibiotic misuse. Artificial intelligence (AI) offers innovative strategies to address this crisis. For example, AI can analyze genomic data to detect resistance markers early on, enabling early interventions. In addition, AI-powered decision support systems can optimize antibiotic use by recommending the most effective treatments based on patient data and local resistance patterns. AI can accelerate drug discovery by predicting the efficacy of new compounds and identifying potential antibacterial agents. Although progress has been made, challenges persist, including data quality, model interpretability, and real-world implementation. A multidisciplinary approach that integrates AI with other emerging technologies, such as synthetic biology and nanomedicine, could pave the way for effective prevention and mitigation of antimicrobial resistance, preserving the efficacy of antibiotics for future generations.
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Affiliation(s)
- Francesco Branda
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, 00128 Rome, Italy
| | - Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
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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.
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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
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7
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Cao X, Tang L, Song J. Circular Single-Stranded DNA: Discovery, Biological Effects, and Applications. ACS Synth Biol 2024; 13:1038-1058. [PMID: 38501391 DOI: 10.1021/acssynbio.4c00040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The field of nucleic acid therapeutics has witnessed a significant surge in recent times, as evidenced by the increasing number of approved genetic drugs. However, current platform technologies containing plasmids, lipid nanoparticle-mRNAs, and adeno-associated virus vectors encounter various limitations and challenges. Thus, we are devoted to finding a novel nucleic acid vector and have directed our efforts toward investigating circular single-stranded DNA (CssDNA), an ancient form of nucleic acid. CssDNAs are ubiquitous, but generally ignored. Accumulating evidence suggests that CssDNAs possess exceptional properties as nucleic acid vectors, exhibiting great potential for clinical applications in genetic disorders, gene editing, and immune cell therapy. Here, we comprehensively review the discovery and biological effects of CssDNAs as well as their applications in the field of biomedical research for the first time. Undoubtedly, as an ancient form of DNA, CssDNA holds immense potential and promises novel insights for biomedical research.
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Affiliation(s)
- Xisen Cao
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Linlin Tang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, China
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, China
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8
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Zorea A, Pellow D, Levin L, Pilosof S, Friedman J, Shamir R, Mizrahi I. Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases. Nat Commun 2024; 15:3147. [PMID: 38605009 PMCID: PMC11009399 DOI: 10.1038/s41467-024-47272-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 03/25/2024] [Indexed: 04/13/2024] Open
Abstract
Plasmids are pivotal in driving bacterial evolution through horizontal gene transfer. Here, we investigated 3467 human gut microbiome samples across continents and disease states, analyzing 11,086 plasmids. Our analyses reveal that plasmid dispersal is predominantly stochastic, indicating neutral processes as the primary driver of their wide distribution. We find that only 20-25% of plasmid DNA is being selected in various disease states, constraining its distribution across hosts. Selective pressures shape specific plasmid segments with distinct ecological functions, influenced by plasmid mobilization lifestyle, antibiotic usage, and inflammatory gut diseases. Notably, these elements are more commonly shared within groups of individuals with similar health conditions, such as Inflammatory Bowel Disease (IBD), regardless of geographic location across continents. These segments contain essential genes such as iron transport mechanisms- a distinctive gut signature of IBD that impacts the severity of inflammation. Our findings shed light on mechanisms driving plasmid dispersal and selection in the human gut, highlighting their role as carriers of vital gene pools impacting bacterial hosts and ecosystem dynamics.
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Affiliation(s)
- Alvah Zorea
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel
| | - David Pellow
- Blavatnik School of Computer Science, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Liron Levin
- Bioinformatics Core Facility, llse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel
| | - Shai Pilosof
- Department of Life Sciences, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel
| | - Jonathan Friedman
- Institute of Environmental Sciences, Hebrew University, Rehovot, Israel
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Itzhak Mizrahi
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel.
- Department of Life Sciences, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel.
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel.
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9
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Gupta S, Pal D. Detection of intrinsic transcription termination sites in bacteria: consensus from hairpin detection approaches. J Biomol Struct Dyn 2024:1-11. [PMID: 38605579 DOI: 10.1080/07391102.2024.2325107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 02/23/2024] [Indexed: 04/13/2024]
Abstract
We compare the WebGeSTer and INtrinsic transcription TERmination hairPIN (INTERPIN) databases used for intrinsic transcription termination (ITT) site prediction in bacteria. The former deploys inverted nucleotide repeat detection for identification of RNA hairpin, while the latter a pair-potential function - the hairpin energy score evaluation being identical for both. We find INTERPIN more sensitive than WebGeSTer with about 6% and 51% additional predictions for ITTs in chromosomal and plasmid operons, respectively. INTERPIN hairpins are relatively shorter in length with ungapped stem, and even located in AT-rich segments, compared to GC-rich longer hairpins with a gapped stem in WebGeSTer. The GC%, length, and energy score from INTERPIN transcription units (TUs) are best inter-correlated while the lowest energy single hairpins from WebGeSTer, considered suitable for ITT, being the worst. Around 72% TUs from the two databases overlap, and ∼60% of all alternate ITT sites downstream of TUs overlap, of which 65% are cluster hairpins. This helps highlight hairpin features that can be used to identify termination sites in bacteria across different prediction methods. Overall, the pair-potential-function-based hairpins screened appear to be more consistent with the kinetic and thermodynamics processes of ITT known to date.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Swati Gupta
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, India
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, India
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Yi L, Yu K, Gao G, Zhang R, Lv L, Yu D, Yang J, Liu JH. Successful spread of mcr-1-bearing IncX4 plasmids is associated with variant in replication protein of IncX4 plasmids. J Glob Antimicrob Resist 2024; 36:365-370. [PMID: 38280721 DOI: 10.1016/j.jgar.2024.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/21/2023] [Accepted: 01/05/2024] [Indexed: 01/29/2024] Open
Abstract
IncX4 plasmids are one of the most epidemiologically successful vehicles for mcr-1 spread. Here we found that the IncX4 plasmids carried two different replication proteins encoded by genes pir-1 and pir-2, respectively, but mcr-1 was only carried by IncX4 plasmid encoding pir-1. The copy number of pir-2 encoding plasmids (3.15 ± 0.9 copies) are higher than that of pir-1 encoding plasmids (0.85 ± 0.5 copies). When mcr-1 was cloned into IncX4 plasmid encoding pir-2, the higher copy number of these plasmids resulted in increased expression of mcr-1 and a greater fitness burden on their host cells. However, these plasmids exhibited a lower rate of invasion into the bacterial population compared with mcr-1-positive plasmids encoding the pir-1 gene. These findings collectively explain the absence of mcr-1 in all IncX4 plasmids encoding pir-2. Our results further confirmed that low-copy numbers are important for the spread of mcr-1 plasmid from the perspective of natural evolution.
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Affiliation(s)
- Lingxian Yi
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kaiyang Yu
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Guangzhou, China
| | - Guolong Gao
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Guangzhou, China
| | - Rongmin Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Guangzhou, China
| | - Luchao Lv
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Guangzhou, China
| | - Daojin Yu
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jun Yang
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Guangzhou, China
| | - Jian-Hua Liu
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Guangzhou, China.
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11
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Yu MK, Fogarty EC, Eren AM. Diverse plasmid systems and their ecology across human gut metagenomes revealed by PlasX and MobMess. Nat Microbiol 2024; 9:830-847. [PMID: 38443576 PMCID: PMC10914615 DOI: 10.1038/s41564-024-01610-3] [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: 07/21/2022] [Accepted: 01/17/2024] [Indexed: 03/07/2024]
Abstract
Plasmids alter microbial evolution and lifestyles by mobilizing genes that often confer fitness in changing environments across clades. Yet our ecological and evolutionary understanding of naturally occurring plasmids is far from complete. Here we developed a machine-learning model, PlasX, which identified 68,350 non-redundant plasmids across human gut metagenomes and organized them into 1,169 evolutionarily cohesive 'plasmid systems' using our sequence containment-aware network-partitioning algorithm, MobMess. Individual plasmids were often country specific, yet most plasmid systems spanned across geographically distinct human populations. Cargo genes in plasmid systems included well-known determinants of fitness, such as antibiotic resistance, but also many others including enzymes involved in the biosynthesis of essential nutrients and modification of transfer RNAs, revealing a wide repertoire of likely fitness determinants in complex environments. Our study introduces computational tools to recognize and organize plasmids, and uncovers the ecological and evolutionary patterns of diverse plasmids in naturally occurring habitats through plasmid systems.
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Affiliation(s)
- Michael K Yu
- Toyota Technological Institute at Chicago, Chicago, IL, USA.
| | - Emily C Fogarty
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Committee On Microbiology, University of Chicago, Chicago, IL, USA
| | - A Murat Eren
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA.
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany.
- Marine 'Omics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.
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12
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Fogarty EC, Schechter MS, Lolans K, Sheahan ML, Veseli I, Moore RM, Kiefl E, Moody T, Rice PA, Yu MK, Mimee M, Chang EB, Ruscheweyh HJ, Sunagawa S, Mclellan SL, Willis AD, Comstock LE, Eren AM. A cryptic plasmid is among the most numerous genetic elements in the human gut. Cell 2024; 187:1206-1222.e16. [PMID: 38428395 DOI: 10.1016/j.cell.2024.01.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 10/03/2023] [Accepted: 01/25/2024] [Indexed: 03/03/2024]
Abstract
Plasmids are extrachromosomal genetic elements that often encode fitness-enhancing features. However, many bacteria carry "cryptic" plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes and is 14 times as numerous as crAssphage, currently established as the most abundant extrachromosomal genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one's mother. pBI143 can transfer between Bacteroidales, and although it does not appear to impact bacterial host fitness in vivo, it can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an alternative approach to track human colonic inflammatory states.
