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Gao H, Wang Y, Huang Z, Yu F, Hu X, Ning D, Xu X. Development of Leptolyngbya sp. BL0902 into a model organism for synthetic biological research in filamentous cyanobacteria. Front Microbiol 2024; 15:1409771. [PMID: 39104590 PMCID: PMC11298460 DOI: 10.3389/fmicb.2024.1409771] [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: 04/01/2024] [Accepted: 07/10/2024] [Indexed: 08/07/2024] Open
Abstract
Cyanobacteria have great potential in CO2-based bio-manufacturing and synthetic biological studies. The filamentous cyanobacterium, Leptolyngbya sp. strain BL0902, is comparable to Arthrospira (Spirulina) platensis in commercial-scale cultivation while proving to be more genetically tractable. Here, we report the analyses of the whole genome sequence, gene inactivation/overexpression in the chromosome and deletion of non-essential chromosomal regions in this strain. The genetic manipulations were performed via homologous double recombination using either an antibiotic resistance marker or the CRISPR/Cpf1 editing system for positive selection. A desD-overexpressing strain produced γ-linolenic acid in an open raceway photobioreactor with the productivity of 0.36 g·m-2·d-1. Deletion mutants of predicted patX and hetR, two genes with opposite effects on cell differentiation in heterocyst-forming species, were used to demonstrate an analysis of the relationship between regulatory genes in the non-heterocystous species. Furthermore, a 50.8-kb chromosomal region was successfully deleted in BL0902 with the Cpf1 system. These results supported that BL0902 can be developed into a stable photosynthetic cell factory for synthesizing high value-added products, or used as a model strain for investigating the functions of genes that are unique to filamentous cyanobacteria, and could be systematically modified into a genome-streamlined chassis for synthetic biological purposes.
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Affiliation(s)
- Hong Gao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yali Wang
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Ziling Huang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Feiqi Yu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Xi Hu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Degang Ning
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xudong Xu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- School of Life Sciences, Central China Normal University, Wuhan, China
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2
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Alves J, Dry I, White JH, Dryden DT, Lynskey NN. Generation of tools for expression and purification of the phage-encoded Type I restriction enzyme inhibitor, Ocr. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001465. [PMID: 39042422 PMCID: PMC11317969 DOI: 10.1099/mic.0.001465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 05/21/2024] [Indexed: 07/24/2024]
Abstract
DNA manipulation is an essential tool in molecular microbiology research that is dependent on the ability of bacteria to take up and preserve foreign DNA by horizontal gene transfer. This process can be significantly impaired by the activity of bacterial restriction modification systems; bacterial operons comprising paired enzymatic activities that protectively methylate host DNA, while cleaving incoming unmodified foreign DNA. Ocr is a phage-encoded protein that inhibits Type I restriction modification systems, the addition of which significantly improves bacterial transformation efficiency. We recently established an improved and highly efficient transformation protocol for the important human pathogen group A Streptococcus using commercially available recombinant Ocr protein, manufacture of which has since been discontinued. In order to ensure the continued availability of Ocr protein within the research community, we have generated tools and methods for in-house Ocr production and validated the activity of the purified recombinant protein.
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Affiliation(s)
- Joana Alves
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Scotland, EH25 9RG, UK
| | - Inga Dry
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Scotland, EH25 9RG, UK
| | - John H. White
- EaStCHEM School of Chemistry, University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3FJ, UK
| | - David T.F. Dryden
- Department of Biosciences, University of Durham, South Road, DH1 3LE, UK
| | - Nicola N. Lynskey
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Scotland, EH25 9RG, UK
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3
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Wang Y, Ge F, Liu J, Hu W, Liu G, Deng Z, He X. The binding affinity-dependent inhibition of cell growth and viability by DNA sulfur-binding domains. Mol Microbiol 2024; 121:971-983. [PMID: 38480679 DOI: 10.1111/mmi.15249] [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: 01/31/2024] [Revised: 03/01/2024] [Accepted: 03/02/2024] [Indexed: 05/16/2024]
Abstract
Increasing evidence suggests that DNA phosphorothioate (PT) modification serves several purposes in the bacterial host, and some restriction enzymes specifically target PT-DNA. PT-dependent restriction enzymes (PDREs) bind PT-DNA through their DNA sulfur binding domain (SBD) with dissociation constants (KD) of 5 nM~1 μM. Here, we report that SprMcrA, a PDRE, failed to dissociate from PT-DNA after cleavage due to high binding affinity, resulting in low DNA cleavage efficiency. Expression of SBDs in Escherichia coli cells with PT modification induced a drastic loss of cell viability at 25°C when both DNA strands of a PT site were bound, with one SBD on each DNA strand. However, at this temperature, SBD binding to only one PT DNA strand elicited a severe growth lag rather than lethality. This cell growth inhibition phenotype was alleviated by raising the growth temperature. An in vitro assay mimicking DNA replication and RNA transcription demonstrated that the bound SBD hindered the synthesis of new DNA and RNA when using PT-DNA as the template. Our findings suggest that DNA modification-targeting proteins might regulate cellular processes involved in DNA metabolism in addition to being components of restriction-modification systems and epigenetic readers.
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Affiliation(s)
- Yuli Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Fulin Ge
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Jinling Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Wenyue Hu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Xinyi He
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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4
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Zhang H, Liu L, Li M. Mini-review of DNA Methylation Detection Techniques and Their Potential Applications in Disease Diagnosis, Prognosis, and Treatment. ACS Sens 2024; 9:1089-1103. [PMID: 38365574 DOI: 10.1021/acssensors.3c02328] [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: 02/18/2024]
Abstract
DNA methylation is the dominant epigenetic mechanism for regulating gene expression in mammals, playing crucial roles in development, differentiation, and tissue homeostasis. Aberrations in DNA methylation are closely associated with the potential onset of various diseases. Consequently, numerous DNA methylation detection techniques have been successively developed. These methods not only facilitate the exploration of disease mechanisms but also hold significant promise for the development of diagnostic and prognostic strategies. In this Perspective, we present a comprehensive overview of commonly employed DNA methylation detection techniques as well as biosensing based on their underlying analytical techniques. For its medical applications, we begin by examining the pathogenesis of different diseases and then proceed to discuss how relevant technologies are applied in the context of these specific medical conditions. Additionally, we briefly discuss the current limitations of these techniques and highlight future challenges in advancing methylation detection and analysis methodologies.
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Affiliation(s)
- Huaming Zhang
- Institute for Advanced Materials, School of Materials Science and Engineering, Jiangsu University, Zhenjiang 212013, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Liu
- Institute for Advanced Materials, School of Materials Science and Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Min Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
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5
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Ghadirian N, Morgan RD, Horton NC. DNA Sequence Control of Enzyme Filamentation and Activation of the SgrAI Endonuclease. Biochemistry 2024; 63:326-338. [PMID: 38207281 DOI: 10.1021/acs.biochem.3c00313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Enzyme polymerization (also known as filamentation) has emerged as a new layer of enzyme regulation. SgrAI is a sequence-dependent DNA endonuclease that forms polymeric filaments with enhanced DNA cleavage activity as well as altered DNA sequence specificity. To better understand this unusual regulatory mechanism, full global kinetic modeling of the reaction pathway, including the enzyme filamentation steps, has been undertaken. Prior work with the primary DNA recognition sequence cleaved by SgrAI has shown how the kinetic rate constants of each reaction step are tuned to maximize activation and DNA cleavage while minimizing the extent of DNA cleavage to the host genome. In the current work, we expand on our prior study by now including DNA cleavage of a secondary recognition sequence, to understand how the sequence of the bound DNA modulates filamentation and activation of SgrAI. The work shows that an allosteric equilibrium between low and high activity states is modulated by the sequence of bound DNA, with primary sequences more prone to activation and filament formation, while SgrAI bound to secondary recognition sequences favor the low (and nonfilamenting) state by up to 40-fold. In addition, the degree of methylation of secondary sequences in the host organism, Streptomyces griseus, is now reported for the first time and shows that as predicted, these sequences are left unprotected from the SgrAI endonuclease making sequence specificity critical in this unusual filament-forming enzyme.
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Affiliation(s)
- Niloofar Ghadirian
- Department of Chemistry & Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Richard D Morgan
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, United States
| | - Nancy C Horton
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, United States
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Nucifora D, Mehta ND, Giguere DJ, Karas BJ. An Expanded Genetic Toolbox to Accelerate the Creation of Acholeplasma laidlawii Driven by Synthetic Genomes. ACS Synth Biol 2024; 13:45-53. [PMID: 38113213 PMCID: PMC10805103 DOI: 10.1021/acssynbio.3c00399] [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: 06/30/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/21/2023]
Abstract
We have developed genetic tools for the atypical bacterium Acholeplasma laidlawii. A. laidlawii is a member of the class Mollicutes, which lacks cell walls, has small genomes, and has limited metabolic capabilities, requiring many metabolites from their hosts. Several of these traits have facilitated the development of genome transplantation for some Mollicutes, consequently enabling the generation of synthetic cells. Here, we propose the development of genome transplantation for A. laidlawii. We first investigated a donor-recipient relationship between two strains, PG-8A and PG-8195, through whole-genome sequencing. We then created multihost shuttle plasmids and used them to optimize an electroporation protocol. We also evolved a superior strain for DNA uptake via electroporation. We created a PG-8A donor strain with a Tn5 transposon carrying a tetracycline resistance gene. These tools will enhance Acholeplasma research and accelerate the effort toward creating A. laidlawii strains with synthetic genomes.
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Affiliation(s)
- Daniel
P. Nucifora
- Department
of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Nidhi D. Mehta
- Department
of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Daniel J. Giguere
- Department
of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Bogumil J. Karas
- Department
of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
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Alonso-del Valle A, Toribio-Celestino L, Quirant A, Pi CT, DelaFuente J, Canton R, Rocha EPC, Ubeda C, Peña-Miller R, San Millan A. Antimicrobial resistance level and conjugation permissiveness shape plasmid distribution in clinical enterobacteria. Proc Natl Acad Sci U S A 2023; 120:e2314135120. [PMID: 38096417 PMCID: PMC10741383 DOI: 10.1073/pnas.2314135120] [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: 08/27/2023] [Accepted: 10/26/2023] [Indexed: 12/18/2023] Open
Abstract
Conjugative plasmids play a key role in the dissemination of antimicrobial resistance (AMR) genes across bacterial pathogens. AMR plasmids are widespread in clinical settings, but their distribution is not random, and certain associations between plasmids and bacterial clones are particularly successful. For example, the globally spread carbapenem resistance plasmid pOXA-48 can use a wide range of enterobacterial species as hosts, but it is usually associated with a small number of specific Klebsiella pneumoniae clones. These successful associations represent an important threat for hospitalized patients. However, knowledge remains limited about the factors determining AMR plasmid distribution in clinically relevant bacteria. Here, we combined in vitro and in vivo experimental approaches to analyze pOXA-48-associated AMR levels and conjugation dynamics in a collection of wild-type enterobacterial strains isolated from hospitalized patients. Our results revealed significant variability in these traits across different bacterial hosts, with Klebsiella spp. strains showing higher pOXA-48-mediated AMR and conjugation frequencies than Escherichia coli strains. Using experimentally determined parameters, we developed a simple mathematical model to interrogate the contribution of AMR levels and conjugation permissiveness to plasmid distribution in bacterial communities. The simulations revealed that a small subset of clones, combining high AMR levels and conjugation permissiveness, play a critical role in stabilizing the plasmid in different polyclonal microbial communities. These results help to explain the preferential association of plasmid pOXA-48 with K. pneumoniae clones in clinical settings. More generally, our study reveals that species- and strain-specific variability in plasmid-associated phenotypes shape AMR evolution in clinically relevant bacterial communities.
