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Zimmerman EH, Ramsey EL, Hunter KE, Villadelgado SM, Phillips CM, Shipman RT, Forsyth MH. The Helicobacter pylori methylome is acid-responsive due to regulation by the two-component system ArsRS and the type I DNA methyltransferase HsdM1 (HP0463). J Bacteriol 2024; 206:e0030923. [PMID: 38179929 PMCID: PMC10810217 DOI: 10.1128/jb.00309-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/14/2023] [Indexed: 01/06/2024] Open
Abstract
In addition to its role in genome protection, DNA methylation can regulate gene expression. In this study, we characterized the impact of acidity, phase variation, and the ArsRS TCS on the expression of the Type I m6A DNA methyltransferase HsdM1 (HP0463) of Helicobacter pylori 26695 and their subsequent effects on the methylome. Transcription of hsdM1 increases at least fourfold in the absence of the sensory histidine kinase ArsS, the major acid-sensing protein of H. pylori. hsdM1 exists in the phase-variable operon hsdR1-hsdM1. Phase-locking hsdR1 (HP0464), the restriction endonuclease gene, has significant impacts on the transcription of hsdM1. To determine the impacts of methyltransferase transcription patterns on the methylome, we conducted methylome sequencing on samples cultured at pH 7 or pH 5. We found differentially methylated motifs between these growth conditions and that deletions of arsS and/or hsdM1 interfere with the epigenetic acid response. Deletion of arsS leads to altered activity of HsdM1 and multiple other methyltransferases under both pH conditions indicating that the ArsRS TCS, in addition to direct effects on regulon transcription during acid acclimation, may also indirectly impact gene expression via regulation of the methylome. We determined the target motif of HsdM1 (HP0463) to be the complementary bipartite sequence pair 5'-TCAm6AVN6TGY-3' and 3'-AGTN6GAm6ACA-5'. This complex regulation of DNA methyltransferases, and thus differential methylation patterns, may have implications for the decades-long persistent infection by H. pylori. IMPORTANCE This study expands the possibilities for complex, epigenomic regulation in Helicobacter pylori. We demonstrate that the H. pylori methylome is plastic and acid sensitive via the two-component system ArsRS and the DNA methyltransferase HsdM1. The control of a methyltransferase by ArsRS may allow for a layered response to changing acidity. Likely, an early response whereby ArsR~P affects regulon expression, including the methyltransferase hsdM1. Then, a somewhat later effect as the altered methylome, due to altered HsdM1 expression, subsequently alters the expression of other genes involved in acclimation. The intermediate methylation of certain motifs supports the hypothesis that methyltransferases play a regulatory role. Untangling this additional web of regulation could play a key role in understanding H. pylori colonization and persistence.
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Affiliation(s)
| | - Erin L. Ramsey
- Department of Biology, William & Mary, Williamsburg, Virginia, USA
| | | | | | | | - Ryan T. Shipman
- Department of Biology, William & Mary, Williamsburg, Virginia, USA
| | - Mark H. Forsyth
- Department of Biology, William & Mary, Williamsburg, Virginia, USA
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2
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Ailloud F, Gottschall W, Suerbaum S. Methylome evolution suggests lineage-dependent selection in the gastric pathogen Helicobacter pylori. Commun Biol 2023; 6:839. [PMID: 37573385 PMCID: PMC10423294 DOI: 10.1038/s42003-023-05218-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 08/04/2023] [Indexed: 08/14/2023] Open
Abstract
The bacterial pathogen Helicobacter pylori, the leading cause of gastric cancer, is genetically highly diverse and harbours a large and variable portfolio of restriction-modification systems. Our understanding of the evolution and function of DNA methylation in bacteria is limited. Here, we performed a comprehensive analysis of the methylome diversity in H. pylori, using a dataset of 541 genomes that included all known phylogeographic populations. The frequency of 96 methyltransferases and the abundance of their cognate recognition sequences were strongly influenced by phylogeographic structure and were inter-correlated, positively or negatively, for 20% of type II methyltransferases. Low density motifs were more likely to be affected by natural selection, as reflected by higher genomic instability and compositional bias. Importantly, direct correlation implied that methylation patterns can be actively enriched by positive selection and suggests that specific sites have important functions in methylation-dependent phenotypes. Finally, we identified lineage-specific selective pressures modulating the contraction and expansion of the motif ACGT, revealing that the genetic load of methylation could be dependent on local ecological factors. Taken together, natural selection may shape both the abundance and distribution of methyltransferases and their specific recognition sequences, likely permitting a fine-tuning of genome-encoded functions not achievable by genetic variation alone.