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Affiliation(s)
- Emily C Fogarty
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Department of Medicine, University of Chicago, Chicago, IL 60637, USA.
| | - Matthew S Schechter
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Karen Lolans
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Madeline L Sheahan
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Department of Microbiology, University of Chicago, Chicago, IL 60637, USA
| | - Iva Veseli
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Ryan M Moore
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Evan Kiefl
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Thomas Moody
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Phoebe A Rice
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Department of Biochemistry, University of Chicago, Chicago, IL 60637, USA
| | - Michael K Yu
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA
| | - Mark Mimee
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Department of Microbiology, University of Chicago, Chicago, IL 60637, USA; Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
| | - Eugene B Chang
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich 8093, Switzerland
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich 8093, Switzerland
| | - Sandra L Mclellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53204, USA
| | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Laurie E Comstock
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Department of Microbiology, University of Chicago, Chicago, IL 60637, USA.
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Marine Biological Laboratory, Woods Hole, MA 02543, USA; Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany; Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129 Oldenburg, Germany; Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany; Helmholtz Institute for Functional Marine Biodiversity, 26129 Oldenburg, Germany.
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13
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Huang J, Liu J, Dong H, Shi J, You X, Zhang Y. Engineering of a Substrate Affinity Reduced S-Adenosyl-methionine Synthetase as a Novel Biosensor for Growth-Coupling Selection of L-Methionine Overproducers. Appl Biochem Biotechnol 2023:10.1007/s12010-023-04807-0. [PMID: 38150159 DOI: 10.1007/s12010-023-04807-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2023] [Indexed: 12/28/2023]
Abstract
Biosensors are powerful tools for monitoring specific metabolites or controlling metabolic flux towards the products in a single cell, which play important roles in microbial cell factory construction. Despite their potential role in metabolic flux monitoring, the development of biosensors for small molecules is still limited. Reported biosensors often exhibit bottlenecks of poor specificity and a narrow dynamic range. Moreover, fine-tuning the substrate binding affinity of a crucial enzyme can decrease its catalytic activity, which ultimately results in the repression of the corresponding essential metabolite biosynthesis and impairs cell growth. However, increasing intracellular substrate concentration can elevate the availability of the essential metabolite and may lead to restore cellular growth. Herein, a new strategy was proposed for constructing whole-cell biosensors based on enzyme encoded by essential gene that offer inherent specificity and universality. Specifically, S-adenosyl-methionine synthetase (MetK) in E. coli was chosen as the crucial enzyme, and a series of MetK variants were identified that were sensitive to L-methionine concentration. This occurrence enabled the engineered cell to sense L-methionine and exhibit L-methionine dose-dependent cell growth. To improve the biosensor's dynamic range, an S-adenosyl-methionine catabolic enzyme was overexpressed to reduce the intracellular availability of S-adenosyl-methionine. The resulting whole-cell biosensor effectively coupled the intracellular concentration of L-methionine with growth and was successfully applied to select strains with enhanced L-methionine biosynthesis from random mutagenesis libraries. Overall, our study presents a universal strategy for designing and constructing growth-coupled biosensors based on crucial enzyme, which can be applied to select strains overproducing high value-added metabolites in cellular metabolism.
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Affiliation(s)
- Jianfeng Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, People's Republic of China
| | - Jinhui Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
- Henan Engineering Research Center of Food Microbiology, College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, People's Republic of China
| | - Huaming Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, People's Republic of China
| | - Jingjing Shi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, People's Republic of China
| | - Xiaoyan You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.
- Henan Engineering Research Center of Food Microbiology, College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, People's Republic of China.
| | - Yanfei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, People's Republic of China.
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14
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Eddins AJ, Bednar RM, Jana S, Pung AH, Mbengi L, Meyer K, Perona JJ, Cooley RB, Karplus PA, Mehl RA. Truncation-Free Genetic Code Expansion with Tetrazine Amino Acids for Quantitative Protein Ligations. Bioconjug Chem 2023; 34:2243-2254. [PMID: 38047550 DOI: 10.1021/acs.bioconjchem.3c00380] [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] [Indexed: 12/05/2023]
Abstract
Quantitative labeling of biomolecules is necessary to advance areas of antibody-drug conjugation, super-resolution microscopy imaging of molecules in live cells, and determination of the stoichiometry of protein complexes. Bio-orthogonal labeling to genetically encodable noncanonical amino acids (ncAAs) offers an elegant solution; however, their suboptimal reactivity and stability hinder the utility of this method. Previously, we showed that encoding stable 1,2,4,5-tetrazine (Tet)-containing ncAAs enables rapid, complete conjugation, yet some expression conditions greatly limited the quantitative reactivity of the Tet-protein. Here, we demonstrate that reduction of on-protein Tet ncAAs impacts their reactivity, while the leading cause of the unreactive protein is near-cognate suppression (NCS) of UAG codons by endogenous aminoacylated tRNAs. To overcome incomplete conjugation due to NCS, we developed a more catalytically efficient tRNA synthetase and developed a series of new machinery plasmids harboring the aminoacyl tRNA synthetase/tRNA pair (aaRS/tRNA pair). These plasmids enable robust production of homogeneously reactive Tet-protein in truncation-free cell lines, eliminating the contamination caused by NCS and protein truncation. Furthermore, these plasmid systems utilize orthogonal synthetic origins, which render these machinery vectors compatible with any common expression system. Through developing these new machinery plasmids, we established that the aaRS/tRNA pair plasmid copy-number greatly affects the yields and quality of the protein produced. We then produced quantitatively reactive soluble Tet-Fabs, demonstrating the utility of this system for rapid, homogeneous conjugations of biomedically relevant proteins.
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Affiliation(s)
- Alex J Eddins
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- GCE4All Biomedical Technology Development and Dissemination Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Riley M Bednar
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- GCE4All Biomedical Technology Development and Dissemination Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Subhashis Jana
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- GCE4All Biomedical Technology Development and Dissemination Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Abigail H Pung
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- GCE4All Biomedical Technology Development and Dissemination Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Lea Mbengi
- Department of Chemistry, Portland State University, Portland, Oregon 97207, United States
| | - Kyle Meyer
- Department of Chemistry, Portland State University, Portland, Oregon 97207, United States
| | - John J Perona
- Department of Chemistry, Portland State University, Portland, Oregon 97207, United States
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- GCE4All Biomedical Technology Development and Dissemination Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- GCE4All Biomedical Technology Development and Dissemination Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- GCE4All Biomedical Technology Development and Dissemination Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
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15
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Tarasova E, Khayat R. Dynamics and Conformations of a Full-Length CRESS-DNA Replicase. Viruses 2023; 15:2393. [PMID: 38140634 PMCID: PMC10747457 DOI: 10.3390/v15122393] [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: 10/28/2023] [Revised: 12/03/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses encode for a Replicase (Rep) that is essential for viral replication. Rep is a helicase with three domains: an endonuclease, an oligomeric, and an ATPase domain (ED, OD, and AD). Our recent cryo-EM structure of the porcine circovirus 2 (PCV2) Rep provided the first structure of a CRESS-DNA Rep. The structure visualized the ED to be highly mobile, Rep to form a homo-hexamer, bound ssDNA and nucleotides, and the AD to adopt a staircase arrangement around the ssDNA. We proposed a hand-over-hand mechanism by the ADs for ssDNA translocation. The hand-over-hand mechanism requires extensive movement of the AD. Here, we scrutinize this mechanism using all-atom Molecular Dynamics (MD) simulation of Rep in three states: (1) Rep bound to ssDNA and ADP, (2) Rep bound to ssDNA, and (3) Rep by itself. Each of the 700 nsec simulations converges within 200 nsec and provides important insight into the dynamics of Rep, the dynamics of Rep in the presence of these biomolecules, and the importance of ssDNA and ADP in driving the AD to adopt the staircase arrangement around the ssDNA. To the best of our knowledge, this is the first example of an all-atom MD simulation of a CRESS-DNA Rep. This study sets the basis of further MD studies aimed at obtaining a chemical understanding of how Rep uses nucleotide binding and hydrolysis to translocate ssDNA.
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Affiliation(s)
- Elvira Tarasova
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA
| | - Reza Khayat
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA
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16
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Tian R, Zhao R, Guo H, Yan K, Wang C, Lu C, Lv X, Li J, Liu L, Du G, Chen J, Liu Y. Engineered bacterial orthogonal DNA replication system for continuous evolution. Nat Chem Biol 2023; 19:1504-1512. [PMID: 37443393 DOI: 10.1038/s41589-023-01387-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 06/16/2023] [Indexed: 07/15/2023]
Abstract
Continuous evolution can generate biomolecules for synthetic biology and enable evolutionary investigation. The orthogonal DNA replication system (OrthoRep) in yeast can efficiently mutate long DNA fragments in an easy-to-operate manner. However, such a system is lacking in bacteria. Therefore, we developed a bacterial orthogonal DNA replication system (BacORep) for continuous evolution. We achieved this by harnessing the temperate phage GIL16 DNA replication machinery in Bacillus thuringiensis with an engineered error-prone orthogonal DNA polymerase. BacORep introduces all 12 types of nucleotide substitution in 15-kilobase genes on orthogonally replicating linear plasmids with a 6,700-fold higher mutation rate than that of the host genome, the mutation rate of which is unchanged. Here we demonstrate the utility of BacORep-based continuous evolution by generating strong promoters applicable to model bacteria, Bacillus subtilis and Escherichia coli, and achieving a 7.4-fold methanol assimilation increase in B. thuringiensis. BacORep is a powerful tool for continuous evolution in prokaryotic cells.
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Affiliation(s)
- Rongzhen Tian
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Science Center for Future Foods, Jiangnan University, Wuxi, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
| | - Runzhi Zhao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Science Center for Future Foods, Jiangnan University, Wuxi, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
| | - Haoyu Guo
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Science Center for Future Foods, Jiangnan University, Wuxi, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
| | - Kun Yan
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Science Center for Future Foods, Jiangnan University, Wuxi, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
| | - Chenyun Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Science Center for Future Foods, Jiangnan University, Wuxi, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
| | - Cheng Lu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Science Center for Future Foods, Jiangnan University, Wuxi, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Jian Chen
- Science Center for Future Foods, Jiangnan University, Wuxi, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.