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Affiliation(s)
- Aida Alonso-del Valle
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, Madrid28049, Spain
| | - Laura Toribio-Celestino
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, Madrid28049, Spain
| | - Anna Quirant
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Valencia46020, Spain
| | - Carles Tardio Pi
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca62209, México
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Unidad Académica Yucatán, Universidad Nacional Autónoma de México, Yucatán04510, México
| | - Javier DelaFuente
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, Madrid28049, Spain
| | - Rafael Canton
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-Instituto Ramon y Cajal de Investigacion Sanitaria, Madrid28034, Spain
- Centro de Investigación Biológica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid28029, Spain
| | - Eduardo P. C. Rocha
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris75015, France
| | - Carles Ubeda
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Valencia46020, Spain
- Centro de Investigación Biológica en Red de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid28029, Spain
| | - Rafael Peña-Miller
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca62209, México
| | - Alvaro San Millan
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, Madrid28049, Spain
- Centro de Investigación Biológica en Red de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid28029, Spain
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Zhou K, Wong TY, Long L, Anantharaman K, Zhang W, Wong WC, Zhang R, Qian PY. Genomic and transcriptomic insights into complex virus-prokaryote interactions in marine biofilms. THE ISME JOURNAL 2023; 17:2303-2312. [PMID: 37875603 PMCID: PMC10689801 DOI: 10.1038/s41396-023-01546-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 10/26/2023]
Abstract
Marine biofilms are complex communities of microorganisms that play a crucial ecological role in oceans. Although prokaryotes are the dominant members of these biofilms, little is known about their interactions with viruses. By analysing publicly available and newly sequenced metagenomic data, we identified 2446 virus-prokaryote connections in 84 marine biofilms. Most of these connections were between the bacteriophages in the Uroviricota phylum and the bacteria of Proteobacteria, Cyanobacteria and Bacteroidota. The network of virus-host pairs is complex; a single virus can infect multiple prokaryotic populations or a single prokaryote is susceptible to several viral populations. Analysis of genomes of paired prokaryotes and viruses revealed the presence of 425 putative auxiliary metabolic genes (AMGs), 239 viral genes related to restriction-modification (RM) systems and 38,538 prokaryotic anti-viral defence-related genes involved in 15 defence systems. Transcriptomic evidence from newly established biofilms revealed the expression of viral genes, including AMGs and RM, and prokaryotic defence systems, indicating the active interplay between viruses and prokaryotes. A comparison between biofilms and seawater showed that biofilm prokaryotes have more abundant defence genes than seawater prokaryotes, and the defence gene composition differs between biofilms and the surrounding seawater. Overall, our study unveiled active viruses in natural biofilms and their complex interplay with prokaryotes, which may result in the blooming of defence strategists in biofilms. The detachment of bloomed defence strategists may reduce the infectivity of viruses in seawater and result in the emergence of a novel role of marine biofilms.
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Affiliation(s)
- Kun Zhou
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Tin Yan Wong
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Lexin Long
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | | | - Weipeng Zhang
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Wai Chuen Wong
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
| | - Pei-Yuan Qian
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
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Van Hofwegen DJ, Hovde CJ, Minnich SA. Comparison of Yersinia enterocolitica DNA Methylation at Ambient and Host Temperatures. EPIGENOMES 2023; 7:30. [PMID: 38131902 PMCID: PMC10742451 DOI: 10.3390/epigenomes7040030] [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: 09/07/2023] [Revised: 11/13/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
Pathogenic bacteria recognize environmental cues to vary gene expression for host adaptation. Moving from ambient to host temperature, Yersinia enterocolitica responds by immediately repressing flagella synthesis and inducing the virulence plasmid (pYV)-encoded type III secretion system. In contrast, shifting from host to ambient temperature requires 2.5 generations to restore motility, suggesting a link to the cell cycle. We hypothesized that differential DNA methylation contributes to temperature-regulated gene expression. We tested this hypothesis by comparing single-molecule real-time (SMRT) sequencing of Y. enterocolitica DNA from cells growing exponentially at 22 °C and 37 °C. The inter-pulse duration ratio rather than the traditional QV scoring was the kinetic metric to compare DNA from cells grown at each temperature. All 565 YenI restriction sites were fully methylated at both temperatures. Among the 27,118 DNA adenine methylase (Dam) sites, 42 had differential methylation patterns, while 17 remained unmethylated regardless of the temperature. A subset of the differentially methylated Dam sites localized to promoter regions of predicted regulatory genes including LysR-type and PadR-like transcriptional regulators and a cyclic-di-GMP phosphodiesterase. The unmethylated Dam sites localized with a bias to the replication terminus, suggesting they were protected from Dam methylase. No cytosine methylation was detected at Dcm sites.
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Affiliation(s)
| | | | - Scott A. Minnich
- Department of Animal Veterinary and Food Science, University of Idaho, Moscow, ID 83843, USA; (D.J.V.H.); (C.J.H.)
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10
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Pisciotta A, Sampino AM, Presentato A, Galardini M, Manteca A, Alduina R. The DNA cytosine methylome revealed two methylation motifs in the upstream regions of genes related to morphological and physiological differentiation in Streptomyces coelicolor A(3)2 M145. Sci Rep 2023; 13:7038. [PMID: 37120673 PMCID: PMC10148868 DOI: 10.1038/s41598-023-34075-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023] Open
Abstract
DNA methylation is an epigenetic modification detected in both prokaryotic and eukaryotic genomic DNAs. In bacteria, the importance of 5-methylcytosine (m5C) in gene expression has been less investigated than in eukaryotic systems. Through dot-blot analysis employing m5C antibodies against chromosomal DNA, we have previously demonstrated that m5C influences the differentiation of Streptomyces coelicolor A(3)2 M145 in solid sporulating and liquid non-sporulating complex media. Here, we mapped the methylated cytosines of the M145 strain growing in the defined Maltose Glutamate (MG) liquid medium. Sequencing of the M145 genome after bisulfite treatment (BS-sequencing) evidenced 3360 methylated cytosines and the two methylation motifs, GGCmCGG and GCCmCG, in the upstream regions of 321 genes. Besides, the role of cytosine methylation was investigated using the hypo-methylating agent 5'-aza-2'-deoxycytidine (5-aza-dC) in S. coelicolor cultures, demonstrating that m5C affects both growth and antibiotic biosynthesis. Finally, quantitative reverse-transcription polymerase-chain-reaction (RT-qPCR) analysis of genes containing the methylation motifs in the upstream regions showed that 5-aza-dC treatment influenced their transcriptional levels and those of the regulatory genes for two antibiotics. To the best of our knowledge, this is the first study that reports the cytosine methylome of S. coelicolor M145, supporting the crucial role ascribed to cytosine methylation in controlling bacterial gene expression.
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Affiliation(s)
- Annalisa Pisciotta
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128, Palermo, Italy
| | - Alessia Maria Sampino
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128, Palermo, Italy
| | - Alessandro Presentato
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128, Palermo, Italy
| | - Marco Galardini
- Department of Biology, University of Florence, Florence, Italy
- EMBL-EBI, Wellcome Genome Campus, Cambridge, UK
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture Between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Angel Manteca
- Área de Microbiología, Departamento de Biología Funcional, IUOPA and ISPA, Facultad de Medicina, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Rosa Alduina
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128, Palermo, Italy.
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11
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Mani I, Singh V. Applications of bioinformatics in epigenetics. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 198:1-13. [PMID: 37225316 DOI: 10.1016/bs.pmbts.2023.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Epigenetic modifications such as DNA methylation, post-translational chromatin modifications and non-coding RNA-mediated mechanisms are responsible for epigenetic inheritance. Change in gene expression due to these epigenetic modifications are responsible for new traits in different organisms leading to various diseases including cancer, diabetic kidney disease (DKD), diabetic nephropathy (DN) and renal fibrosis. Bioinformatics is an effective approach for epigenomic profiling. These epigenomic data can be analyzed by a large number of bioinformatics tools and software. Many databases are available online, which comprises huge amount of information regarding these modifications. Recent methodologies include many sequencing and analytical techniques to extrapolate different types of epigenetic data. This data can be used to design drugs against diseases linked to epigenetic modifications. This chapter briefly highlights different epigenetics databases (MethDB, REBASE, Pubmeth, MethPrimerDB, Histone Database, ChromDB, MeInfoText database, EpimiR, Methylome DB, and dbHiMo), and tools (compEpiTools, CpGProD, MethBlAST, EpiExplorer, and BiQ analyzer), which are being utilized to retrieve the data and mechanistically analysis of epigenetics modifications.
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Affiliation(s)
- Indra Mani
- Department of Microbiology, Gargi College, University of Delhi, New Delhi, India.
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
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12
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Luo L, Ma X, Guo R, Jiang T, Wang T, Shao H, He H, Wang H, Liang Y, McMinn A, Guo C, Wang M. Characterization and genomic analysis of a novel Synechococcus phage S-H9-2 belonging to Bristolvirus genus isolated from the Yellow Sea. Virus Res 2023; 328:199072. [PMID: 36781075 DOI: 10.1016/j.virusres.2023.199072] [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: 07/30/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023]
Abstract
Cyanophages are known to influence the population dynamics and community structure of cyanobacteria and thus play an important role in biogeochemical cycles in aquatic ecosystems. In this study, a novel Synechococcus phage S-H9-2 infecting Synechococcus sp. WH 8102 was isolated from the coastal water of the Yellow Sea. Synechococcus phage S-H9-2 contains a 187,320 bp genome of double-stranded DNA with a G + C content of 40.3%, 202 potential open reading frames (ORFs), and 15 tRNAs. Phylogenetic analysis and nucleotide-based intergenomic similarity suggest that Synechococcus phage S-H9-2 belongs to the Bristolvirus genus under the family Kyanoviridae. Homologs of the S-H9-2 open reading frame can be found in a variety of marine environments, as shown by the results of mapping the genome sequence of S-H9-2 to the Global Ocean Viromes 2.0 dataset. The presence of auxiliary metabolic genes (AMGs) related to photosynthesis, carbon metabolism, and phosphorus assimilation, as well as phylogenetic relationships based on complete genome sequences, reflect the mechanism of phage-host interaction and host-specific strategies for adaptation to environmental conditions. This study enriches the current genomic database of cyanophage and contributed to our understanding of the virus-host interactions and their adaption to the environment.
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Affiliation(s)
- Lin Luo
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Xiaohong Ma
- Department of Pediatrics, Qingdao Municipal Hospital, Qingdao266011, China
| | - Ruizhe Guo
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Tong Jiang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Tiancong Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Hongbing Shao
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; UMT-OUC Joint Centre for Marine Studies, Qingdao 266003, China
| | - Hui He
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; UMT-OUC Joint Centre for Marine Studies, Qingdao 266003, China
| | - Hualong Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; UMT-OUC Joint Centre for Marine Studies, Qingdao 266003, China
| | - Yantao Liang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; UMT-OUC Joint Centre for Marine Studies, Qingdao 266003, China
| | - Andrew McMinn
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS 7001, SA
| | - Cui Guo
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; UMT-OUC Joint Centre for Marine Studies, Qingdao 266003, China.
| | - Min Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; UMT-OUC Joint Centre for Marine Studies, Qingdao 266003, China; The Affiliated Hospital of Qingdao University, Qingdao 266000, China.
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13
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Nishimura M, Tanaka T, Murata S, Miyabe A, Ishige T, Kawasaki K, Yokoyama M, Hashimoto N, Yamagata K, Nagano H, Tojo-Nishimura S, Matsushita K. Extension of bacterial rDNA sequencing for simultaneous methylation detection and its application in microflora analysis. Sci Rep 2023; 13:5731. [PMID: 37029177 PMCID: PMC10082018 DOI: 10.1038/s41598-023-28706-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/23/2023] [Indexed: 04/09/2023] Open
Abstract
Although polymerase chain reaction (PCR) amplification and sequencing of the bacterial 16S rDNA region has numerous scientific applications, it does not provide DNA methylation information. Herein, we propose a simple extension for bisulfite sequencing to investigate 5-methylcytosine residues in the bacterial 16S rDNA region from clinical isolates or flora. Multiple displacement amplification without DNA denaturation was used to preferentially pre-amplify single-stranded bacterial DNA after bisulfite conversion. Following the pre-amplification, the 16S rDNA region was analyzed using nested bisulfite PCR and sequencing, enabling the simultaneous identification of DNA methylation status and sequence data. We used this approach (termed sm16S rDNA PCR/sequencing) to identify novel methylation sites and a methyltransferase (M. MmnI) in Morganella morganii and different methylation motifs among Enterococcus faecalis strains from small volumes of clinical specimens. Further, our analysis suggested that M. MmnI may be correlated to erythromycin resistance. Thus, sm16S rDNA PCR/sequencing is a useful extension method for analyzing the DNA methylation of 16S rDNA regions in a microflora, providing additional information not provided by conventional PCR. Given the relationship between DNA methylation status and drug resistance in bacteria, we believe this technique can be effectively applied in clinical sample testing.