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Affiliation(s)
- Florent Ailloud
- Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
| | - Wilhelm Gottschall
- Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Sebastian Suerbaum
- Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
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3
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Wang X, Yu D, Chen L. Antimicrobial resistance and mechanisms of epigenetic regulation. Front Cell Infect Microbiol 2023; 13:1199646. [PMID: 37389209 PMCID: PMC10306973 DOI: 10.3389/fcimb.2023.1199646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/26/2023] [Indexed: 07/01/2023] Open
Abstract
The rampant use of antibiotics in animal husbandry, farming and clinical disease treatment has led to a significant issue with pathogen resistance worldwide over the past decades. The classical mechanisms of resistance typically investigate antimicrobial resistance resulting from natural resistance, mutation, gene transfer and other processes. However, the emergence and development of bacterial resistance cannot be fully explained from a genetic and biochemical standpoint. Evolution necessitates phenotypic variation, selection, and inheritance. There are indications that epigenetic modifications also play a role in antimicrobial resistance. This review will specifically focus on the effects of DNA modification, histone modification, rRNA methylation and the regulation of non-coding RNAs expression on antimicrobial resistance. In particular, we highlight critical work that how DNA methyltransferases and non-coding RNAs act as transcriptional regulators that allow bacteria to rapidly adapt to environmental changes and control their gene expressions to resist antibiotic stress. Additionally, it will delve into how Nucleolar-associated proteins in bacteria perform histone functions akin to eukaryotes. Epigenetics, a non-classical regulatory mechanism of bacterial resistance, may offer new avenues for antibiotic target selection and the development of novel antibiotics.
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Affiliation(s)
- Xinrui Wang
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
- National Health Commission Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
| | - Donghong Yu
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
- National Health Commission Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
| | - Lu Chen
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
- National Health Commission Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
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4
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Nahar N, Tram G, Jen FEC, Phillips ZN, Weinert L, Bossé J, Jabbari J, Gouil Q, Du MM, Ritchie M, Bowden R, Langford P, Tucker A, Jennings M, Turni C, Blackall P, Atack J. Actinobacillus pleuropneumoniae encodes multiple phase-variable DNA methyltransferases that control distinct phasevarions. Nucleic Acids Res 2023; 51:3240-3260. [PMID: 36840716 PMCID: PMC10123105 DOI: 10.1093/nar/gkad091] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 02/26/2023] Open
Abstract
Actinobacillus pleuropneumoniae is the cause of porcine pleuropneumonia, a severe respiratory tract infection that is responsible for major economic losses to the swine industry. Many host-adapted bacterial pathogens encode systems known as phasevarions (phase-variable regulons). Phasevarions result from variable expression of cytoplasmic DNA methyltransferases. Variable expression results in genome-wide methylation differences within a bacterial population, leading to altered expression of multiple genes via epigenetic mechanisms. Our examination of a diverse population of A. pleuropneumoniae strains determined that Type I and Type III DNA methyltransferases with the hallmarks of phase variation were present in this species. We demonstrate that phase variation is occurring in these methyltransferases, and show associations between particular Type III methyltransferase alleles and serovar. Using Pacific BioSciences Single-Molecule, Real-Time (SMRT) sequencing and Oxford Nanopore sequencing, we demonstrate the presence of the first ever characterised phase-variable, cytosine-specific Type III DNA methyltransferase. Phase variation of distinct Type III DNA methyltransferase in A. pleuropneumoniae results in the regulation of distinct phasevarions, and in multiple phenotypic differences relevant to pathobiology. Our characterisation of these newly described phasevarions in A. pleuropneumoniae will aid in the selection of stably expressed antigens, and direct and inform development of a rationally designed subunit vaccine against this major veterinary pathogen.