- Science Center for Future Foods, Jiangnan University, Wuxi, China.
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, China.
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, China.
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17
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Song X, Lei S, Liu S, Liu Y, Fu P, Zeng Z, Yang K, Chen Y, Li M, She Q, Han W. Catalytically inactive long prokaryotic Argonaute systems employ distinct effectors to confer immunity via abortive infection. Nat Commun 2023; 14:6970. [PMID: 37914725 PMCID: PMC10620215 DOI: 10.1038/s41467-023-42793-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 10/20/2023] [Indexed: 11/03/2023] Open
Abstract
Argonaute proteins (Agos) bind short nucleic acids as guides and are directed by them to recognize target complementary nucleic acids. Diverse prokaryotic Agos (pAgos) play potential functions in microbial defense. The functions and mechanisms of a group of full-length yet catalytically inactive pAgos, long-B pAgos, remain unclear. Here, we show that most long-B pAgos are functionally connected with distinct associated proteins, including nucleases, Sir2-domain-containing proteins and trans-membrane proteins, respectively. The long-B pAgo-nuclease system (BPAN) is activated by guide RNA-directed target DNA recognition and performs collateral DNA degradation in vitro. In vivo, the system mediates genomic DNA degradation after sensing invading plasmid, which kills the infected cells and results in the depletion of the invader from the cell population. Together, the BPAN system provides immunoprotection via abortive infection. Our data also suggest that the defense strategy is employed by other long-B pAgos equipped with distinct associated proteins.
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Affiliation(s)
- Xinmi Song
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Sheng Lei
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Shunhang Liu
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Yanqiu Liu
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Pan Fu
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zhifeng Zeng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Ke Yang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Yu Chen
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Ming Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, 266237, Jimo, Qingdao, China
| | - Wenyuan Han
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China.
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18
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Chen BC, Chen YZ, Lin HY. An Introduced RNA-Only Approach for Plasmid Curing via the CRISPR-Cpf1 System in Saccharomyces cerevisiae. Biomolecules 2023; 13:1561. [PMID: 37892243 PMCID: PMC10604987 DOI: 10.3390/biom13101561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/13/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
The CRISPR-Cas system has been widely used for genome editing due to its convenience, simplicity and flexibility. Using a plasmid-carrying Cas protein and crRNA or sgRNA expression cassettes is an efficient strategy in the CRISPR-Cas genome editing system. However, the plasmid remains in the cells after genome editing. Development of general plasmid-curing strategies is necessary. Based on our previous CRISPR-Cpf1 genome-editing system in Saccharomyces cerevisiae, the crRNA, designed for the replication origin of the CRISPR-Cpf1 plasmid, and the ssDNA, as a template for homologous recombination, were introduced for plasmid curing. The efficiency of the plasmid curing was 96 ± 4%. In addition, we further simplified the plasmid curing system by transforming only one crRNA into S. cerevisiae, and the curing efficiency was about 70%. In summary, we have developed a CRISPR-mediated plasmid-curing system. The RNA-only plasmid curing system is fast and easy. This plasmid curing strategy can be applied in broad hosts by designing crRNA specific for the replication origin of the plasmid. The plasmid curing system via CRISPR-Cas editing technology can be applied to produce traceless products without foreign genes and to perform iterative processes in multiple rounds of genome editing.
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Affiliation(s)
- Bo-Chou Chen
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu 300, Taiwan;
| | - Yu-Zhen Chen
- Department of Food Science and Technology, Hungkuang University, Taichung 433, Taiwan;
| | - Huan-Yu Lin
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu 300, Taiwan;
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19
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Souza SSR, Smith JT, Bruce SA, Gibson R, Martin IW, Andam CP. Multi-host infection and phylogenetically diverse lineages shape the recombination and gene pool dynamics of Staphylococcus aureus. BMC Microbiol 2023; 23:235. [PMID: 37626313 PMCID: PMC10463932 DOI: 10.1186/s12866-023-02985-9] [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: 03/21/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Staphylococcus aureus can infect and adapt to multiple host species. However, our understanding of the genetic and evolutionary drivers of its generalist lifestyle remains inadequate. This is particularly important when considering local populations of S. aureus, where close physical proximity between bacterial lineages and between host species may facilitate frequent and repeated interactions between them. Here, we aim to elucidate the genomic differences between human- and animal-derived S. aureus from 437 isolates sampled from disease cases in the northeast region of the United States. RESULTS Multi-locus sequence typing revealed the existence of 75 previously recognized sequence types (ST). Our population genomic analyses revealed heterogeneity in the accessory genome content of three dominant S. aureus lineages (ST5, ST8, ST30). Genes related to antimicrobial resistance, virulence, and plasmid types were differentially distributed among isolates according to host (human versus non-human) and among the three major STs. Across the entire population, we identified a total of 1,912 recombination events that occurred in 765 genes. The frequency and impact of homologous recombination were comparable between human- and animal-derived isolates. Low-frequency STs were major donors of recombined DNA, regardless of the identity of their host. The most frequently recombined genes (clfB, aroA, sraP) function in host infection and virulence, which were also frequently shared between the rare lineages. CONCLUSIONS Taken together, these results show that frequent but variable patterns of recombination among co-circulating S. aureus lineages, including the low-frequency lineages, that traverse host barriers shape the structure of local gene pool and the reservoir of host-associated genetic variants. Our study provides important insights to the genetic and evolutionary factors that contribute to the ability of S. aureus to colonize and cause disease in multiple host species. Our study highlights the importance of continuous surveillance of S. aureus circulating in different ecological host niches and the need to systematically sample from them. These findings will inform development of effective measures to control S. aureus colonization, infection, and transmission across the One Health continuum.
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Affiliation(s)
- Stephanie S R Souza
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA.
| | - Joshua T Smith
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Spencer A Bruce
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA
| | - Robert Gibson
- New Hampshire Veterinary Diagnostic Laboratory, Durham, NH, USA
| | - Isabella W Martin
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH, USA
| | - Cheryl P Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA.
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20
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Nitipan S, Saithong P. Characterization and sequencing analysis of pLP2.5-11 and pLP3.0-4 novel cryptic plasmids from Lactiplantibacillus plantarum WP72/27. 3 Biotech 2023; 13:263. [PMID: 37408733 PMCID: PMC10317920 DOI: 10.1007/s13205-023-03684-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 06/25/2023] [Indexed: 07/07/2023] Open
Abstract
We sequenced and described two cryptic plasmids from Lactiplantibacillus plantarum strain WP72/27, termed pLP2.5-11 (OP831909) and pLP3.0-4 (OP831910). Nucleotide sequencing gave the sizes of pLP2.5-11 and pLP3.0-4 as 2754 and 3197 base pairs, with G + C contents 38.89% and 40.88% and predicted two and eight putative open reading frames, respectively. The RepA protein of pLP2.5-11 shared a 99% identity with pC30il, pLP1 and pC30il, whereas the RepB protein of pLP3.0-4 shared a 98% identity with pXY3, a member of the rolling-circle replication (RCR) pC194 family. The origin of plasmid replication was predicted to consist of inverted and directed repeat sequences upstream of the Rep genes. Sequence analysis predicted that both pLP2.5-11 and pLP3.0-4 plasmids replicate via a rolling-circle process. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03684-y.
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Affiliation(s)
- Supachai Nitipan
- Department of Biology, Faculty of Science, Thaksin University, Phattalung Campus, Phattalung, 93210 Thailand
- Microbial Technology for Agriculture, Food and Environment Research Center, Thaksin University, Phatthalung Campus, Phatthalung, 93210 Thailand
| | - Pramuan Saithong
- Department of Applied Microbiology, Institute of Food Research and Product Development, Kasetsart University, Bangkok, 10900 Thailand
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21
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Dewan I, Uecker H. A mathematician's guide to plasmids: an introduction to plasmid biology for modellers. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001362. [PMID: 37505810 PMCID: PMC10433428 DOI: 10.1099/mic.0.001362] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/03/2023] [Indexed: 07/29/2023]
Abstract
Plasmids, extrachromosomal DNA molecules commonly found in bacterial and archaeal cells, play an important role in bacterial genetics and evolution. Our understanding of plasmid biology has been furthered greatly by the development of mathematical models, and there are many questions about plasmids that models would be useful in answering. In this review, we present an introductory, yet comprehensive, overview of the biology of plasmids suitable for modellers unfamiliar with plasmids who want to get up to speed and to begin working on plasmid-related models. In addition to reviewing the diversity of plasmids and the genes they carry, their key physiological functions, and interactions between plasmid and host, we also highlight selected plasmid topics that may be of particular interest to modellers and areas where there is a particular need for theoretical development. The world of plasmids holds a great variety of subjects that will interest mathematical biologists, and introducing new modellers to the subject will help to expand the existing body of plasmid theory.