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Affiliation(s)
- Motoi Nishimura
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, Chiba, Japan.
| | - Tomoaki Tanaka
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
- Research Institute of Disaster Medicine, Chiba University, Chiba, Japan
| | - Syota Murata
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, Chiba, Japan
| | - Akiko Miyabe
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, Chiba, Japan
| | - Takayuki Ishige
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, Chiba, Japan
| | - Kenji Kawasaki
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, Chiba, Japan
| | - Masataka Yokoyama
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Naoko Hashimoto
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
- Research Institute of Disaster Medicine, Chiba University, Chiba, Japan
| | - Kazuyuki Yamagata
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hidekazu Nagano
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Satomi Tojo-Nishimura
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kazuyuki Matsushita
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, Chiba, Japan
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14
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Breckell GL, Silander OK. Growth condition-dependent differences in methylation imply transiently differentiated DNA methylation states in Escherichia coli. G3 (BETHESDA, MD.) 2022; 13:6858946. [PMID: 36454087 PMCID: PMC9911048 DOI: 10.1093/g3journal/jkac310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 09/14/2022] [Accepted: 09/28/2022] [Indexed: 12/05/2022]
Abstract
DNA methylation in bacteria frequently serves as a simple immune system, allowing recognition of DNA from foreign sources, such as phages or selfish genetic elements. However, DNA methylation also affects other cell phenotypes in a heritable manner (i.e. epigenetically). While there are several examples of methylation affecting transcription in an epigenetic manner in highly localized contexts, it is not well-established how frequently methylation serves a more general epigenetic function over larger genomic scales. To address this question, here we use Oxford Nanopore sequencing to profile DNA modification marks in three natural isolates of Escherichia coli. We first identify the DNA sequence motifs targeted by the methyltransferases in each strain. We then quantify the frequency of methylation at each of these motifs across the entire genome in different growth conditions. We find that motifs in specific regions of the genome consistently exhibit high or low levels of methylation. Furthermore, we show that there are replicable and consistent differences in methylated regions across different growth conditions. This suggests that during growth, E. coli transiently differentiate into distinct methylation states that depend on the growth state, raising the possibility that measuring DNA methylation alone can be used to infer bacterial growth states without additional information such as transcriptome or proteome data. These results show the utility of using Oxford Nanopore sequencing as an economic means to infer DNA methylation status. They also provide new insights into the dynamics of methylation during bacterial growth and provide evidence of differentiated cell states, a transient analog to what is observed in the differentiation of cell types in multicellular organisms.
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Affiliation(s)
- Georgia L Breckell
- Corresponding author: School of Natural and Sciences, Massey University, Auckland 0745, New Zealand. ; Corresponding author: School of Natural and Sciences, Massey University, Auckland 0745, New Zealand. Present address: Ministry for Primary Industries, Auckland 2022, New Zealand
| | - Olin K Silander
- Corresponding author: School of Natural and Sciences, Massey University, Auckland 0745, New Zealand. ; Corresponding author: School of Natural and Sciences, Massey University, Auckland 0745, New Zealand. Present address: Ministry for Primary Industries, Auckland 2022, New Zealand
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15
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DNA Methyltransferase Regulates Nitric Oxide Homeostasis and Virulence in a Chronically Adapted Pseudomonas aeruginosa Strain. mSystems 2022; 7:e0043422. [PMID: 36106744 PMCID: PMC9600465 DOI: 10.1128/msystems.00434-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Opportunistic pathogens such as Pseudomonas aeruginosa adapt their genomes rapidly during chronic infections. Understanding their epigenetic regulation may provide biomarkers for diagnosis and reveal novel regulatory mechanisms. We performed single-molecule real-time sequencing (SMRT-seq) to characterize the methylome of a chronically adapted P. aeruginosa clinical strain, TBCF10839. Two N6-methyladenine (6mA) methylation recognition motifs (RCCANNNNNNNTGAR and TRGANNNNNNTGC [modification sites are in bold]) were identified and predicted as new type I methylation sites using REBASE analysis. We confirmed that the motif TRGANNNNNNTGC was methylated by the methyltransferase (MTase) M.PaeTBCFII, according to methylation sensitivity assays in vivo and vitro. Transcriptomic analysis showed that a ΔpaeTBCFIIM knockout mutant significantly downregulated nitric oxide reductase (NOR) regulation and expression of coding genes such as nosR and norB, which contain methylated motifs in their promoters or coding regions. The ΔpaeTBCFIIM strain exhibited reduced intercellular survival capacity in NO-producing RAW264.7 macrophages and attenuated virulence in a Galleria mellonella infection model; the complemented strain recovered these defective phenotypes. Further phylogenetic analysis demonstrated that homologs of M.PaeTBCFII occur frequently in P. aeruginosa as well as other bacterial species. Our work therefore provided new insights into the relationship between DNA methylation, NO detoxification, and bacterial virulence, laying a foundation for further exploring the molecular mechanism of DNA methyltransferase in regulating the pathogenicity of P. aeruginosa. IMPORTANCE Pseudomonas aeruginosa is an opportunistic pathogen which causes acute and chronic infections that are difficult to treat. Comparative genomic analysis has showed broad genome diversity among P. aeruginosa clinical strains and revealed their different regulatory traits compared to the laboratory strains. While current investigation of the epigenetics of P. aeruginosa is still lacking, understanding epigenetic regulation may provide biomarkers for diagnosis and facilitate development of novel therapies. Denitrification capability is critical for microbial versatility in response to different environmental stress conditions, including the bacterial infection process, where nitric oxide (NO) can be generated by phagocytic cells. The denitrification regulation mechanisms have been studied intensively at genetic and biochemical levels. However, there is very little evidence about the epigenetic regulation of bacterial denitrification mechanism. P. aeruginosa TBCF10839 is a chronically host-adapted strain isolated from a cystic fibrosis (CF) patient with special antiphagocytosis characteristics. Here, we investigated the regulatory effect of an orphan DNA MTase, M.PaeTBCFII, in P. aeruginosa TBCF10839. We demonstrated that the DNA MTase regulates the transcription of denitrification genes represented by NOR and affects antiphagocytic ability in bacteria. In silico analysis suggested that DNA methylation modification may enhance gene expression by affecting the binding of transacting factors such as DNR and RpoN. Our findings not only deepen the understanding of the role of DNA MTase in transcriptional regulation in P. aeruginosa but also provide a theoretical foundation for the in-depth study of the molecular mechanism of the epigenetic regulation on denitrification, virulence, and host-pathogen interaction.
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16
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Zhang X, Wang R, Xie X, Hu Y, Wang J, Sun Q, Feng X, Lin W, Tong S, Yan W, Wen H, Wang M, Zhai S, Sun C, Wang F, Niu Q, Kropinski A, Cui Y, Jiang X, Peng S, Li S, Tong Y. Mining bacterial NGS data vastly expands the complete genomes of temperate phages. NAR Genom Bioinform 2022; 4:lqac057. [PMID: 35937545 PMCID: PMC9346568 DOI: 10.1093/nargab/lqac057] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 06/13/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Temperate phages (active prophages induced from bacteria) help control pathogenicity, modulate community structure, and maintain gut homeostasis. Complete phage genome sequences are indispensable for understanding phage biology. Traditional plaque techniques are inapplicable to temperate phages due to their lysogenicity, curbing their identification and characterization. Existing bioinformatics tools for prophage prediction usually fail to detect accurate and complete temperate phage genomes. This study proposes a novel computational temperate phage detection method (TemPhD) mining both the integrated active prophages and their spontaneously induced forms (temperate phages) from next-generation sequencing raw data. Applying the method to the available dataset resulted in 192 326 complete temperate phage genomes with different host species, expanding the existing number of complete temperate phage genomes by more than 100-fold. The wet-lab experiments demonstrated that TemPhD can accurately determine the complete genome sequences of the temperate phages, with exact flanking sites, outperforming other state-of-the-art prophage prediction methods. Our analysis indicates that temperate phages are likely to function in the microbial evolution by (i) cross-infecting different bacterial host species; (ii) transferring antibiotic resistance and virulence genes and (iii) interacting with hosts through restriction-modification and CRISPR/anti-CRISPR systems. This work provides a comprehensively complete temperate phage genome database and relevant information, which can serve as a valuable resource for phage research.
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Affiliation(s)
- Xianglilan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing 100071, People's Republic of China
| | - Ruohan Wang
- Department of Computer Science, City University of Hong Kong , Hong Kong 999077, People's Republic of China
| | - Xiangcheng Xie
- College of Computer, National University of Defense Technology , Changsha 410073, People's Republic of China
| | - Yunjia Hu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, People's Republic of China
- School of Medicine, Shanghai University , Shanghai 200444, People's Republic of China
| | - Jianping Wang
- Department of Computer Science, City University of Hong Kong , Hong Kong 999077, People's Republic of China
| | - Qiang Sun
- The 964th Hospital , Changchun 130021, People's Republic of China
| | - Xikang Feng
- School of Software, Northwestern Polytechnical University , Xi’an 710072, People's Republic of China
| | - Wei Lin
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, People's Republic of China
| | - Shanwei Tong
- Bioinformatics Graduate Program, University of British Columbia , Vancouver BC V6T 1Z4, Canada
- Faculty of Health Sciences, Simon Fraser University , Burnaby , BC V5A 1S6, Canada
| | - Wei Yan
- National Library of Medicine, National Institutes of Health , Bethesda , MD 20894, USA
| | - Huiqi Wen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing 100071, People's Republic of China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, People's Republic of China
| | - Mengyao Wang
- Department of Computer Science, City University of Hong Kong , Hong Kong 999077, People's Republic of China
| | - Shixiang Zhai
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences , Yantai 264003, People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049, People's Republic of China
- Center for Ocean Mega-Science, Chinese Academy of Sciences , Qingdao 266071, People's Republic of China
| | - Cheng Sun
- School of Computer Science and Electronic Engineering, Hunan University , Changsha 410082, People's Republic of China
| | - Fangyi Wang
- Department of Statistics, the Ohio State University , Columbus, OH 43210, USA
| | - Qi Niu
- School of Computer Science and Electronic Engineering, Hunan University , Changsha 410082, People's Republic of China
| | - Andrew M Kropinski
- Departments of Food Science, and Pathobiology, University of Guelph , Guelph , ON N1G 2W1 , Canada
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing 100071, People's Republic of China
| | - Xiaofang Jiang
- National Library of Medicine, National Institutes of Health , Bethesda , MD 20894, USA
| | - Shaoliang Peng
- School of Computer Science and Electronic Engineering, Hunan University , Changsha 410082, People's Republic of China
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong , Hong Kong 999077, People's Republic of China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, People's Republic of China
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17
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Plant DNA Methylation Responds to Nutrient Stress. Genes (Basel) 2022; 13:genes13060992. [PMID: 35741754 PMCID: PMC9222553 DOI: 10.3390/genes13060992] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/23/2022] [Accepted: 05/30/2022] [Indexed: 12/16/2022] Open
Abstract
Nutrient stress as abiotic stress has become one of the important factors restricting crop yield and quality. DNA methylation is an essential epigenetic modification that can effectively regulate genome stability. Exploring DNA methylation responses to nutrient stress could lay the foundation for improving plant tolerance to nutrient stress. This article summarizes the plant DNA methylation patterns, the effects of nutrient stress, such as nitrogen, phosphorus, iron, zinc and sulfur stress, on plant DNA methylation and research techniques for plant DNA methylation, etc. Our discussion provides insight for further research on epigenetics response to nutrient stress in the future.