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Affiliation(s)
- Ian Dewan
- Research Group Stochastic Evolutionary Dynamics, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Hildegard Uecker
- Research Group Stochastic Evolutionary Dynamics, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
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22
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Chen XM, Zhao YY, Liu XC, Han YY, Zhang YH, Hou CY, Zheng LL, Ma SJ, Chen HY. Molecular detection and genetic characteristics of a novel porcine circovirus (porcine circovirus 4) and porcine reproductive and respiratory syndrome virus in Shaanxi and Henan Provinces of China. Comp Immunol Microbiol Infect Dis 2023; 98:102009. [PMID: 37390696 DOI: 10.1016/j.cimid.2023.102009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/18/2023] [Accepted: 06/19/2023] [Indexed: 07/02/2023]
Abstract
Porcine circovirus 4 (PCV4) is a recently discovered circovirus that was first reported in 2019 in several pigs with severe clinical disease in Hunan province of China, and also identified in pigs infected with porcine reproductive and respiratory syndrome virus (PRRSV). To further investigate the epidemic profile and genetic characteristics of the two viruses, 150 clinical samples were collected from 9 swine farms in Shaanxi and Henan provinces of China, and a SYBR Green I-based duplex quantitative real-time polymerase chain reaction (qPCR) was developed for detecting PCV4 and PRRSV simultaneously. The results showed the limits of detection were 41.1 copies/μL and 81.5 copies/μL for PCV4 and PRRSV, respectively. The detection rates of PCV4 and PRRSV were 8.00% (12/150) and 12.00% (18/150) respectively, and a case of co-infection with PCV4 and PRRSV was found in the lung tissue of a suckling pig with respiratory symptom. Subsequently, the complete genomic sequences of five PCV4 strains were obtained, of which one PCV4 strain (SX-ZX) was from Shaanxi province, and these strains were 1770 nucleotides in length and had 97.7%-99.4% genomic identity with 59 PCV4 reference strains. The genome characteristic of the SX-ZX strain was evaluated from three aspects, a "stem-loop" structure, ORF1 and ORF2. As essential elements for the replication, the 17-bp iterative sequence was predicted as the stem structure, in which three non-tandem hexamers were found at downstream with H1/H2 (12-CGGCACACTTCGGCAC-27) as the minimal binding site. Three of the five PCV4 strains were clustered into PCV4b, which was composed of Suidae, fox, dairy cow, dog and raccoon dog. Phylogenetic analysis revealed that seven PRRSV strains from the present study were clustered into the PRRSV-2 genotype. Collectively, these data extend our understanding of the genome characteristic of PCV4 as well as the molecular epidemiology and the genetic profile of PCV4 and PRRSV.
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Affiliation(s)
- Xi-Meng Chen
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, People's Republic of China
| | - You-Yi Zhao
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, People's Republic of China
| | - Xiao-Chen Liu
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, People's Republic of China
| | - Ying-Ying Han
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, People's Republic of China
| | - Yuan-Hang Zhang
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, People's Republic of China
| | - Cheng-Yao Hou
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, People's Republic of China
| | - Lan-Lan Zheng
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, People's Republic of China
| | - Shi-Jie Ma
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, People's Republic of China.
| | - Hong-Ying Chen
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, People's Republic of China.
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23
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Habermann D, Klempt M, Franz CMAP. Identification and Characterization of Novel SPHINX/BMMF-like DNA Sequences Isolated from Non-Bovine Foods. Genes (Basel) 2023; 14:1307. [PMID: 37510212 PMCID: PMC10378824 DOI: 10.3390/genes14071307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Sixteen novel circular rep-encoding DNA sequences with high sequence homologies to previously described SPHINX and BMMF sequences were isolated for the first time from non-bovine foods (pork, wild boar, chicken meat, Alaska pollock, pangasius, black tiger shrimp, apple, carrot, and sprouts from alfalfa, radish, and broccoli). The phylogenetic analysis of the full-length circular genomes grouped these together with previously described representatives of SPHINX/BMMF group 1 and 2 sequences (eight in each group). The characterization of genome lengths, genes present, and conserved structures confirmed their relationship to the known SPHINX/BMMF sequences. Further analysis of iteron-like tandem repeats of SPHINX/BMMF group 1-related genomes revealed a correlation with both full-length sequence tree branches as well as Rep protein sequence tree branches and was able to differentiate subtypes of SPHINX/BMMF group 1 members. For the SPHINX/BMMF group 2 members, a distinct grouping of sequences into two clades (A and B) with subgroups could be detected. A deeper investigation of potential functional regions upstream of the rep gene of the new SPHINX/BMMF group 2 sequences revealed homologies to the dso and sso regions of known plasmid groups that replicate via the rolling circle mechanism. Phylogenetic analyses were accomplished by a Rep protein sequence analysis of different ssDNA viruses, pCRESS, and plasmids with the known replication mechanism, as this yielded deeper insights into the relationship of SPHINX/BMMF group 1 and 2 Rep proteins. A clear relation of these proteins to the Rep proteins of plasmids could be confirmed. Interestingly, for SPHINX/BMMF group 2 members, the relationship to rolling circle replication plasmids could also be verified. Furthermore, a relationship of SPHINX/BMMF group 1 Rep proteins to theta-replicating plasmid Reps is discussed.
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Affiliation(s)
- Diana Habermann
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Martin Klempt
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
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24
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Cronin JM, Yu AM. Recombinant Technologies Facilitate Drug Metabolism, Pharmacokinetics, and General Biomedical Research. Drug Metab Dispos 2023; 51:685-699. [PMID: 36948592 PMCID: PMC10197202 DOI: 10.1124/dmd.122.001008] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/24/2023] Open
Abstract
The development of safe and effective medications requires a profound understanding of their pharmacokinetic (PK) and pharmacodynamic properties. PK studies have been built through investigation of enzymes and transporters that drive drug absorption, distribution, metabolism, and excretion (ADME). Like many other disciplines, the study of ADME gene products and their functions has been revolutionized through the invention and widespread adoption of recombinant DNA technologies. Recombinant DNA technologies use expression vectors such as plasmids to achieve heterologous expression of a desired transgene in a specified host organism. This has enabled the purification of recombinant ADME gene products for functional and structural characterization, allowing investigators to elucidate their roles in drug metabolism and disposition. This strategy has also been used to offer recombinant or bioengineered RNA (BioRNA) agents to investigate the posttranscriptional regulation of ADME genes. Conventional research with small noncoding RNAs such as microRNAs (miRNAs) and small interfering RNAs has been dependent on synthetic RNA analogs that are known to carry a range of chemical modifications expected to improve stability and PK properties. Indeed, a novel transfer RNA fused pre-miRNA carrier-based bioengineering platform technology has been established to offer consistent and high-yield production of unparalleled BioRNA molecules from Escherichia coli fermentation. These BioRNAs are produced and processed inside living cells to better recapitulate the properties of natural RNAs, representing superior research tools to investigate regulatory mechanisms behind ADME. SIGNIFICANCE STATEMENT: This review article summarizes recombinant DNA technologies that have been an incredible boon in the study of drug metabolism and PK, providing investigators with powerful tools to express nearly any ADME gene products for functional and structural studies. It further overviews novel recombinant RNA technologies and discusses the utilities of bioengineered RNA agents for the investigation of ADME gene regulation and general biomedical research.
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Affiliation(s)
- Joseph M Cronin
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA (J.M.C., A.-M.Y.)
| | - Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA (J.M.C., A.-M.Y.)
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25
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Stockdale SR, Hill C. Incorporating plasmid biology and metagenomics into a holistic model of the human gut microbiome. Curr Opin Microbiol 2023; 73:102307. [PMID: 37002975 DOI: 10.1016/j.mib.2023.102307] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 02/14/2023] [Accepted: 03/05/2023] [Indexed: 04/01/2023]
Abstract
The human gut microbiome is often described as the collection of bacteria, archaea, fungi, protists, and viruses associated with an individual, with no acknowledgement of the plasmid constituents. However, like viruses, plasmids are autonomous intracellular replicating entities that can influence the genotype and phenotype of their host and mediate trans-kingdom interactions. Plasmids are frequently noted as vehicles for horizontal gene transfer and for spreading antibiotic resistance, yet their multifaceted contribution to mutualistic and antagonistic interactions within the human microbiome and impact on human health is overlooked. In this review, we highlight the importance of plasmids and their biological properties as overlooked components of microbiomes. Subsequent human microbiome studies should include dedicated analyses of plasmids, particularly as a holistic understanding of human-microbial interactions is required before effective and safe interventions can be implemented to improve human well-being.
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26
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Prity FT, Tobin LA, Maharajan R, Paulsen IT, Cain AK, Hamidian M. The evolutionary tale of eight novel plasmids in a colistin-resistant environmental Acinetobacter baumannii isolate. Microb Genom 2023; 9. [PMID: 37171842 DOI: 10.1099/mgen.0.001010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
Acinetobacter baumannii is an important opportunistic pathogen known for its high levels of resistance to many antibiotics, particularly those considered last resorts such as colistin and carbapenems. Plasmids of this organism are increasingly associated with the spread of clinically important antibiotic resistance genes. Although A. baumannii is a ubiquitous organism, to date, most of the focus has been on studying strains recovered from clinical samples ignoring those isolated in the environment (soil, water, food, etc.). Here, we analysed the genetic structures of eight novel plasmids carried by an environmental colistin-resistant A. baumannii (strain E-072658) recovered in a recycled fibre pulp in a paper mill in Finland. It was shown that E-072658 carries a new variant of the mcr-4 colistin resistance gene (mcr-4.7) in a novel Tn3-family transposon (called Tn6926) carried by a novel plasmid p8E072658. E-072658 is also resistant to sulphonamide compounds; consistent with this, the sul2 sulphonamide resistance gene was found in a pdif module. E-072658 also carries six additional plasmids with no antibiotic resistance genes, but they contained several pdif modules shared with plasmids carried by clinical strains. Detailed analysis of the genetic structure of all eight plasmids carried by E-072658 showed a complex evolutionary history revealing genetic exchange events within the genus Acinetobacter beyond the clinical or environmental origin of the strains. This work provides evidence that environmental strains might act as a source for some of the clinically significant antibiotic resistance genes.
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Affiliation(s)
- Farzana T Prity
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Liam A Tobin
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Ram Maharajan
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Ian T Paulsen
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Amy K Cain
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Mehrad Hamidian
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, NSW, 2007, Australia
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27
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Taylor JC, Kumar R, Xu J, Xu Y. A pathogenicity locus of Streptococcus gallolyticus subspecies gallolyticus. Sci Rep 2023; 13:6291. [PMID: 37072463 PMCID: PMC10113328 DOI: 10.1038/s41598-023-33178-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 04/08/2023] [Indexed: 05/03/2023] Open
Abstract
Streptococcus gallolyticus subspecies gallolyticus (Sgg) is known to be strongly associated with colorectal cancer (CRC). Recent functional studies further demonstrated that Sgg actively stimulates CRC cell proliferation and promotes the development of colon tumors. However, the Sgg factors important for the pro-proliferative and pro-tumor activities of Sgg remain unclear. Here, we identified a chromosomal locus in Sgg strain TX20005. Deletion of this locus significantly reduced Sgg adherence to CRC cells and abrogated the ability of Sgg to stimulate CRC cell proliferation. Thus, we designate this locus as the Sgg pathogenicity-associated region (SPAR). More importantly, we found that SPAR is important for Sgg pathogenicity in vivo. In a gut colonization model, mice exposed to the SPAR deletion mutant showed significantly reduced Sgg load in the colonic tissues and fecal materials, suggesting that SPAR contributes to the colonization capacity of Sgg. In a mouse model of CRC, deletion of SPAR abolished the ability of Sgg to promote the development of colon tumors growth. Taken together, these results highlight SPAR as a critical pathogenicity determinant of Sgg.
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Affiliation(s)
- John Culver Taylor
- Center for Infectious and Inflammatory Diseases, Texas A&M Health Science Center Institute of Biosciences of Technology, Houston, TX, USA
| | - Ritesh Kumar
- Center for Infectious and Inflammatory Diseases, Texas A&M Health Science Center Institute of Biosciences of Technology, Houston, TX, USA
- IFF Health and Biosciences, Madison, USA
| | - Juan Xu
- Center for Infectious and Inflammatory Diseases, Texas A&M Health Science Center Institute of Biosciences of Technology, Houston, TX, USA
| | - Yi Xu
- Center for Infectious and Inflammatory Diseases, Texas A&M Health Science Center Institute of Biosciences of Technology, Houston, TX, USA.
- Department of Microbiology and Molecular Genetics, McGovern Medical School, UT Health, Houston, TX, USA.
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas, USA.
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28
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Fogarty EC, Schechter MS, Lolans K, Sheahan ML, Veseli I, Moore R, Kiefl E, Moody T, Rice PA, Yu MK, Mimee M, Chang EB, Mclellan SL, Willis AD, Comstock LE, Eren AM. A highly conserved and globally prevalent cryptic plasmid is among the most numerous mobile genetic elements in the human gut. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.25.534219. [PMID: 36993556 PMCID: PMC10055365 DOI: 10.1101/2023.03.25.534219] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Plasmids are extrachromosomal genetic elements that often encode fitness enhancing features. However, many bacteria carry 'cryptic' plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes, and is 14 times as numerous as crAssphage, currently established as the most abundant genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one's mother. pBI143 can transfer between Bacteroidales and although it does not appear to impact bacterial host fitness in vivo, can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an inexpensive alternative for detecting human colonic inflammatory states.
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Affiliation(s)
- Emily C Fogarty
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Matthew S Schechter
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Karen Lolans
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Madeline L. Sheahan
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Microbiology, University of Chicago, Chicago, IL, 60637, USA
| | - Iva Veseli
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Ryan Moore
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Evan Kiefl
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Thomas Moody
- Department of Systems Biology, Columbia University, New York, NY, 10032 USA
| | - Phoebe A Rice
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
- Department of Biochemistry, University of Chicago, Chicago, IL, 60637, USA
| | | | - Mark Mimee
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
- Department of Microbiology, University of Chicago, Chicago, IL, 60637, USA
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
| | - Eugene B Chang
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Sandra L Mclellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53204, USA
| | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Laurie E Comstock
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Microbiology, University of Chicago, Chicago, IL, 60637, USA
| | - A Murat Eren
- Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129 Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity, 26129 Oldenburg, Germany
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29
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Kazi TA, Mukhopadhyay BC, Mandal S, Biswas SR. Molecular characterization of five novel plasmids from Enterococcus italicus SD1 isolated from fermented milk: An insight into understanding plasmid incompatibility. Gene 2023; 856:147154. [PMID: 36574936 DOI: 10.1016/j.gene.2022.147154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/15/2022] [Accepted: 12/23/2022] [Indexed: 12/25/2022]
Abstract
Enterococcal plasmids have attracted considerable interest because of their indispensable role in the pathogenesis and dissemination of multidrug-resistance. In this work, five novel plasmids pSRB2, pSRB3, pSRB4, pSRB5 and pSRB7 have been identified and characterised, coexisting in Eneterococcus italicus SD1 from fermented milk. The plasmids pSRB2, pSRB3 and pSRB5 were found to replicate via theta mode of replication while pSRB4 and pSRB7 were rolling-circle plasmids. Comparative analysis of SD1-plasmids dictated that the plasmids are mosaic with novel architecture. Plasmids pSRB2 and pSRB5 are comprised of a typical iteron-based class-A theta type origin of replication, whereas pSRB3 has a Class-D theta type replication origin like pAMβ1. The plasmids pSRB4 and pSRB7 shared similar ori as in pWV01. The SD1 class-A theta type plasmids shared significant homology between their replication proteins with differences in their DNA-binding domain and comprises of distinct iterons. The differences in their iterons and replication proteins restricts the "handcuff" formation for inhibition of plasmid replication, rendering to their compatibility to coexist. Similarly, for SD1 rolling circle plasmids the differences in the replication protein binding site in the origin and the replication protein supports their coexistence by inhibiting the crosstalk between the origins and replication proteins. The phylogenetic tree of their replication proteins revealed their distant kinship. The results indicate that the identified plasmids are unique to E. italicus SD1, providing further opportunities to study their utility in designing multiple gene expression systems for the simultaneous production of proteins in enterococci with the renewed concept of plasmid incompatibility.
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Affiliation(s)
- Tawsif Ahmed Kazi
- Department of Botany, Visva-Bharati University, Santiniketan 731235, West Bengal, India
| | | | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700019, India
| | - Swadesh Ranjan Biswas
- Department of Botany, Visva-Bharati University, Santiniketan 731235, West Bengal, India.
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30
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Lossouarn J, Nesbø CL, Bienvenu N, Geslin C. Plasmid pMO1 from Marinitoga okinawensis, first non-cryptic plasmid reported within Thermotogota. Res Microbiol 2023; 174:104044. [PMID: 36805054 DOI: 10.1016/j.resmic.2023.104044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/19/2023]
Abstract
Mobile genetic elements (MGEs), such as viruses and plasmids, drive the evolution and adaptation of their cellular hosts from all three domains of life. This includes microorganisms thriving in the most extreme environments, like deep-sea hydrothermal vents. However, our knowledge about MGEs still remains relatively sparse in these abyssal ecosystems. Here we report the isolation, sequencing, assembly, and functional annotation of pMO1, a 28.2 kbp plasmid associated with the reference strain Marinitoga okinawensis. Carrying restriction/modification and chemotaxis protein-encoding genes, pMO1 likely affects its host's phenotype and represents the first non-cryptic plasmid described among the phylum Thermotogota.
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Affiliation(s)
- Julien Lossouarn
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.
| | - Camilla L Nesbø
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada; Biozone, Department of Chemical Engineering and Applied Chemistry and BioZone, University of Toronto, 200 College Street, Toronto, Ontario, Canada, M5S 3E5.
| | - Nadège Bienvenu
- Univ Brest, Ifremer, CNRS, Unité Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France.
| | - Claire Geslin
- Univ Brest, Ifremer, CNRS, Unité Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France. mailto:
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31
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Genomic Analysis of Non-B Nucleic Acids Structures in SARS-CoV-2: Potential Key Roles for These Structures in Mutability, Translation, and Replication? Genes (Basel) 2023; 14:genes14010157. [PMID: 36672896 PMCID: PMC9859294 DOI: 10.3390/genes14010157] [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: 12/09/2022] [Revised: 01/01/2023] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Non-B nucleic acids structures have arisen as key contributors to genetic variation in SARS-CoV-2. Herein, we investigated the presence of defining spike protein mutations falling within inverted repeats (IRs) for 18 SARS-CoV-2 variants, discussed the potential roles of G-quadruplexes (G4s) in SARS-CoV-2 biology, and identified potential pseudoknots within the SARS-CoV-2 genome. Surprisingly, there was a large variation in the number of defining spike protein mutations arising within IRs between variants and these were more likely to occur in the stem region of the predicted hairpin stem-loop secondary structure. Notably, mutations implicated in ACE2 binding and propagation (e.g., ΔH69/V70, N501Y, and D614G) were likely to occur within IRs, whilst mutations involved in antibody neutralization and reduced vaccine efficacy (e.g., T19R, ΔE156, ΔF157, R158G, and G446S) were rarely found within IRs. We also predicted that RNA pseudoknots could predominantly be found within, or next to, 29 mutations found in the SARS-CoV-2 spike protein. Finally, the Omicron variants BA.2, BA.4, BA.5, BA.2.12.1, and BA.2.75 appear to have lost two of the predicted G4-forming sequences found in other variants. These were found in nsp2 and the sequence complementary to the conserved stem-loop II-like motif (S2M) in the 3' untranslated region (UTR). Taken together, non-B nucleic acids structures likely play an integral role in SARS-CoV-2 evolution and genetic diversity.
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32
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Juhas M. The World of Microorganisms. BRIEF LESSONS IN MICROBIOLOGY 2023:1-16. [DOI: 10.1007/978-3-031-29544-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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33
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Abstract
In the late 1950s, a number of laboratories took up the study of plasmids once the discovery was made that extrachromosomal antibiotic resistance (R) factors are the responsible agents for the transmissibility of multiple antibiotic resistance among the enterobacteria. The use of incompatibility for the classification of plasmids is now widespread. It seems clear now on the basis of the limited studies to date that the number of incompatibility groups of plasmids will likely be extremely large when one includes plasmids obtained from bacteria that are normal inhabitants of poorly studied natural environments. The presence of both linear chromosomes and linear plasmids is now established for several Streptomyces species. One of the more fascinating developments in plasmid biology was the discovery of linear plasmids in the 1980s. A remarkable feature of the Ti plasmids of Agrobacterium tumefaciens is the presence of two DNA transfer systems. A definitive demonstration that plasmids consisted of duplex DNA came from interspecies conjugal transfer of plasmids followed by separation of plasmid DNA from chromosomal DNA by equilibrium buoyant density centrifugation. The formation of channels for DNA movement and the actual steps involved in DNA transport offer many opportunities for the discovery of proteins with novel activities and for establishing fundamentally new concepts of macromolecular interactions between DNA and specific proteins, membranes, and the peptidoglycan matrix.