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18
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Zhanga S, Yao Y, Wang J, Liang Y. Identification of DNA N4-methylcytosine sites based on multi-source features and gradient boosting decision tree. Anal Biochem 2022; 652:114746. [DOI: 10.1016/j.ab.2022.114746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/13/2022] [Accepted: 05/18/2022] [Indexed: 11/16/2022]
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19
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Cohen H, Hoede C, Scharte F, Coluzzi C, Cohen E, Shomer I, Mallet L, Holbert S, Serre RF, Schiex T, Virlogeux-Payant I, Grassl GA, Hensel M, Chiapello H, Gal-Mor O. Intracellular Salmonella Paratyphi A is motile and differs in the expression of flagella-chemotaxis, SPI-1 and carbon utilization pathways in comparison to intracellular S. Typhimurium. PLoS Pathog 2022; 18:e1010425. [PMID: 35381053 PMCID: PMC9012535 DOI: 10.1371/journal.ppat.1010425] [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: 10/18/2021] [Revised: 04/15/2022] [Accepted: 03/09/2022] [Indexed: 12/21/2022] Open
Abstract
Although Salmonella Typhimurium (STM) and Salmonella Paratyphi A (SPA) belong to the same phylogenetic species, share large portions of their genome and express many common virulence factors, they differ vastly in their host specificity, the immune response they elicit, and the clinical manifestations they cause. In this work, we compared their intracellular transcriptomic architecture and cellular phenotypes during human epithelial cell infection. While transcription induction of many metal transport systems, purines, biotin, PhoPQ and SPI-2 regulons was similar in both intracellular SPA and STM, we identified 234 differentially expressed genes that showed distinct expression patterns in intracellular SPA vs. STM. Surprisingly, clear expression differences were found in SPI-1, motility and chemotaxis, and carbon (mainly citrate, galactonate and ethanolamine) utilization pathways, indicating that these pathways are regulated differently during their intracellular phase. Concurring, on the cellular level, we show that while the majority of STM are non-motile and reside within Salmonella-Containing Vacuoles (SCV), a significant proportion of intracellular SPA cells are motile and compartmentalized in the cytosol. Moreover, we found that the elevated expression of SPI-1 and motility genes by intracellular SPA results in increased invasiveness of SPA, following exit from host cells. These findings demonstrate unexpected flagellum-dependent intracellular motility of a typhoidal Salmonella serovar and intriguing differences in intracellular localization between typhoidal and non-typhoidal salmonellae. We propose that these differences facilitate new cycles of host cell infection by SPA and may contribute to the ability of SPA to disseminate beyond the intestinal lamina propria of the human host during enteric fever. Salmonella enterica is a ubiquitous, facultative intracellular animal and human pathogen. Although non-typhoidal Salmonella (NTS) and typhoidal Salmonella serovars belong to the same phylogenetic species and share many virulence factors, the disease they cause in humans is very different. While the underlying mechanisms for these differences are not fully understood, one possible reason expected to contribute to their different pathogenicity is a distinct expression pattern of genes involved in host-pathogen interactions. Here, we compared the global gene expression and intracellular phenotypes, during human epithelial cell infection of S. Paratyphi A (SPA) and S. Typhimurium (STM), as prototypical serovars of typhoidal and NTS, respectively. Interestingly, we identified different expression patterns in key virulence and metabolic pathways, cytosolic motility and increased reinvasion of SPA, following exit from infected cells. We hypothesize that these differences contribute to the invasive and systemic disease developed following SPA infection in humans.
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Affiliation(s)
- Helit Cohen
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | - Claire Hoede
- Université Fédérale de Toulouse, INRAE, BioinfOmics, UR MIAT, GenoToul Bioinformatics facility, 31326, Castanet-Tolosan, France
| | - Felix Scharte
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Charles Coluzzi
- INRAE, Université Paris-Saclay, MaIAGE, Jouy-en-Josas, France
| | - Emiliano Cohen
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | - Inna Shomer
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | - Ludovic Mallet
- Université Fédérale de Toulouse, INRAE, BioinfOmics, UR MIAT, GenoToul Bioinformatics facility, 31326, Castanet-Tolosan, France
| | | | | | - Thomas Schiex
- Université Fédérale de Toulouse, ANITI, INRAE, Toulouse, France
| | | | - Guntram A. Grassl
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School and German Center for Infection Research (DZIF), Hanover, Germany
| | - Michael Hensel
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
- CellNanOs–Center of Cellular Nanoanalytics Osnabrück, Universität Osnabrück, Osnabrück, Germany
- * E-mail: (MH); (HC); (OG-M)
| | - Hélène Chiapello
- Université Fédérale de Toulouse, INRAE, BioinfOmics, UR MIAT, GenoToul Bioinformatics facility, 31326, Castanet-Tolosan, France
- INRAE, Université Paris-Saclay, MaIAGE, Jouy-en-Josas, France
- * E-mail: (MH); (HC); (OG-M)
| | - Ohad Gal-Mor
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- * E-mail: (MH); (HC); (OG-M)
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20
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Alsheikh-Hussain AS, Ben Zakour NL, Forde BM, Silayeva O, Barnes AC, Beatson SA. A high-quality reference genome for the fish pathogen Streptococcus iniae. Microb Genom 2022; 8:000777. [PMID: 35229712 PMCID: PMC9176272 DOI: 10.1099/mgen.0.000777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fish mortality caused by Streptococcus iniae is a major economic problem in aquaculture in warm and temperate regions globally. There is also risk of zoonotic infection by S. iniae through handling of contaminated fish. In this study, we present the complete genome sequence of S. iniae strain QMA0248, isolated from farmed barramundi in South Australia. The 2.12 Mb genome of S. iniae QMA0248 carries a 32 kb prophage, a 12 kb genomic island and 92 discrete insertion sequence (IS) elements. These include nine novel IS types that belong mostly to the IS3 family. Comparative and phylogenetic analysis between S. iniae QMA0248 and publicly available complete S. iniae genomes revealed discrepancies that are probably due to misassembly in the genomes of isolates ISET0901 and ISNO. Long-range PCR confirmed five rRNA loci in the PacBio assembly of QMA0248, and, unlike S. iniae 89353, no tandemly repeated rRNA loci in the consensus genome. However, we found sequence read evidence that the tandem rRNA repeat existed within a subpopulation of the original QMA0248 culture. Subsequent nanopore sequencing revealed that the tandem rRNA repeat was the most prevalent genotype, suggesting that there is selective pressure to maintain fewer rRNA copies under uncertain laboratory conditions. Our study not only highlights assembly problems in existing genomes, but provides a high-quality reference genome for S. iniae QMA0248, including manually curated mobile genetic elements, that will assist future S. iniae comparative genomic and evolutionary studies.
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Affiliation(s)
- Areej S. Alsheikh-Hussain
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Nouri L. Ben Zakour
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
- The Westmead Institute for Medical Research and the University of Sydney, Sydney, New South Wales, Australia
| | - Brian M. Forde
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Oleksandra Silayeva
- School of Biological Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Andrew C. Barnes
- School of Biological Science, The University of Queensland, Brisbane, Queensland, Australia
- *Correspondence: Andrew C. Barnes,
| | - Scott A. Beatson
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
- *Correspondence: Scott A. Beatson,
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21
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Genomic Features and Pervasive Negative Selection in Rhodanobacter Strains Isolated from Nitrate and Heavy Metal Contaminated Aquifer. Microbiol Spectr 2022; 10:e0259121. [PMID: 35107332 PMCID: PMC8809349 DOI: 10.1128/spectrum.02591-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Rhodanobacter species dominate in the Oak Ridge Reservation (ORR) subsurface environments contaminated with acids, nitrate, metal radionuclides, and other heavy metals. To uncover the genomic features underlying adaptations to these mixed-waste environments and to guide genetic tool development, we sequenced the whole genomes of eight Rhodanobacter strains isolated from the ORR site. The genome sizes ranged from 3.9 to 4.2 Mb harboring 3,695 to 4,035 protein-coding genes and GC contents approximately 67%. Seven strains were classified as R. denitrificans and one strain, FW510-R12, as R. thiooxydans based on full length 16S rRNA sequences. According to gene annotation, the top two Cluster of Orthologous Groups (COGs) with high pan-genome expansion rates (Pan/Core gene ratio) were “replication, recombination and repair” and “defense mechanisms.” The denitrifying genes had high DNA homologies except the predicted protein structure variances in NosZ. In contrast, heavy metal resistance genes were diverse with between 7 to 34% of them were located in genomic islands, and these results suggested origins from horizontal gene transfer. Analysis of the methylation patterns in four strains revealed the unique 5mC methylation motifs. Most orthologs (78%) had ratios of nonsynonymous to synonymous substitutions (dN/dS) less than one when compared to the type strain 2APBS1, suggesting the prevalence of negative selection. Overall, the results provide evidence for the important roles of horizontal gene transfer and negative selection in genomic adaptation at the contaminated field site. The complex restriction-modification system genes and the unique methylation motifs in Rhodanobacter strains suggest the potential recalcitrance to genetic manipulation. IMPORTANCE Despite the dominance of Rhodanobacter species in the subsurface of the contaminated Oak Ridge Reservation (ORR) site, very little is known about the mechanisms underlying their adaptions to the various stressors present at ORR. Recently, multiple Rhodanobacter strains have been isolated from the ORR groundwater samples from several wells with varying geochemical properties. Using Illumina, PacBio, and Oxford Nanopore sequencing platforms, we obtained the whole genome sequences of eight Rhodanobacter strains. Comparison of the whole genomes demonstrated the genetic diversity, and analysis of the long nanopore reads revealed the heterogeneity of methylation patterns in strains isolated from the same well. Although all strains contained a complete set of denitrifying genes, the predicted tertiary structures of NosZ differed. The sequence comparison results demonstrate the important roles of horizontal gene transfer and negative selection in adaptation. In addition, these strains may be recalcitrant to genetic manipulation due to the complex restriction-modification systems and methylations.
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Tellgren-Roth C, Couturier M. Detecting DNA Methylations in the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius Using SMRT Sequencing. Methods Mol Biol 2022; 2516:39-50. [PMID: 35922620 DOI: 10.1007/978-1-0716-2413-5_3] [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
DNA methylations are one of the most well-known epigenetic modifications along with histone modifications and noncoding RNAs. They are found at specific sites along the DNA in all domains of life, with 5-mC and 6-mA/4-mC being well-characterized in eukaryotes and bacteria respectively, and they have not only been described as contributing to the structure of the double helix itself but also as regulators of DNA-based processes such as replication, transcription, and recombination. Different methods have been developed to accurately identify and/or map methylated motifs to decipher the involvement of DNA methylations in regulatory networks that affect the cellular state.Although DNA methylations have been detected along archaeal genomes, their involvement as regulators of DNA-based processes remains the least known. To highlight the importance of DNA methylations in the control of key cellular mechanisms and their dynamics in archaea cells, we have used single-molecule real-time (SMRT) sequencing. This sequencing technology allows the identification and direct mapping of the methylated motifs along the genome of an organism. In this chapter, we present a step-by-step protocol for detecting DNA methylations in the hyperthermophilic crenarchaeon Sulfolobus acidocaldarius using SMRT sequencing. This protocol can easily be adapted to other prokaryotes.
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Affiliation(s)
- Christian Tellgren-Roth
- Department of Immunology, Genetics and Pathology, National Genomics Infrastructure, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mohea Couturier
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.
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23
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Characterization of the Type I Restriction Modification System Broadly Conserved among Group A Streptococci. mSphere 2021; 6:e0079921. [PMID: 34787444 PMCID: PMC8597746 DOI: 10.1128/msphere.00799-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although prokaryotic DNA methylation investigations have long focused on immunity against exogenous DNA, it has been recently recognized that DNA methylation impacts gene expression and phase variation in Streptococcus pneumoniae and Streptococcus suis. A comprehensive analysis of DNA methylation is lacking for beta-hemolytic streptococci, and thus we sought to examine DNA methylation in the major human pathogen group A Streptococcus (GAS). Using a database of 224 GAS genomes encompassing 80 emm types, we found that nearly all GAS strains encode a type I restriction modification (RM) system that lacks the hsdS′ alleles responsible for impacting gene expression in S. pneumoniae and S. suis. The GAS type I system is located on the core chromosome, while sporadically present type II orphan methyltransferases were identified on prophages. By combining single-molecule real-time (SMRT) analyses of 10 distinct emm types along with phylogenomics of 224 strains, we were able to assign 13 methylation patterns to the GAS population. Inactivation of the type I RM system, occurring either naturally through phage insertion or through laboratory-induced gene deletion, abrogated DNA methylation detectable via either SMRT or MinION sequencing. Contrary to a previous report, inactivation of the type I system did not impact transcript levels of the gene (mga) encoding the key multigene activator protein (Mga) or Mga-regulated genes. Inactivation of the type I system significantly increased plasmid transformation rates. These data delineate the breadth of the core chromosomal type I RM system in the GAS population and clarify its role in immunity rather than impacting Mga regulon expression. IMPORTANCE The advent of whole-genome approaches capable of detecting DNA methylation has markedly expanded appreciation of the diverse roles of epigenetic modification in prokaryotic physiology. For example, recent studies have suggested that DNA methylation impacts gene expression in some streptococci. The data described herein are from the first systematic analysis of DNA methylation in a beta-hemolytic streptococcus and one of the few analyses to comprehensively characterize DNA methylation across hundreds of strains of the same bacterial species. We clarify that DNA methylation in group A Streptococcus (GAS) is primarily due to a type I restriction modification (RM) system present in the core genome and does not impact mga-regulated virulence gene expression, but does impact immunity against exogenous DNA. The identification of the DNA motifs recognized by each type I RM system may assist with optimizing methods for GAS genetic manipulation and help us understand how bacterial pathogens acquire exogenous DNA elements.