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Affiliation(s)
- Donald R. Helinski
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
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34
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Valenzuela-Aviles P, Torrealba D, Figueroa C, Mercado L, Dixon B, Conejeros P, Gallardo-Matus J. Why vaccines fail against Piscirickettsiosis in farmed salmon and trout and how to avoid it: A review. Front Immunol 2022; 13:1019404. [PMID: 36466828 PMCID: PMC9714679 DOI: 10.3389/fimmu.2022.1019404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/24/2022] [Indexed: 09/28/2023] Open
Abstract
Piscirickettsiosis is the most severe, persistent, and damaging disease that has affected the Chilean salmon industry since its origins in the 1980s. As a preventive strategy for this disease, different vaccines have been developed and used over the last 30 years. However, vaccinated salmon and trout frequently die in the sea cages and the use of antibiotics is still high demonstrating the low efficiency of the available vaccines. The reasons why the vaccines fail so often are still debated, but it could involve different extrinsic and intrinsic factors. Among the extrinsic factors, mainly associated with chronic stress, we can distinguish: 1) biotic including coinfection with sea lice, sealions attacks or harmful algal blooms; 2) abiotic including low oxygen or high temperature; and 3) farm-management factors including overcrowding or chemical delousing treatments. Among the intrinsic factors, we can distinguish: 1) fish-related factors including host's genetic variability (species, population and individual), sex or age; 2) pathogen-related factors including their variability and ability to evade host immune responses; and 3) vaccine-related factors including low immunogenicity and poor matches with the circulating pathogen strain. Based on the available evidence, in order to improve the development and the efficacy of vaccines against P. salmonis we recommend: a) Do not perform efficacy evaluations by intraperitoneal injection of pathogens because they generate an artificial protective immune response, instead cohabitation or immersion challenges must be used; b) Evaluate the diversity of pathogen strains in the field and ensure a good antigenic match with the vaccines; c) Investigate whether host genetic diversity could be improved, e.g. through selection, in favor of better and longer responses to vaccination; d) To reduce the stressful effects at the cage level, controlling the co-infection of pathogens and avoiding fish overcrowding. To date, we do not know the immunological mechanisms by which the vaccines against P. salmonis may or may not generate protection. More studies are required to identify what type of response, cellular or molecular, is required to develop effective vaccines.
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Affiliation(s)
- Paula Valenzuela-Aviles
- Laboratorio de Genética y Genómica Aplicada, Escuela de Ciencias del Mar, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Débora Torrealba
- Laboratorio de Genética y Genómica Aplicada, Escuela de Ciencias del Mar, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Carolina Figueroa
- Laboratorio de Genética y Genómica Aplicada, Escuela de Ciencias del Mar, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Luis Mercado
- Grupo de Marcadores Inmunológicos en Organismos Acuáticos, Pontificia Universidad Católica de Valparaíso, Instituto de Biología, Valparaíso, Chile
| | - Brian Dixon
- Department of Biology, Faculty of Science, University of Waterloo, Waterloo, Canada
| | - Pablo Conejeros
- Centro de Investigación y Gestión de Recursos Naturales (CIGREN), Facultad de Ciencias, Instituto de Biología, Universidad de Valparaíso, Valparaíso, Chile
| | - José Gallardo-Matus
- Laboratorio de Genética y Genómica Aplicada, Escuela de Ciencias del Mar, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
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Klanschnig M, Cserjan-Puschmann M, Striedner G, Grabherr R. CRISPRactivation-SMS, a message for PAM sequence independent gene up-regulation in Escherichia coli. Nucleic Acids Res 2022; 50:10772-10784. [PMID: 36134715 PMCID: PMC9561276 DOI: 10.1093/nar/gkac804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/10/2022] [Accepted: 09/08/2022] [Indexed: 12/26/2022] Open
Abstract
Governance of the endogenous gene regulatory network enables the navigation of cells towards beneficial traits for recombinant protein production. CRISPRactivation and interference provides the basis for gene expression modulation but is primarily applied in eukaryotes. Particularly the lack of wide-ranging prokaryotic CRISPRa studies might be attributed to intrinsic limitations of bacterial activators and Cas9 proteins. While bacterial activators need accurate spatial orientation and distancing towards the target promoter to be functional, Cas9-based CRISPR tools only bind sites adjacent to NGG PAM sequences. These circumstances hampered Cas9-guided activators from mediating the up-regulation of endogenous genes at precise positions in bacteria. We could overcome this limitation by combining the PAM independent Cas9 variant SpRY and a CRISPRa construct using phage protein MCP fused to transcriptional activator SoxS. This CRISPRa construct, referred to as SMS, was compared with previously reported CRISPRa constructs and showed up-regulation of a reporter gene library independent of its PAM sequence in Escherichia coli. We also demonstrated down-regulation and multi-gene expression control with SMS at non-NGG PAM sites. Furthermore, we successfully applied SMS to up-regulate endogenous genes, and transgenes at non-NGG PAM sites, which was impossible with the previous CRISPRa construct.
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Affiliation(s)
- Marco Klanschnig
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Gerald Striedner
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Reingard Grabherr
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
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Haines MC, Carling B, Marshall J, Shenshin VA, Baldwin GS, Freemont P, Storch M. basicsynbio and the BASIC SEVA collection: software and vectors for an established DNA assembly method. Synth Biol (Oxf) 2022; 7:ysac023. [PMID: 36381610 PMCID: PMC9664905 DOI: 10.1093/synbio/ysac023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 09/06/2022] [Accepted: 10/10/2022] [Indexed: 10/19/2023] Open
Abstract
Standardized deoxyribonucleic acid (DNA) assembly methods utilizing modular components provide a powerful framework to explore designs and iterate through Design-Build-Test-Learn cycles. Biopart Assembly Standard for Idempotent Cloning (BASIC) DNA assembly uses modular parts and linkers, is highly accurate, easy to automate, free for academic and commercial use and enables hierarchical assemblies through an idempotent format. These features enable applications including pathway engineering, ribosome binding site (RBS) tuning, fusion protein engineering and multiplexed guide ribonucleic acid (RNA) expression. In this work, we present basicsynbio, open-source software encompassing a Web App (https://basicsynbio.web.app/) and Python Package (https://github.com/LondonBiofoundry/basicsynbio), enabling BASIC construct design via simple drag-and-drop operations or programmatically. With basicsynbio, users can access commonly used BASIC parts and linkers while designing new parts and assemblies with exception handling for common errors. Users can export sequence data and create instructions for manual or acoustic liquid-handling platforms. Instruction generation relies on the BasicBuild Open Standard, which is parsed for bespoke workflows and is serializable in JavaScript Object Notation for transfer and storage. We demonstrate basicsynbio, assembling 30 vectors using sequences including modules from the Standard European Vector Architecture (SEVA). The BASIC SEVA vector collection is compatible with BASIC and Golden Gate using BsaI. Vectors contain one of six antibiotic resistance markers and five origins of replication from different compatibility groups. The collection is available via Addgene under an OpenMTA agreement. Furthermore, vector sequences are available from within the basicsynbio application programming interface with other collections of parts and linkers, providing a powerful environment for designing assemblies for bioengineering applications. Graphical Abstract.
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Affiliation(s)
- Matthew C Haines
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, London SW7 2AZ, UK
- London Biofoundry, Imperial College Translation and Innovation Hub, London W12 0BZ, UK
| | - Benedict Carling
- Department of Bioengineering, Imperial College London, London, Westminster SW7 2AZ, UK
| | - James Marshall
- Department of Bioengineering, Imperial College London, London, Westminster SW7 2AZ, UK
| | - Vasily A Shenshin
- Department of Life Sciences, Imperial College London, London, Westminster SW7 2AZ, UK
| | - Geoff S Baldwin
- Department of Life Sciences, Imperial College London, London, Westminster SW7 2AZ, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Paul Freemont
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, London SW7 2AZ, UK
- London Biofoundry, Imperial College Translation and Innovation Hub, London W12 0BZ, UK
- UK DRI Care Research and Technology Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Marko Storch
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, London SW7 2AZ, UK
- London Biofoundry, Imperial College Translation and Innovation Hub, London W12 0BZ, UK
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Thomsen J, Schmitz RA. Generating a Small Shuttle Vector for Effective Genetic Engineering of Methanosarcina mazei Allowed First Insights in Plasmid Replication Mechanism in the Methanoarchaeon. Int J Mol Sci 2022; 23:ijms231911910. [PMID: 36233214 PMCID: PMC9569500 DOI: 10.3390/ijms231911910] [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: 09/08/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/16/2022] Open
Abstract
Due to their role in methane production, methanoarchaea are of high ecological relevance and genetic systems have been ever more established in the last two decades. The system for protein expression in Methanosarcina using a comprehensive shuttle vector is established; however, details about its replication mechanism in methanoarchaea remain unknown. Here, we report on a significant optimisation of the rather large shuttle vector pWM321 (8.9 kbp) generated by Metcalf through a decrease in its size by about 35% by means of the deletion of several non-coding regions and the ssrA gene. The resulting plasmid (pRS1595) still stably replicates in M. mazei and—most likely due to its reduced size—shows a significantly higher transformation efficiency compared to pWM321. In addition, we investigate the essential gene repA, coding for a rep type protein. RepA was heterologously expressed in Escherichia coli, purified and characterised, demonstrating the significant binding and nicking activity of supercoiled plasmid DNA. Based on our findings we propose that the optimised shuttle vector replicates via a rolling circle mechanism with RepA as the initial replication protein in Methanosarcina. On the basis of bioinformatic comparisons, we propose the presence and location of a double-strand and a single-strand origin, which need to be further verified.
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Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD + depletion. Nat Microbiol 2022; 7:1857-1869. [PMID: 36192537 DOI: 10.1038/s41564-022-01239-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 08/26/2022] [Indexed: 02/02/2023]
Abstract
Argonaute (Ago) proteins are found in all three domains of life. The so-called long Agos are composed of four major domains (N, PAZ, MID and PIWI) and contribute to RNA silencing in eukaryotes (eAgos) or defence against invading mobile genetic elements in prokaryotes (pAgos). The majority (~60%) of pAgos identified bioinformatically are shorter (comprising only MID and PIWI domains) and are typically associated with Sir2, Mrr or TIR domain-containing proteins. The cellular function and mechanism of short pAgos remain enigmatic. Here we show that Geobacter sulfurreducens short pAgo and the NAD+-bound Sir2 protein form a stable heterodimeric complex. The GsSir2/Ago complex presumably recognizes invading plasmid or phage DNA and activates the Sir2 subunit, which triggers endogenous NAD+ depletion and cell death, and prevents the propagation of invading DNA. We reconstituted NAD+ depletion activity in vitro and showed that activated GsSir2/Ago complex functions as a NADase that hydrolyses NAD+ to ADPR. Thus, short Sir2-associated pAgos provide defence against phages and plasmids, underscoring the diversity of mechanisms of prokaryotic Agos.
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Pöschel L, Gehr E, Buchhaupt M. A pBBR1-based vector with IncP group plasmid compatibility for Methylorubrum extorquens. Microbiologyopen 2022; 11:e1325. [PMID: 36314759 PMCID: PMC9531332 DOI: 10.1002/mbo3.1325] [Citation(s) in RCA: 1] [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: 08/09/2022] [Revised: 09/23/2022] [Accepted: 09/23/2022] [Indexed: 11/06/2022] Open
Abstract
Plasmids are one of the most important genetic tools for basic research and biotechnology, as they enable rapid genetic manipulation. Here we present a novel pBBR1-based plasmid for Methylorubrum extorquens, a model methylotroph that is used for the development of C1-based microbial cell factories. To develop a vector with compatibility to the so far mainly used pCM plasmid system, we transferred the pBBR1-based plasmid pMiS1, which showed an extremely low transformation rate and caused a strong growth defect. Isolation of a suppressor mutant with improved growth led to the isolation of the variant pMis1_1B. Its higher transformation rate and less pronounced growth defect phenotype could be shown to be the result of a mutation in the promotor region of the rep gene. Moreover, cotransformation of pMis1_1B and pCM160 was possible, but the resulting transformants showed stronger growth defects in comparison with a single pMis1_1B transformant. Surprisingly, cotransformants carrying pCM160 and a pMis1_1B derivative containing a mCherry reporter construct showed higher fluorescence levels than strains containing only the pMis1_1B-based reporter plasmids or a corresponding pCM160 derivative. Relative plasmid copy number determination experiments confirmed our hypothesis of an increased copy number of pMis1_1B in the strain carrying both plasmids. Despite the slight metabolic burden caused by pMis1_1B, the plasmid strongly expands the genetic toolbox for M. extorquens.
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Affiliation(s)
- Laura Pöschel
- DECHEMA-Forschungsinstitut, Microbial Biotechnology, Frankfurt am Main, Germany
- Department of Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Elisabeth Gehr
- DECHEMA-Forschungsinstitut, Microbial Biotechnology, Frankfurt am Main, Germany
| | - Markus Buchhaupt
- DECHEMA-Forschungsinstitut, Microbial Biotechnology, Frankfurt am Main, Germany
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Antibiotics Resistance Pattern of Food-Borne Bacteria Isolated from Ice Cream in Bangladesh: A Multidisciplinary Study. J FOOD QUALITY 2022. [DOI: 10.1155/2022/5016795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Ice cream is one of the most popular food items consumed during the summer season in Bangladesh by all ages but mostly school-going students. Due to the ingredients and handling process of ice cream, it acts as a good shelter for pathogenic and nonpathogenic microorganisms. Therefore, we aimed to investigate the microbial count, prevalence, isolate and characterize multidrug-resistant bacteria in ice cream samples collected from nearby shops of schools in Tangail district, Bangladesh. Ice-cream consumer and nonconsumer students were selected by providing questionnaires. Total viable count (TVC) and total coliform count (TCC) were determined by pour plate methods, where conventional methods were performed for bacterial identification. The Kirby-Bauer disk diffusion method was used to determine the antimicrobial susceptibility of bacterial isolates. Kado and Liu method, with some modifications, was used to extract plasmid from the isolated bacteria and visualized through gel electrophoresis. The demographic characteristics showed that the degree of symptoms regarding microorganisms mediated disorders and rate of antibiotics intake in ice cream consumers were significantly higher than the nonconsumers. The range of TVC and TCC in the ice cream samples was found 0–9.9 × 109 CFU/ml and 0–900 CFU/ml, respectively. Interestingly, 93.75% of the total ice cream samples also showed fungal positive. A total of 12 different bacterial species were identified, including Proteus spp, E. coli, V.cholera, Pseudomonas spp, Shigella spp, Klebsiella spp, Aeromonas spp, V. Parahemolyticus. Salmonella paratyphi, Citrobacterspp, Plesiomonasspp, and Staphylococcus aureus. The antimicrobial susceptibility assay showed the multiple resistance frequency of these isolates to different antimicrobial drugs. All individual isolates were screened for plasmid DNA, and we found that seven strains harbored a single or more than two plasmids sized approximately between 1.9 and 140 MDa, indicating a possible connection between resistance phenotype pattern and genotype.
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Abstract
Plasmids are one of the most commonly used platforms for genetic engineering and recombinant gene expression in bacteria. The range of available copy numbers for cloning vectors is largely restricted to the handful of Origins of Replication (ORIs) that have been isolated from plasmids found in nature. Here, we introduce two systems that allow for the continuous, finely-tuned control of plasmid copy number between 1 and 800 copies per cell: a plasmid with an anhydrotetracycline-controlled copy number, and a parallelized assay that is used to generate a continuous spectrum of 1194 ColE1-based copy number variants. Using these systems, we investigate the effects of plasmid copy number on cellular growth rates, gene expression, biosynthesis, and genetic circuit performance. We perform single-cell timelapse measurements to characterize plasmid loss, runaway plasmid replication, and quantify the impact of plasmid copy number on the variability of gene expression. Using our assay, we find that each plasmid imposes a 0.063% linear metabolic burden on their hosts, hinting at a simple relationship between metabolic burdens and plasmid DNA synthesis. Our systems enable the precise control of gene expression, and our results highlight the importance of tuning plasmid copy number as a powerful tool for the optimization of synthetic biological systems.
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Kazi TA, Acharya A, Mukhopadhyay BC, Mandal S, Arukha AP, Nayak S, Biswas SR. Plasmid-Based Gene Expression Systems for Lactic Acid Bacteria: A Review. Microorganisms 2022; 10:1132. [PMID: 35744650 PMCID: PMC9229153 DOI: 10.3390/microorganisms10061132] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 01/27/2023] Open
Abstract
Lactic acid bacteria (LAB) play a very vital role in food production, preservation, and as probiotic agents. Some of these species can colonize and survive longer in the gastrointestinal tract (GIT), where their presence is crucially helpful to promote human health. LAB has also been used as a safe and efficient incubator to produce proteins of interest. With the advent of genetic engineering, recombinant LAB have been effectively employed as vectors for delivering therapeutic molecules to mucosal tissues of the oral, nasal, and vaginal tracks and for shuttling therapeutics for diabetes, cancer, viral infections, and several gastrointestinal infections. The most important tool needed to develop genetically engineered LABs to produce proteins of interest is a plasmid-based gene expression system. To date, a handful of constitutive and inducible vectors for LAB have been developed, but their limited availability, host specificity, instability, and low carrying capacity have narrowed their spectrum of applications. The current review discusses the plasmid-based vectors that have been developed so far for LAB; their functionality, potency, and constraints; and further highlights the need for a new, more stable, and effective gene expression platform for LAB.
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Affiliation(s)
- Tawsif Ahmed Kazi
- Department of Botany, Visva-Bharati University, Santiniketan 731235, West Bengal, India; (T.A.K.); (A.A.); (B.C.M.)
| | - Aparupa Acharya
- Department of Botany, Visva-Bharati University, Santiniketan 731235, West Bengal, India; (T.A.K.); (A.A.); (B.C.M.)
| | - Bidhan Chandra Mukhopadhyay
- Department of Botany, Visva-Bharati University, Santiniketan 731235, West Bengal, India; (T.A.K.); (A.A.); (B.C.M.)
| | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700019, West Bengal, India;
| | - Ananta Prasad Arukha
- Researcher 5 Department of Neurosurgery, Medical School, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Subhendu Nayak
- Sr. Scientist, Clorox, Better Health VMS, Durham, NC 27701, USA;
| | - Swadesh Ranjan Biswas
- Department of Botany, Visva-Bharati University, Santiniketan 731235, West Bengal, India; (T.A.K.); (A.A.); (B.C.M.)
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Zhang X, An X. Adaptation by Type III CRISPR-Cas Systems: Breakthrough Findings and Open Questions. Front Microbiol 2022; 13:876174. [PMID: 35495695 PMCID: PMC9048733 DOI: 10.3389/fmicb.2022.876174] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/03/2022] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems acquire heritable defense memory against invading nucleic acids through adaptation. Type III CRISPR-Cas systems have unique and intriguing features of defense and are important in method development for Genetics research. We started to understand the common and unique properties of type III CRISPR-Cas adaptation in recent years. This review summarizes our knowledge regarding CRISPR-Cas adaptation with the emphasis on type III systems and discusses open questions for type III adaptation studies.