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24
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Cheng Y, Jiang Y, Ren Z, Fu Y, Xu C. Development of an in vivo methylation system for transformation of Ruminiclostridium cellulolyticum. J Appl Microbiol 2021; 132:1926-1935. [PMID: 34787948 DOI: 10.1111/jam.15367] [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: 05/23/2021] [Revised: 09/06/2021] [Accepted: 10/04/2021] [Indexed: 11/30/2022]
Abstract
AIMS Ruminiclostridium cellulolyticum, an anaerobic cellulolytic bacterium producing an efficient cellulolytic extracellular complex named cellulosome, is a promising host for biofuel production from lignocellulose. This study aims to develop a rapid transformation method for R. cellulolyticum avoiding its restriction system. METHODS AND RESULTS The CceI restriction system is a major barrier to introduction of foreign DNA into R. cellulolyticum cells. To improve the transformation efficiency of R. cellulolyticum, the gene encoding CceI methyltransferase (M.CceI) of R. cellulolyticum H10 was functionally expressed in Escherichia coli, resulting in an in vivo methylation system for transformation of R. cellulolyticum. The electrotransformation experiments of R. cellulolyticum H10 with the E. coli-Clostridium shuttle plasmid pMTC6 showed that the transformation efficiency reached up to 2.6 × 103 ±0.23 × 103 CFU per μg plasmid DNA. The results demonstrated that the system is able to confer the M.CceI-specific DNA methylation pattern to its resident plasmid, which makes the plasmid resistant to the CceI restriction and efficiently transferred into R. cellulolyticum. CONCLUSIONS In this study, we generated an in vivo methylation system of R. cellulolyticum, allowing interspecies DNA transfer and improving transformation efficiency. SIGNIFICANCE AND IMPACT OF THE STUDY This research result will greatly facilitate the metabolic engineering of R. cellulolyticum for biofuel production directly from cellulose.
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Affiliation(s)
- Ying Cheng
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, Shanxi Province, China
| | - Yuanyuan Jiang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, Shanxi Province, China
| | - Zhenxing Ren
- Institute of Applied Chemistry, Shanxi University, Taiyuan, Shanxi Province, China
| | - Yuejun Fu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, Shanxi Province, China
| | - Chenggang Xu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, Shanxi Province, China
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25
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Dimitriu T, Szczelkun MD, Westra ER. Evolutionary Ecology and Interplay of Prokaryotic Innate and Adaptive Immune Systems. Curr Biol 2021; 30:R1189-R1202. [PMID: 33022264 DOI: 10.1016/j.cub.2020.08.028] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Like many organisms, bacteria and archaea have both innate and adaptive immune systems to defend against infection by viruses and other parasites. Innate immunity most commonly relies on the endonuclease-mediated cleavage of any incoming DNA that lacks a specific epigenetic modification, through a system known as restriction-modification. CRISPR-Cas-mediated adaptive immunity relies on the insertion of short DNA sequences from parasite genomes into CRISPR arrays on the host genome to provide sequence-specific protection. The discovery of each of these systems has revolutionised our ability to carry out genetic manipulations, and, as a consequence, the enzymes involved have been characterised in exquisite detail. In comparison, much less is known about the importance of these two arms of the defence for the ecology and evolution of prokaryotes and their parasites. Here, we review our current ecological and evolutionary understanding of these systems in isolation, and discuss the need to study how innate and adaptive immune responses are integrated when they coexist in the same cell.
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Affiliation(s)
- Tatiana Dimitriu
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK.
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK.
| | - Edze R Westra
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK.
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26
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Wang N, Gao J, Liu Y, Wang Q, Zhuang X, Zhuang G. Realizing the role of N-acyl-homoserine lactone-mediated quorum sensing in nitrification and denitrification: A review. CHEMOSPHERE 2021; 274:129970. [PMID: 33979914 DOI: 10.1016/j.chemosphere.2021.129970] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Nitrification and denitrification are crucial processes in the nitrogen cycle, a vital microbially driven biogeochemical cycle. N-acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) is widespread in bacteria and plays a key role in their physiological status. Recently, there has been an increase in research into how the AHL-mediated QS system is involved in nitrification and denitrification. Consequentially, the AHL-mediated QS system has been considered a promising regulatory approach in nitrogen metabolism processes, with high potential for real-world applications. In this review, the universal presence of QS in nitrifiers and denitrifiers is summarized. Many microorganisms taking part in nitrification and denitrification harbor QS genes, and they may produce AHLs with different chain lengths. The phenotypes and processes affected by QS in real-world applications are also reviewed. In wastewater bioreactors, QS could affect nitrogen metabolism efficiency, granule aggregation, and biofilm formation. Furthermore, methods commonly used to identify the existence and functions of QS, including physiological tests, genetic manipulation and omics analyses are discussed.
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Affiliation(s)
- Na Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie Gao
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Ying Liu
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Qiuying Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuliang Zhuang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guoqiang Zhuang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
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27
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Wachter J, Martens C, Barbian K, Rego ROM, Rosa P. Epigenomic Landscape of Lyme Disease Spirochetes Reveals Novel Motifs. mBio 2021; 12:e0128821. [PMID: 34156261 PMCID: PMC8262957 DOI: 10.1128/mbio.01288-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 05/07/2021] [Indexed: 11/20/2022] Open
Abstract
Borrelia burgdorferi, the etiological agent of Lyme disease, persists in nature through an enzootic cycle consisting of a vertebrate host and an Ixodes tick vector. The sequence motifs modified by two well-characterized restriction/modification (R/M) loci of B. burgdorferi type strain B31 were recently described, but the methylation profiles of other Lyme disease Borrelia bacteria have not been characterized. Here, the methylomes of B. burgdorferi type strain B31 and 7 clonal derivatives, along with B. burgdorferi N40, B. burgdorferi 297, B. burgdorferi CA-11, B. afzelii PKo, B. afzelii BO23, and B. garinii PBr, were defined through PacBio single-molecule real-time (SMRT) sequencing. This analysis revealed 9 novel sequence motifs methylated by the plasmid-encoded restriction/modification enzymes of these Borrelia strains. Furthermore, while a previous analysis of B. burgdorferi B31 revealed an epigenetic impact of methylation on the global transcriptome, the current data contradict those findings; our analyses of wild-type B. burgdorferi B31 revealed no consistent differences in gene expression among isogenic derivatives lacking one or more restriction/modification enzymes. IMPORTANCE The principal causative agent of Lyme disease in humans in the United States is Borrelia burgdorferi, while B. burgdorferi, B. afzelii, and B. garinii, collectively members of the Borrelia burgdorferi sensu lato species complex, cause Lyme disease in Europe and Asia. Two plasmid-encoded restriction/modification systems have been shown to limit the genetic transformation of B. burgdorferi type strain B31 with foreign DNA, but little is known about the restriction/modification systems of other Lyme disease Borrelia bacteria. This paper describes the methylation motifs present on genomic DNAs of multiple B. burgdorferi, B. afzelii, and B. garinii strains. Contrary to a previous report, we did not find evidence for an epigenetic impact on gene expression by methylation. Knowledge of the motifs recognized and methylated by the restriction/modification enzymes of Lyme disease Borrelia will facilitate molecular genetic investigations of these important human pathogens. Additionally, the similar motifs methylated by orthologous restriction/modification systems of Lyme disease Borrelia bacteria and the presence of these motifs within recombinogenic loci suggest a biological role for these ubiquitous restriction/modification systems in horizontal gene transfer.
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Affiliation(s)
- Jenny Wachter
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Craig Martens
- Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Kent Barbian
- Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Ryan O. M. Rego
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Patricia Rosa
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
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Szewczuk M, Boguszewska K, Kaźmierczak-Barańska J, Karwowski BT. The Influence of 5' R and 5' S cdA and cdG on the Activity of BsmAI and SspI Restriction Enzymes. Molecules 2021; 26:molecules26123750. [PMID: 34205449 PMCID: PMC8234751 DOI: 10.3390/molecules26123750] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/11/2021] [Accepted: 06/15/2021] [Indexed: 01/03/2023] Open
Abstract
Restriction endonucleases (REs) are intra-bacterial scissors that are considered tools in the fight against foreign genetic material. SspI and BsmAI, examined in this study, cleave dsDNA at their site of recognition or within a short distance of it. Both enzymes are representatives of type II REs, which have played an extremely important role in research on the genetics of organisms and molecular biology. Therefore, the study of agents affecting their activity has become highly important. Ionizing radiation may damage basic cellular mechanisms by inducing lesions in the genome, with 5',8-cyclo-2'-deoxypurines (cdPus) as a model example. Since cdPus may become components of clustered DNA lesions (CDLs), which are unfavorable for DNA repair pathways, their impact on other cellular mechanisms is worthy of attention. This study investigated the influence of cdPus on the elements of the bacterial restriction-modification system. In this study, it was shown that cdPus present in DNA affect the activity of REs. SspI was blocked by any cdPu lesion present at the enzyme's recognition site. When lesions were placed near the recognition sequence, the SspI was inhibited up to 46%. Moreover, (5'S)-5',8-cyclo-2'-deoxyadenosine (ScdA) present in the oligonucleotide sequence lowered BsmAI activity more than (5'R)-5',8-cyclo-2'-deoxyadenosine (RcdA). Interestingly, in the case of 5',8-cyclo-2'-deoxyguanosine (cdG), both 5'S and 5'R diastereomers inhibited BsmAI activity (up to 55% more than cdA). The inhibition was weaker when cdG was present at the recognition site rather than the cleavage site.
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29
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Nutrient Loading and Viral Memory Drive Accumulation of Restriction Modification Systems in Bloom-Forming Cyanobacteria. mBio 2021; 12:e0087321. [PMID: 34060332 PMCID: PMC8262939 DOI: 10.1128/mbio.00873-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The mechanisms driving cyanobacterial harmful algal blooms (HABs) like those caused by Microcystis aeruginosa remain elusive, but improved defense against viral predation has been implicated for success in eutrophic environments. Our genus-level analyses of 139,023 genomes revealed that HAB-forming cyanobacteria carry vastly more restriction modification systems per genome (RMPG) than nearly all other prokaryotic genera, suggesting that viral defense is a cornerstone of their ecological success. In contrast, picocyanobacteria that numerically dominate nutrient-poor systems have the fewest RMPG within the phylum Cyanobacteria. We used classic resource competition models to explore the hypothesis that nutrient enrichments drive ecological selection for high RMPG due to increased host-phage contact rate. These classic models, agnostic to the mechanism of defense, explain how nutrient loading can select for increased RMPG but, importantly, fail to explain the extreme accumulation of these defense systems. However, extreme accumulation of RMPG can be achieved in a novel “memory” model that accounts for a unique activity of restriction modification systems: the accidental methylation of viral DNA by the methyltransferase. The methylated virus “remembers” the RM defenses of its former host and can evade these defenses if they are present in the next host. This viral memory leads to continual RM system devaluation; RMs accumulate extensively because the benefit of each addition is diminished. Our modeling leads to the hypothesis that nutrient loading and virion methylation drive the extreme accumulation of RMPG in HAB-forming cyanobacteria. Finally, our models suggest that hosts with different RMPG values can coexist when hosts have unique sets of RM systems.
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30
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Qu J, Cai Z, Liu Y, Duan X, Han S, Liu J, Zhu Y, Jiang Z, Zhang Y, Zhuo C, Liu Y, Liu Y, Liu L, Yang L. Persistent Bacterial Coinfection of a COVID-19 Patient Caused by a Genetically Adapted Pseudomonas aeruginosa Chronic Colonizer. Front Cell Infect Microbiol 2021; 11:641920. [PMID: 33816347 PMCID: PMC8010185 DOI: 10.3389/fcimb.2021.641920] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/08/2021] [Indexed: 12/20/2022] Open
Abstract
Pseudomonas aeruginosa is a biofilm-forming opportunistic pathogen which causes chronic infections in immunocompromised patients and leads to high mortality rate. It is identified as a common coinfecting pathogen in COVID-19 patients causing exacerbation of illness. In our hospital, P. aeruginosa is one of the top coinfecting bacteria identified among COVID-19 patients. We collected a strong biofilm-forming P. aeruginosa strain displaying small colony variant morphology from a severe COVID-19 patient. Genomic and transcriptomic sequencing analyses were performed with phenotypic validation to investigate its adaptation in SARS-CoV-2 infected environment. Genomic characterization predicted specific genomic islands highly associated with virulence, transcriptional regulation, and DNA restriction-modification systems. Epigenetic analysis revealed a specific N6-methyl adenine (m6A) methylating pattern including methylation of alginate, flagellar and quorum sensing associated genes. Differential gene expression analysis indicated that this isolate formed excessive biofilm by reducing flagellar formation (7.4 to 1,624.1 folds) and overproducing extracellular matrix components including CdrA (4.4 folds), alginate (5.2 to 29.1 folds) and Pel (4.8–5.5 folds). In summary, we demonstrated that P. aeuginosa clinical isolates with novel epigenetic markers could form excessive biofilm, which might enhance its antibiotic resistance and in vivo colonization in COVID-19 patients.