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Affiliation(s)
- Xinfu Zhang
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, GA, United States
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Research Center of Tree breeding and Ecological Remediation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- *Correspondence: Xinfu Zhang,
| | - Xinmin An
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Research Center of Tree breeding and Ecological Remediation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Xinmin An,
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Immethun CM, Kathol M, Changa T, Saha R. Synthetic Biology Tool Development Advances Predictable Gene Expression in the Metabolically Versatile Soil Bacterium Rhodopseudomonas palustris. Front Bioeng Biotechnol 2022; 10:800734. [PMID: 35372317 PMCID: PMC8966681 DOI: 10.3389/fbioe.2022.800734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 02/16/2022] [Indexed: 11/13/2022] Open
Abstract
Harnessing the unique biochemical capabilities of non-model microorganisms would expand the array of biomanufacturing substrates, process conditions, and products. There are non-model microorganisms that fix nitrogen and carbon dioxide, derive energy from light, catabolize methane and lignin-derived aromatics, are tolerant to physiochemical stresses and harsh environmental conditions, store lipids in large quantities, and produce hydrogen. Model microorganisms often only break down simple sugars and require low stress conditions, but they have been engineered for the sustainable manufacture of numerous products, such as fragrances, pharmaceuticals, cosmetics, surfactants, and specialty chemicals, often by using tools from synthetic biology. Transferring complex pathways has proven to be exceedingly difficult, as the cofactors, cellular conditions, and energy sources necessary for this pathway to function may not be present in the host organism. Utilization of unique biochemical capabilities could also be achieved by engineering the host; although, synthetic biology tools developed for model microbes often do not perform as designed in other microorganisms. The metabolically versatile Rhodopseudomonas palustris CGA009, a purple non-sulfur bacterium, catabolizes aromatic compounds derived from lignin in both aerobic and anaerobic conditions and can use light, inorganic, and organic compounds for its source of energy. R. palustris utilizes three nitrogenase isozymes to fulfill its nitrogen requirements while also generating hydrogen. Furthermore, the bacterium produces two forms of RuBisCo in response to carbon dioxide/bicarbonate availability. While this potential chassis harbors many beneficial traits, stable heterologous gene expression has been problematic due to its intrinsic resistance to many antibiotics and the lack of synthetic biology parts investigated in this microbe. To address these problems, we have characterized gene expression and plasmid maintenance for different selection markers, started a synthetic biology toolbox specifically for the photosynthetic R. palustris, including origins of replication, fluorescent reporters, terminators, and 5′ untranslated regions, and employed the microbe’s endogenous plasmid for exogenous protein production. This work provides essential synthetic biology tools for engineering R. palustris’ many unique biochemical processes and has helped define the principles for expressing heterologous genes in this promising microbe through a methodology that could be applied to other non-model microorganisms.
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Harnessing plasmid replication mechanism to enable dynamic control of gene copy in bacteria. Metab Eng 2022; 70:67-78. [PMID: 35033655 PMCID: PMC8844098 DOI: 10.1016/j.ymben.2022.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/17/2021] [Accepted: 01/09/2022] [Indexed: 01/03/2023]
Abstract
Dynamic regulation has been proved efficient in controlling gene expression at transcriptional, translational, and post-translational level. However, the dynamic regulation at gene replication level has been rarely explored so far. In this study, we established dynamic regulation at gene copy level through engineering controllable plasmid replication to dynamically control the gene expression. Prototypic genetic circuits with different control logic were applied to enable diversified dynamic behaviors of gene copy. To explore the applicability of this strategy, the dynamic gene copy control was employed in regulating the biosynthesis of p-coumaric acid, which resulted in an up to 78% increase in p-coumaric acid titer to 1.69 g/L in shake flasks. These results indicated the great potential of applying dynamic gene copy control for engineering biosynthesis of valuable compounds in metabolic engineering.
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Miller CA, Ho JML, Bennett MR. Strategies for Improving Small-Molecule Biosensors in Bacteria. BIOSENSORS 2022; 12:bios12020064. [PMID: 35200325 PMCID: PMC8869690 DOI: 10.3390/bios12020064] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 05/03/2023]
Abstract
In recent years, small-molecule biosensors have become increasingly important in synthetic biology and biochemistry, with numerous new applications continuing to be developed throughout the field. For many biosensors, however, their utility is hindered by poor functionality. Here, we review the known types of mechanisms of biosensors within bacterial cells, and the types of approaches for optimizing different biosensor functional parameters. Discussed approaches for improving biosensor functionality include methods of directly engineering biosensor genes, considerations for choosing genetic reporters, approaches for tuning gene expression, and strategies for incorporating additional genetic modules.
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Affiliation(s)
- Corwin A. Miller
- Department of Biosciences, Rice University MS-140, 6100 Main St., Houston, TX 77005, USA; (C.A.M.); (J.M.L.H.)
| | - Joanne M. L. Ho
- Department of Biosciences, Rice University MS-140, 6100 Main St., Houston, TX 77005, USA; (C.A.M.); (J.M.L.H.)
| | - Matthew R. Bennett
- Department of Biosciences, Rice University MS-140, 6100 Main St., Houston, TX 77005, USA; (C.A.M.); (J.M.L.H.)
- Department of Bioengineering, Rice University MS-140, 6100 Main St., Houston, TX 77005, USA
- Correspondence:
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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’.
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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
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48
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Breger JC, Ellis GA, Walper SA, Susumu K, Medintz IL. Implementing Multi-Enzyme Biocatalytic Systems Using Nanoparticle Scaffolds. Methods Mol Biol 2022; 2487:227-262. [PMID: 35687240 DOI: 10.1007/978-1-0716-2269-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Interest in multi-enzyme synthesis outside of cells (in vitro) is becoming far more prevalent as the field of cell-free synthetic biology grows exponentially. Such synthesis would allow for complex chemical transformations based on the exquisite specificity of enzymes in a "greener" manner as compared to organic chemical transformations. Here, we describe how nanoparticles, and in this specific case-semiconductor quantum dots, can be used to both stabilize enzymes and further allow them to self-assemble into nanocomplexes that facilitate high-efficiency channeling phenomena. Pertinent protocol information is provided on enzyme expression, choice of nanoparticulate material, confirmation of enzyme attachment to nanoparticles, assay format and tracking, data analysis, and optimization of assay formats to draw the best analytical information from the underlying processes.
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Affiliation(s)
- Joyce C Breger
- Center for Bio/Molecular Science and Engineering, Code 6900, Washington, DC, USA
| | - Gregory A Ellis
- Center for Bio/Molecular Science and Engineering, Code 6900, Washington, DC, USA
| | - Scott A Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, Washington, DC, USA
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, DC, USA
- Jacobs Corporation, Hanover, MD, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, Washington, DC, USA.
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49
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A Structural Perspective of Reps from CRESS-DNA Viruses and Their Bacterial Plasmid Homologues. Viruses 2021; 14:v14010037. [PMID: 35062241 PMCID: PMC8780604 DOI: 10.3390/v14010037] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 11/17/2022] Open
Abstract
Rolling circle replication (RCR) is ubiquitously used by cellular and viral systems for genome and plasmid replication. While the molecular mechanism of RCR has been described, the structural mechanism is desperately lacking. Circular-rep encoded single stranded DNA (CRESS-DNA) viruses employ a viral encoded replicase (Rep) to initiate RCR. The recently identified prokaryotic homologues of Reps may also be responsible for initiating RCR. Reps are composed of an endonuclease, oligomerization, and ATPase domain. Recent structural studies have provided structures for all these domains such that an overall mechanism of RCR initiation can begin to be synthesized. However, structures of Rep in complex with its various DNA substrates and/or ligands are lacking. Here we provide a 3D bioinformatic review of the current structural information available for Reps. We combine an excess of 1590 sequences with experimental and predicted structural data from 22 CRESS-DNA groups to identify similarities and differences between Reps that lead to potentially important functional sites. Experimental studies of these sites may shed light on how Reps execute their functions. Furthermore, we identify Rep-substrate or Rep-ligand structures that are urgently needed to better understand the structural mechanism of RCR.
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50
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Zhang X, Garrett S, Graveley BR, Terns MP. Unique properties of spacer acquisition by the type III-A CRISPR-Cas system. Nucleic Acids Res 2021; 50:1562-1582. [PMID: 34893878 PMCID: PMC8860593 DOI: 10.1093/nar/gkab1193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/12/2021] [Accepted: 11/19/2021] [Indexed: 12/11/2022] Open
Abstract
Type III CRISPR-Cas systems have a unique mode of interference, involving crRNA-guided recognition of nascent RNA and leading to DNA and RNA degradation. How type III systems acquire new CRISPR spacers is currently not well understood. Here, we characterize CRISPR spacer uptake by a type III-A system within its native host, Streptococcus thermophilus. Adaptation by the type II-A system in the same host provided a basis for comparison. Cas1 and Cas2 proteins were critical for type III adaptation but deletion of genes responsible for crRNA biogenesis or interference did not detectably change spacer uptake patterns, except those related to host counter-selection. Unlike the type II-A system, type III spacers are acquired in a PAM- and orientation-independent manner. Interestingly, certain regions of plasmids and the host genome were particularly well-sampled during type III-A, but not type II-A, spacer uptake. These regions included the single-stranded origins of rolling-circle replicating plasmids, rRNA and tRNA encoding gene clusters, promoter regions of expressed genes and 5′ UTR regions involved in transcription attenuation. These features share the potential to form DNA secondary structures, suggesting a preferred substrate for type III adaptation. Lastly, the type III-A system adapted to and protected host cells from lytic phage infection.
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Affiliation(s)
- Xinfu Zhang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Sandra Garrett
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.,Department of Microbiology, University of Georgia, Athens, GA 30602, USA.,Department of Genetics, University of Georgia, Athens, GA 30602, USA
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