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Affiliation(s)
- Jiuxin Qu
- Department of Clinical Laboratory, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, National Clinical Research Center for Infectious Diseases, Shenzhen, China
| | - Zhao Cai
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Yumei Liu
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Xiangke Duan
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Shuhong Han
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Jihong Liu
- School of Medicine, Southern University of Science and Technology, Shenzhen, China.,Medical Research Center, Southern University of Science and Technology Hospital, Shenzhen, China
| | - Yuao Zhu
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Zhaofang Jiang
- Department of Clinical Laboratory, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, National Clinical Research Center for Infectious Diseases, Shenzhen, China
| | - Yingdan Zhang
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Chao Zhuo
- The State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yang Liu
- Medical Research Center, Southern University of Science and Technology Hospital, Shenzhen, China
| | - Yingxia Liu
- Department of Clinical Laboratory, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, National Clinical Research Center for Infectious Diseases, Shenzhen, China.,Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Lei Liu
- Department of Clinical Laboratory, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, National Clinical Research Center for Infectious Diseases, Shenzhen, China.,Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology, Shenzhen, China.,Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, China
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31
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Tarique M, Ahmad S, Malik A, Ahmad I, Saeed M, Almatroudi A, Qadah T, Murad MA, Mashraqi M, Alam Q, Al-Saleh Y. Novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) and Other Coronaviruses: A Genome-wide Comparative Annotation and Analysis. Mol Cell Biochem 2021; 476:2203-2217. [PMID: 33564990 PMCID: PMC7872828 DOI: 10.1007/s11010-020-04027-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/22/2020] [Indexed: 11/06/2022]
Abstract
Novel strain of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) causes mild to severe respiratory illness. The early symptoms may be fever, dry cough, sour throat, and difficulty in breathing which may lead to death in severe cases. Compared to previous outbreaks like SARS-CoV and Middle East Respiratory Syndrome (MERS), SARS-CoV2 disease (COVID-19) outbreak has been much distressing due to its high rate of infection but low infection fatality rate (IFR) with 1.4% around the world. World Health Organization (WHO) has declared (COVID-19) a pandemic on March 11, 2020. In the month of January 2020, the whole genome of SARS-CoV2 was sequenced which made work easy for researchers to develop diagnostic kits and to carry out drug repurposing to effectively alleviate the pandemic situation in the world. Now, it is important to understand why this virus has high rate of infectivity or is there any factor involved at the genome level which actually facilitates this virus infection globally? In this study, we have extensively analyzed the whole genomes of different coronaviruses infecting humans and animals in different geographical locations around the world. The main aim of the study is to identify the similarity and the mutational adaptation of the coronaviruses from different host and geographical locations to the SARS-CoV2 and provide a better strategy to understand the mutational rate for specific target-based drug designing. This study is focused to every annotation in a comparative manner which includes SNPs, repeat analysis with the different categorization of the short-sequence repeats and long-sequence repeats, different UTR’s, transcriptional factors, and the predicted matured peptides with the specific length and positions on the genomes. The extensive analysis on SNPs revealed that Wuhan SARS-CoV2 and Indian SARS-CoV2 are having only eight SNPs. Collectively, phylogenetic analysis, repeat analysis, and the polymorphism revealed the genomic conserveness within the SARS-CoV2 and few other coronaviruses with very less mutational chances and the huge distance and mutations from the few other species.
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Affiliation(s)
- Mohammed Tarique
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
| | - Shaban Ahmad
- Department of Computer Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Arshi Malik
- Department of Clinical Biochemistry, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Irfan Ahmad
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia.,Research Centre for Advanced Materials Science, King Khalid University, Abha, Saudi Arabia
| | - Mohd Saeed
- Department of Biology College of Sciences, University of Hail, Hail, Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, 51431, Saudi Arabia
| | - Talal Qadah
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80324, Postcode 21589, Jeddah, Saudi Arabia
| | - Manal Abdulaziz Murad
- Department Family Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mutaib Mashraqi
- Department of Clinical Laboratory Sciences, College of Applied Medical Science, Najran University, Najran, Saudi Arabia
| | - Qamre Alam
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, 11426, Saudi Arabia
| | - Yousef Al-Saleh
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, 22490, Saudi Arabia.,King Abdullah International Medical Research Center, Riyadh, 11481, Saudi Arabia.,Department of Medicine, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs, Riyadh, 14611, Saudi Arabia
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32
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Abstract
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a widely used technique in the global analysis of epigenetic DNA modifications. The high-resolution chromatographic separation along with sensitive MS detection permits the identification and quantification of deoxyribonucleosides with precision and reliability. Although there have been tremendous advances in LC and MS instrumentation in recent years, sample preparation has not experienced a similar rate of development and is often a bottleneck to chemical analysis. Here we present a protocol for identification and quantification of cytosine modifications that combines a robust and efficient method to generate single nucleosides from genomic DNA samples followed by direct LC-MS/MS analysis.
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Zhao X, Zheng H, Zhen J, Shu W, Yang S, Xu J, Song H, Ma Y. Multiplex genetic engineering improves endogenous expression of mesophilic α-amylase gene in a wild strain Bacillus amyloliquefaciens 205. Int J Biol Macromol 2020; 165:609-618. [PMID: 33010275 DOI: 10.1016/j.ijbiomac.2020.09.210] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 12/17/2022]
Abstract
A wild strain Bacillus amyloliquefaciens 205 was screened for its high activity of α-amylase. A mesophilic α-amylase encoding gene amyE-205 was revealed and analyzed by genome sequencing. In order to facilitate plasmid transformation to strain 205, an interspecific plasmid transformation method was improved with 5-13 times higher in transformants than that of electronic transformation. A series of CRISPR genome editing tools have been successfully constructed for gene knockout, transcript repression and activation in 205 genome. At this basis, sporulation related genes spo0A and spoIIAC were knockout and suppressed with CRISPR/Cas9 and CRISPR/dCas9 respectively. The double knockout strain 205spo- was eliminated sporulation with 22.8% increasing of α-amylase activity. The optimal binding site G8 for dCas9-ω has been confirmed in the transcript activation. When amyE-205 was over-expressed with high copy plasmid pUC980-2, its whole upstream sequences containing G8 were also cloned. Whereafter, dCas9-ω was used to activate amyE-205 expression both at genome and plasmid. The final engineered strain 205PG8spo- achieved 784.3% promotion on α-amylase activity than the starting strain 205. The novel genetic tool box containing an efficient interspecific transformation method and functional CRISPR systems, superadded the multiplex regulation strategies used in strain modification would be also applicative in many Bacillus species.
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Affiliation(s)
- Xingya Zhao
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Hongchen Zheng
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
| | - Jie Zhen
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Wenju Shu
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Shibin Yang
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jianyong Xu
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Hui Song
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
| | - Yanhe Ma
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
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34
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Matsumura I. Methylase-assisted subcloning for high throughput BioBrick assembly. PeerJ 2020; 8:e9841. [PMID: 32974095 PMCID: PMC7489255 DOI: 10.7717/peerj.9841] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/10/2020] [Indexed: 12/02/2022] Open
Abstract
The BioBrick standard makes possible iterated pairwise assembly of cloned parts without any depletion of unique restriction sites. Every part that conforms to the standard is compatible with every other part, thereby fostering a worldwide user community. The assembly methods, however, are labor intensive or inefficient compared to some newer ones so the standard may be falling out of favor. An easier way to assemble BioBricks is described herein. Plasmids encoding BioBrick parts are purified from Escherichia coli cells that express a foreign site-specific DNA methyltransferase, so that each is subsequently protected in vitro from the activity of a particular restriction endonuclease. Each plasmid is double-digested and all resulting restriction fragments are ligated together without gel purification. The ligation products are subsequently double-digested with another pair of restriction endonucleases so only the desired insert-recipient vector construct retains the capacity to transform E. coli. This 4R/2M BioBrick assembly protocol is more efficient and accurate than established workflows including 3A assembly. It is also much easier than gel purification to miniaturize, automate and perform more assembly reactions in parallel. As such, it should streamline DNA assembly for the existing community of BioBrick users, and possibly encourage others to join.
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Affiliation(s)
- Ichiro Matsumura
- Emory University School of Medicine, Department of Biochemistry, Atlanta, GA, United States of America
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35
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Saak CC, Dinh CB, Dutton RJ. Experimental approaches to tracking mobile genetic elements in microbial communities. FEMS Microbiol Rev 2020; 44:606-630. [PMID: 32672812 PMCID: PMC7476777 DOI: 10.1093/femsre/fuaa025] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022] Open
Abstract
Horizontal gene transfer is an important mechanism of microbial evolution and is often driven by the movement of mobile genetic elements between cells. Due to the fact that microbes live within communities, various mechanisms of horizontal gene transfer and types of mobile elements can co-occur. However, the ways in which horizontal gene transfer impacts and is impacted by communities containing diverse mobile elements has been challenging to address. Thus, the field would benefit from incorporating community-level information and novel approaches alongside existing methods. Emerging technologies for tracking mobile elements and assigning them to host organisms provide promise for understanding the web of potential DNA transfers in diverse microbial communities more comprehensively. Compared to existing experimental approaches, chromosome conformation capture and methylome analyses have the potential to simultaneously study various types of mobile elements and their associated hosts. We also briefly discuss how fermented food microbiomes, given their experimental tractability and moderate species complexity, make ideal models to which to apply the techniques discussed herein and how they can be used to address outstanding questions in the field of horizontal gene transfer in microbial communities.
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Affiliation(s)
- Christina C Saak
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Cong B Dinh
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Rachel J Dutton
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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36
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Gong Z, Wang G, Zeng J, Stojkoska A, Huang H, Xie J. Differential DNA methylomes of clinical MDR, XDR and XXDR Mycobacterium tuberculosis isolates revealed by using single-molecule real-time sequencing. J Drug Target 2020; 29:69-77. [PMID: 32672115 DOI: 10.1080/1061186x.2020.1797049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Post-replicative DNA methylation is essential for diverse biological processes in both eukaryotes and prokaryotes. Mycobacterium tuberculosis (M. tuberculosis), the causative agent of tuberculosis, remains one of the most formidable threats worldwide. Although DNA methylation of M. tuberculosis has been documented, little information is available for clinical drug-resistant M. tuberculosis. Single-molecule real-time (SMRT) sequencing was used to profile the core methylome of three clinical isolates, namely multidrug-resistant (MDR), extensively drug-resistant (XDR) and extremely drug-resistant (XXDR) strains. 3812, 6808 and 6041 DNA methylated sites were identified in MDR-MTB, XDR-MTB and XXDR-MTB genome, respectively. There are two types of methylated motifs, namely N6-methyladenine (m6A) and N4-methylcytosine (m4C). A novel widespread 6 mA methylation motif 5'-CACGCAG-3' was found in XDR-MTB and XXDR-MTB. The methylated genes are involved in multiple cellular processes, especially metabolic enzymes engaged in glucose metabolism, fatty acid and TCA cycle. Many methylated genes are involved in mycobacterial virulence, antibiotic resistance and tolerance. This provided a comprehensive list of methylated genes in drug-resistant clinical isolates and the basis for further functional elucidation.
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Affiliation(s)
- Zhen Gong
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
| | - Guirong Wang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Jie Zeng
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
| | - Andrea Stojkoska
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
| | - Hairong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Jianping Xie
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
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37
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Weissman JL, Stoltzfus A, Westra ER, Johnson PLF. Avoidance of Self during CRISPR Immunization. Trends Microbiol 2020; 28:543-553. [PMID: 32544441 DOI: 10.1016/j.tim.2020.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/05/2020] [Accepted: 02/25/2020] [Indexed: 02/07/2023]
Abstract
The battle between microbes and their viruses is ancient and ongoing. Clustered regularly interspaced short palindromic repeat (CRISPR) immunity, the first and, to date, only form of adaptive immunity found in prokaryotes, represents a flexible mechanism to recall past infections while also adapting to a changing pathogenic environment. Critical to the role of CRISPR as an adaptive immune mechanism is its capacity for self versus non-self recognition when acquiring novel immune memories. Yet, CRISPR systems vary widely in both how and to what degree they can distinguish foreign from self-derived genetic material. We document known and hypothesized mechanisms that bias the acquisition of immune memory towards non-self targets. We demonstrate that diversity is the rule, with many widespread but no universal mechanisms for self versus non-self recognition.
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Affiliation(s)
- Jake L Weissman
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Arlin Stoltzfus
- Office of Data and Informatics, Material Measurement Laboratory, NIST, Gaithersburg, MD 20899, USA; Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Edze R Westra
- Environment and Sustainability Institute, Centre for Ecology and Conservation, University of Exeter, Biosciences, Penryn, Cornwall, UK
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38
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Shi J, Shi Z, Dong Y, Wu F, Liu D. Responsive DNA-Based Supramolecular Hydrogels. ACS APPLIED BIO MATERIALS 2020; 3:2827-2837. [DOI: 10.1021/acsabm.0c00081] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jiezhong Shi
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ziwei Shi
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Yuanchen Dong
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Fen Wu
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China
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39
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Huang T, Xiong T, Peng Z, Xiao YS, Liu ZG, Hu M, Xie MY. Genomic analysis revealed adaptive mechanism to plant-related fermentation of Lactobacillus plantarum NCU116 and Lactobacillus spp. Genomics 2020; 112:703-711. [DOI: 10.1016/j.ygeno.2019.05.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/23/2019] [Accepted: 05/08/2019] [Indexed: 11/26/2022]
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40
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Weissman JL, Fagan WF, Johnson PLF. Linking high GC content to the repair of double strand breaks in prokaryotic genomes. PLoS Genet 2019; 15:e1008493. [PMID: 31703064 PMCID: PMC6867656 DOI: 10.1371/journal.pgen.1008493] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 11/20/2019] [Accepted: 10/25/2019] [Indexed: 01/21/2023] Open
Abstract
Genomic GC content varies widely among microbes for reasons unknown. While mutation bias partially explains this variation, prokaryotes near-universally have a higher GC content than predicted solely by this bias. Debate surrounds the relative importance of the remaining explanations of selection versus biased gene conversion favoring GC alleles. Some environments (e.g. soils) are associated with a high genomic GC content of their inhabitants, which implies that either high GC content is a selective adaptation to particular habitats, or that certain habitats favor increased rates of gene conversion. Here, we report a novel association between the presence of the non-homologous end joining DNA double-strand break repair pathway and GC content; this observation suggests that DNA damage may be a fundamental driver of GC content, leading in part to the many environmental patterns observed to-date. We discuss potential mechanisms accounting for the observed association, and provide preliminary evidence that sites experiencing higher rates of double-strand breaks are under selection for increased GC content relative to the genomic background. The overall nucleotide composition of an organism’s genome varies greatly between species. Previous work has identified certain environmental factors (e.g., oxygen availability) associated with the relative number of GC bases as opposed to AT bases in the genomes of species. Many of these environments that are associated with high GC content are also associated with relatively high rates of DNA damage. We show that organisms possessing the non-homologous end-joining DNA repair pathway, which is one mechanism to repair DNA double-strand breaks, have an elevated GC content relative to expectation. We also show that certain sites on the genome that are particularly susceptible to double strand breaks have an elevated GC content. This leads us to suggest that an important underlying driver of variability in nucleotide composition across environments is the rate of DNA damage (specifically double-strand breaks) to which an organism living in each environment is exposed.
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Affiliation(s)
- JL Weissman
- Department of Biology, University of Maryland - College Park, College Park, Maryland, United States of America
| | - William F. Fagan
- Department of Biology, University of Maryland - College Park, College Park, Maryland, United States of America
| | - Philip L. F. Johnson
- Department of Biology, University of Maryland - College Park, College Park, Maryland, United States of America
- * E-mail:
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41
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Mtimka S, Pillay P, Rashamuse K, Gildenhuys S, Tsekoa TL. Functional screening of a soil metagenome for DNA endonucleases by acquired resistance to bacteriophage infection. Mol Biol Rep 2019; 47:353-361. [PMID: 31643043 DOI: 10.1007/s11033-019-05137-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/10/2019] [Indexed: 11/27/2022]
Abstract
Endonucleases play a crucial role as reagents in laboratory research and diagnostics. Here, metagenomics was used to functionally screen a fosmid library for endonucleases. A fosmid library was constructed using metagenomic DNA isolated from soil sampled from the unique environment of the Kogelberg Nature Reserve in the Western Cape of South Africa. The principle of acquired immunity against phage infection was used to develop a plate-based screening technique for the isolation of restriction endonucleases from the library. Using next-generation sequencing and bioinformatics tools, sequence data were generated and analysed, revealing 113 novel open reading frames (ORFs) encoding putative endonuclease genes and ORFs of unknown identity and function. One endonuclease designated Endo52 was selected from the putative endonuclease ORFs and was recombinantly produced in Escherichia coli Rosetta™ (DE3) pLysS. Endo52 was purified by immobilised metal affinity chromatography and yielded 0.437 g per litre of cultivation volume. Its enzyme activity was monitored by cleaving lambda DNA and pUC19 plasmid as substrates, and it demonstrated non-specific endonuclease activity. In addition to endonuclease-like genes, the screen identified several unknown genes. These could present new phage resistance mechanisms and are an opportunity for future investigations.
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Affiliation(s)
- Sibongile Mtimka
- Biomanufacturing Technologies, CSIR Future Production: Chemicals, P O Box 395, Pretoria, 0001, South Africa.,Department of Life & Consumer Sciences, College of Agriculture & Environmental Sciences, University of South Africa, Florida Campus (The Science Hub), Florida, P O Box 392, Johannesburg, South Africa
| | - Priyen Pillay
- Biomanufacturing Technologies, CSIR Future Production: Chemicals, P O Box 395, Pretoria, 0001, South Africa
| | - Konanani Rashamuse
- Biomanufacturing Technologies, CSIR Future Production: Chemicals, P O Box 395, Pretoria, 0001, South Africa
| | - Samantha Gildenhuys
- Department of Life & Consumer Sciences, College of Agriculture & Environmental Sciences, University of South Africa, Florida Campus (The Science Hub), Florida, P O Box 392, Johannesburg, South Africa
| | - Tsepo L Tsekoa
- Biomanufacturing Technologies, CSIR Future Production: Chemicals, P O Box 395, Pretoria, 0001, South Africa.
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42
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Gifford I, Vance S, Nguyen G, Berry AM. A Stable Genetic Transformation System and Implications of the Type IV Restriction System in the Nitrogen-Fixing Plant Endosymbiont Frankia alni ACN14a. Front Microbiol 2019; 10:2230. [PMID: 31608043 PMCID: PMC6769113 DOI: 10.3389/fmicb.2019.02230] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 09/11/2019] [Indexed: 12/26/2022] Open
Abstract
Genus Frankia is comprised primarily of nitrogen-fixing actinobacteria that form root nodule symbioses with a group of hosts known as the actinorhizal plants. These plants are evolutionarily closely related to the legumes that are nodulated by the rhizobia. Both host groups utilize homologs of nodulation genes for root-nodule symbiosis, derived from common plant ancestors. The corresponding endosymbionts, Frankia and the rhizobia, however, are distantly related groups of bacteria, leading to questions about their symbiotic mechanisms and evolutionary history. To date, a stable system of electrotransformation has been lacking in Frankia despite numerous attempts by research groups worldwide. We have identified type IV methyl-directed restriction systems, highly-expressed in a range of actinobacteria, as a likely barrier to Frankia transformation. Here we report the successful electrotransformation of the model strain F. alni ACN14a with an unmethylated, broad host-range replicating plasmid, expressing chloramphenicol-resistance for selection and GFP as a marker of gene expression. This system circumvented the type IV restriction barrier and allowed the stable maintenance of the plasmid. During nitrogen limitation, Frankia differentiates into two cell types: the vegetative hyphae and nitrogen-fixing vesicles. When the expression of egfp under the control of the nif gene cluster promoter was localized using fluorescence imaging, the expression of nitrogen fixation in nitrogen-limited culture was localized in Frankia vesicles but not in hyphae. The ability to separate gene expression patterns between Frankia hyphae and vesicles will enable deeper comparisons of molecular signaling and metabolic exchange between Frankia-actinorhizal and rhizobia-legume symbioses to be made, and may broaden potential applications in agriculture. Further downstream applications are possible, including gene knock-outs and complementation, to open up a range of experiments in Frankia and its symbioses. Additionally, in the transcriptome of F. alni ACN14a, type IV restriction enzymes were highly expressed in nitrogen-replete culture but their expression strongly decreased during symbiosis. The down-regulation of type IV restriction enzymes in symbiosis suggests that horizontal gene transfer may occur more frequently inside the nodule, with possible new implications for the evolution of Frankia.
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Affiliation(s)
- Isaac Gifford
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
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43
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Jensen TØ, Tellgren-Roth C, Redl S, Maury J, Jacobsen SAB, Pedersen LE, Nielsen AT. Genome-wide systematic identification of methyltransferase recognition and modification patterns. Nat Commun 2019; 10:3311. [PMID: 31427571 PMCID: PMC6700114 DOI: 10.1038/s41467-019-11179-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 06/27/2019] [Indexed: 01/25/2023] Open
Abstract
Genome-wide analysis of DNA methylation patterns using single molecule real-time DNA sequencing has boosted the number of publicly available methylomes. However, there is a lack of tools coupling methylation patterns and the corresponding methyltransferase genes. Here we demonstrate a high-throughput method for coupling methyltransferases with their respective motifs, using automated cloning and analysing the methyltransferases in vectors carrying a strain-specific cassette containing all potential target sites. To validate the method, we analyse the genomes of the thermophile Moorella thermoacetica and the mesophile Acetobacterium woodii, two acetogenic bacteria having substantially modified genomes with 12 methylation motifs and a total of 23 methyltransferase genes. Using our method, we characterize the 23 methyltransferases, assign motifs to the respective enzymes and verify activity for 11 of the 12 motifs. Single molecule real-time DNA sequencing allows genome-wide identification of DNA methylation patterns. Here, Jensen et al. present a high-throughput method that allows rapid coupling of DNA methylation patterns with their corresponding methyltransferase genes in bacteria.
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Affiliation(s)
- Torbjørn Ølshøj Jensen
- The Novo Nordisk Foundation Center for Biosustainability (CfB), Technical University of Denmark (DTU), DK-2800, Lyngby, Denmark
| | - Christian Tellgren-Roth
- Uppsala Genome Center, National Genomics Infrastructure, SciLifeLab, SE-751 08, Uppsala, Sweden
| | - Stephanie Redl
- The Novo Nordisk Foundation Center for Biosustainability (CfB), Technical University of Denmark (DTU), DK-2800, Lyngby, Denmark.,Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jérôme Maury
- The Novo Nordisk Foundation Center for Biosustainability (CfB), Technical University of Denmark (DTU), DK-2800, Lyngby, Denmark
| | | | - Lasse Ebdrup Pedersen
- The Novo Nordisk Foundation Center for Biosustainability (CfB), Technical University of Denmark (DTU), DK-2800, Lyngby, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability (CfB), Technical University of Denmark (DTU), DK-2800, Lyngby, Denmark.
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44
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Forde BM, McAllister LJ, Paton JC, Paton AW, Beatson SA. SMRT sequencing reveals differential patterns of methylation in two O111:H- STEC isolates from a hemolytic uremic syndrome outbreak in Australia. Sci Rep 2019; 9:9436. [PMID: 31263188 PMCID: PMC6602927 DOI: 10.1038/s41598-019-45760-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 05/23/2019] [Indexed: 11/21/2022] Open
Abstract
In 1995 a severe haemolytic-uremic syndrome (HUS) outbreak in Adelaide occurred. A recent genomic analysis of Shiga toxigenic Escherichia coli (STEC) O111:H- strains 95JB1 and 95NR1 from this outbreak found that the more virulent isolate, 95NR1, harboured two additional copies of the Shiga toxin 2 (Stx2) genes encoded within prophage regions. The structure of the Stx2-converting prophages could not be fully resolved using short-read sequence data alone and it was not clear if there were other genomic differences between 95JB1 and 95NR1. In this study we have used Pacific Biosciences (PacBio) single molecule real-time (SMRT) sequencing to characterise the genome and methylome of 95JB1 and 95NR1. We completely resolved the structure of all prophages including two, tandemly inserted, Stx2-converting prophages in 95NR1 that were absent from 95JB1. Furthermore we defined all insertion sequences and found an additional IS1203 element in the chromosome of 95JB1. Our analysis of the methylome of 95NR1 and 95JB1 identified hemi-methylation of a novel motif (5′-CTGCm6AG-3′) in more than 4000 sites in the 95NR1 genome. These sites were entirely unmethylated in the 95JB1 genome, and included at least 177 potential promoter regions that could contribute to regulatory differences between the strains. IS1203 mediated deactivation of a novel type IIG methyltransferase in 95JB1 is the likely cause of the observed differential patterns of methylation between 95NR1 and 95JB1. This study demonstrates the capability of PacBio SMRT sequencing to resolve complex prophage regions and reveal the genetic and epigenetic heterogeneity within a clonal population of bacteria.
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Affiliation(s)
- Brian M Forde
- Australian Infectious Diseases Centre, The University of Queensland, Brisbane, QLD, Australia.,Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Lauren J McAllister
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
| | - James C Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
| | - Adrienne W Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
| | - Scott A Beatson
- Australian Infectious Diseases Centre, The University of Queensland, Brisbane, QLD, Australia. .,Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
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45
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Weissman JL, Laljani RMR, Fagan WF, Johnson PLF. Visualization and prediction of CRISPR incidence in microbial trait-space to identify drivers of antiviral immune strategy. ISME JOURNAL 2019; 13:2589-2602. [PMID: 31239539 PMCID: PMC6776019 DOI: 10.1038/s41396-019-0411-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 03/15/2019] [Accepted: 03/24/2019] [Indexed: 01/21/2023]
Abstract
Bacteria and archaea are locked in a near-constant battle with their viral pathogens. Despite previous mechanistic characterization of numerous prokaryotic defense strategies, the underlying ecological drivers of different strategies remain largely unknown and predicting which species will take which strategies remains a challenge. Here, we focus on the CRISPR immune strategy and develop a phylogenetically-corrected machine learning approach to build a predictive model of CRISPR incidence using data on over 100 traits across over 2600 species. We discover a strong but hitherto-unknown negative interaction between CRISPR and aerobicity, which we hypothesize may result from interference between CRISPR-associated proteins and non-homologous end-joining DNA repair due to oxidative stress. Our predictive model also quantitatively confirms previous observations of an association between CRISPR and temperature. Finally, we contrast the environmental associations of different CRISPR system types (I, II, III) and restriction modification systems, all of which act as intracellular immune systems.
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Affiliation(s)
- Jake L Weissman
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Rohan M R Laljani
- Department of Biology, University of Maryland, College Park, MD, USA
| | - William F Fagan
- Department of Biology, University of Maryland, College Park, MD, USA
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46
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Wang L, Jiang S, Deng Z, Dedon PC, Chen S. DNA phosphorothioate modification-a new multi-functional epigenetic system in bacteria. FEMS Microbiol Rev 2019; 43:109-122. [PMID: 30289455 PMCID: PMC6435447 DOI: 10.1093/femsre/fuy036] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/03/2018] [Indexed: 12/20/2022] Open
Abstract
Synthetic phosphorothioate (PT) internucleotide linkages, in which a nonbridging oxygen is replaced by a sulphur atom, share similar physical and chemical properties with phosphodiesters but confer enhanced nuclease tolerance on DNA/RNA, making PTs a valuable biochemical and pharmacological tool. Interestingly, PT modification was recently found to occur naturally in bacteria in a sequence-selective and RP configuration-specific manner. This oxygen-sulphur swap is catalysed by the gene products of dndABCDE, which constitute a defence barrier with DndFGH in some bacterial strains that can distinguish and attack non-PT-modified foreign DNA, resembling DNA methylation-based restriction-modification (R-M) systems. Despite their similar defensive mechanisms, PT- and methylation-based R-M systems have evolved to target different consensus contexts in the host cell because when they share the same recognition sequences, the protective function of each can be impeded. The redox and nucleophilic properties of PT sulphur render PT modification a versatile player in the maintenance of cellular redox homeostasis, epigenetic regulation and environmental fitness. The widespread presence of dnd systems is considered a consequence of extensive horizontal gene transfer, whereas the lability of PT during oxidative stress and the susceptibility of PT to PT-dependent endonucleases provide possible explanations for the ubiquitous but sporadic distribution of PT modification in the bacterial world.
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Affiliation(s)
- Lianrong Wang
- Zhongnan Hospital, Wuhan University, 169 Donghu Road, Wuhan 430071, China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 185 Donghu Road, Wuhan 430071, China
| | - Susu Jiang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 185 Donghu Road, Wuhan 430071, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 185 Donghu Road, Wuhan 430071, China
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Masschusetts Avenue, Cambridge, Massachusetts, USA
| | - Shi Chen
- Zhongnan Hospital, Wuhan University, 169 Donghu Road, Wuhan 430071, China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 185 Donghu Road, Wuhan 430071, China
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Xiong L, Liu S, Chen S, Xiao Y, Zhu B, Gao Y, Zhang Y, Chen B, Luo J, Deng Z, Chen X, Wang L, Chen S. A new type of DNA phosphorothioation-based antiviral system in archaea. Nat Commun 2019; 10:1688. [PMID: 30975999 PMCID: PMC6459918 DOI: 10.1038/s41467-019-09390-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 03/07/2019] [Indexed: 01/21/2023] Open
Abstract
Archaea and Bacteria have evolved different defence strategies that target virtually all steps of the viral life cycle. The diversified virion morphotypes and genome contents of archaeal viruses result in a highly complex array of archaea-virus interactions. However, our understanding of archaeal antiviral activities lags far behind our knowledges of those in bacteria. Here we report a new archaeal defence system that involves DndCDEA-specific DNA phosphorothioate (PT) modification and the PbeABCD-mediated halt of virus propagation via inhibition of DNA replication. In contrast to the breakage of invasive DNA by DndFGH in bacteria, DndCDEA-PbeABCD does not degrade or cleave viral DNA. The PbeABCD-mediated PT defence system is widespread and exhibits extensive interdomain and intradomain gene transfer events. Our results suggest that DndCDEA-PbeABCD is a new type of PT-based virus resistance system, expanding the known arsenal of defence systems as well as our understanding of host-virus interactions.
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Affiliation(s)
- Lei Xiong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
- Taihe Hospital, Hubei University of Medicine, 442000, Shiyan, Hubei, China
- Brain Center, Zhongnan Hospital, Wuhan University, 430071, Wuhan, China
| | - Siyi Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
- Brain Center, Zhongnan Hospital, Wuhan University, 430071, Wuhan, China
| | - Si Chen
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, 430023, Wuhan, China
| | - Yao Xiao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
- Brain Center, Zhongnan Hospital, Wuhan University, 430071, Wuhan, China
| | - Bochen Zhu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
- Brain Center, Zhongnan Hospital, Wuhan University, 430071, Wuhan, China
| | - Yali Gao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
- Brain Center, Zhongnan Hospital, Wuhan University, 430071, Wuhan, China
| | - Yujing Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
- Brain Center, Zhongnan Hospital, Wuhan University, 430071, Wuhan, China
| | - Beibei Chen
- College of Life Sciences, Wuhan University, 430071, Wuhan, China
| | - Jie Luo
- Taihe Hospital, Hubei University of Medicine, 442000, Shiyan, Hubei, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
| | - Xiangdong Chen
- College of Life Sciences, Wuhan University, 430071, Wuhan, China
| | - Lianrong Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
- Taihe Hospital, Hubei University of Medicine, 442000, Shiyan, Hubei, China
- Brain Center, Zhongnan Hospital, Wuhan University, 430071, Wuhan, China
| | - Shi Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China.
- Taihe Hospital, Hubei University of Medicine, 442000, Shiyan, Hubei, China.
- Brain Center, Zhongnan Hospital, Wuhan University, 430071, Wuhan, China.
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48
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Ra SR, Kim MS, Paek CIL, Pak YC, Pak SH, Pak HB, Ri KC. Bci528I, a new isoschizomer of EcoRI isolated from Bacillus circulans 528. Folia Microbiol (Praha) 2019; 64:803-808. [DOI: 10.1007/s12223-019-00694-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/28/2019] [Indexed: 10/27/2022]
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49
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Mindlin S, Beletsky A, Mardanov A, Petrova M. Adaptive dif Modules in Permafrost Strains of Acinetobacter lwoffii and Their Distribution and Abundance Among Present Day Acinetobacter Strains. Front Microbiol 2019; 10:632. [PMID: 30984151 PMCID: PMC6449649 DOI: 10.3389/fmicb.2019.00632] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/13/2019] [Indexed: 12/22/2022] Open
Abstract
The dif/Xer system of site-specific recombination allows resolution of chromosomal dimers during bacterial DNA replication. Recently, it was also shown to be involved in horizontal transfer of a few known Xer-dependent mobile elements. Here, we show that plasmids of various Acinetobacter species, including clinically important strains, often contain multiple pdif sites that are mainly located within their accessory regions. Chromosomes of Acinetobacter strains may also contain additional dif sites, and their similarity with plasmid pdif sites is higher than with the main chromosomal site dif1. We further identify putative mobile genetic elements containing pdif sites on both flanks of adaptive genes and analyze their distribution in Acinetobacter species. In total, we describe seven mobile elements containing genes with various adaptive functions from permafrost strains of A. lwoffii group. All of them are also spread in modern plasmids of different Acinetobacter species including A. baumannii. We could not detect pdif sites and corresponding mobile elements in closely related bacterial genera, including Psychrobacter and Moraxella. Thus, the widespread distribution of dif modules is a characteristic feature of Acinetobacter species and may contribute to their high adaptability both in the environment and in the clinic.
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Affiliation(s)
- Sofia Mindlin
- Laboratory of Molecular Genetics of Microorganisms, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Alexey Beletsky
- Laboratory of Microorganism Genomics and Metagenomics, Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Andrey Mardanov
- Laboratory of Microorganism Genomics and Metagenomics, Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Mayya Petrova
- Laboratory of Molecular Genetics of Microorganisms, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
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50
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Barahona CJ, Basantes LE, Tompkins KJ, Heitman DM, Chukwu BI, Sanchez J, Sanchez JL, Ghadirian N, Park CK, Horton NC. The Need for Speed: Run-On Oligomer Filament Formation Provides Maximum Speed with Maximum Sequestration of Activity. J Virol 2019; 93:e01647-18. [PMID: 30518649 PMCID: PMC6384071 DOI: 10.1128/jvi.01647-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 11/26/2018] [Indexed: 01/29/2023] Open
Abstract
Here, we investigate an unusual antiviral mechanism developed in the bacterium Streptomyces griseus SgrAI is a type II restriction endonuclease that forms run-on oligomer filaments when activated and possesses both accelerated DNA cleavage activity and expanded DNA sequence specificity. Mutations disrupting the run-on oligomer filament eliminate the robust antiphage activity of wild-type SgrAI, and the observation that even relatively modest disruptions completely abolish this anti-viral activity shows that the greater speed imparted by the run-on oligomer filament mechanism is critical to its biological function. Simulations of DNA cleavage by SgrAI uncover the origins of the kinetic advantage of this newly described mechanism of enzyme regulation over more conventional mechanisms, as well as the origin of the sequestering effect responsible for the protection of the host genome against damaging DNA cleavage activity of activated SgrAI.IMPORTANCE This work is motivated by an interest in understanding the characteristics and advantages of a relatively newly discovered enzyme mechanism involving filament formation. SgrAI is an enzyme responsible for protecting against viral infections in its host bacterium and was one of the first such enzymes shown to utilize such a mechanism. In this work, filament formation by SgrAI is disrupted, and the effects on the speed of the purified enzyme as well as its function in cells are measured. It was found that even small disruptions, which weaken but do not destroy filament formation, eliminate the ability of SgrAI to protect cells from viral infection, its normal biological function. Simulations of enzyme activity were also performed and show how filament formation can greatly speed up an enzyme's activation compared to that of other known mechanisms, as well as to better localize its action to molecules of interest, such as invading phage DNA.
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Affiliation(s)
- Claudia J Barahona
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - L Emilia Basantes
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Kassidy J Tompkins
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Desirae M Heitman
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Barbara I Chukwu
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Juan Sanchez
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Jonathan L Sanchez
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Niloofar Ghadirian
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Chad K Park
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - N C Horton
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
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