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Affiliation(s)
- Nusrat Nahar
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Greg Tram
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Freda E-C Jen
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Zachary N Phillips
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Janine T Bossé
- Section of Paediatric Infectious Disease, Imperial College London, St Mary's Campus, London W2 1PG, UK
| | - Jafar S Jabbari
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Quentin Gouil
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Mei R M Du
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Matthew E Ritchie
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Rory Bowden
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Paul R Langford
- Section of Paediatric Infectious Disease, Imperial College London, St Mary's Campus, London W2 1PG, UK
| | - Alexander W Tucker
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Michael P Jennings
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Conny Turni
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Patrick J Blackall
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - John M Atack
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
- School of Environment and Science, Griffith University, Gold Coast, Queensland 4222, Australia
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5
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Suerbaum S, Ailloud F. Genome and population dynamics during chronic infection with Helicobacter pylori. Curr Opin Immunol 2023; 82:102304. [PMID: 36958230 DOI: 10.1016/j.coi.2023.102304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/25/2023]
Abstract
Helicobacter pylori is responsible for one of the most prevalent bacterial infections worldwide. Chronic infection typically leads to chronic active gastritis. Clinical sequelae, including peptic ulcers, mucosa-associated lymphoid tissue lymphoma or, most importantly, gastric adenocarcinoma develop in 10-15% of cases. H. pylori is characterized by extensive inter-strain diversity which is the result of a high mutation rate, recombination, and a large repertoire of restriction-modification systems. This diversity is thought to be a major contributor to H. pylori's persistence and exceptional aptitude to adapt to the gastric environment and evade the immune system. This review covers efforts in the last decade to characterize and understand the multiple layers of H. pylori's diversity in different biological contexts.
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Affiliation(s)
- Sebastian Suerbaum
- Max von Pettenkofer Institute for Hygiene and Medical Microbiology, Medical Faculty, LMU Munich, Pettenkoferstr. 9a, 80336 Munich, Germany; DZIF German Centre for Infection Research, Munich Partner Site, Pettenkoferstr. 9a, 80336 Munich, Germany; German National Reference Centre for Helicobacter pylori, Pettenkoferstr. 9a, 80336 Munich, Germany.
| | - Florent Ailloud
- Max von Pettenkofer Institute for Hygiene and Medical Microbiology, Medical Faculty, LMU Munich, Pettenkoferstr. 9a, 80336 Munich, Germany; DZIF German Centre for Infection Research, Munich Partner Site, Pettenkoferstr. 9a, 80336 Munich, Germany
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6
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Garai P, Atack JM, Wills BM, Jennings MP, Bakaletz LO, Brockman KL. Adherence of Nontypeable Haemophilus influenzae to Cells and Substrates of the Airway Is Differentially Regulated by Individual ModA Phasevarions. Microbiol Spectr 2023; 11:e0409322. [PMID: 36511712 PMCID: PMC9927368 DOI: 10.1128/spectrum.04093-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
Adherence of nontypeable Haemophilus influenzae (NTHi) to the host airway is an essential initial step for asymptomatic colonization of the nasopharynx, as well as development of disease. NTHi relies on strict regulation of multiple adhesins for adherence to host substrates encountered in the airway. NTHi encode a phase-variable cytoplasmic DNA methyltransferase, ModA, that regulates expression of multiple genes; a phasevarion (phase-variable regulon). Multiple modA alleles are present in NTHi, in which different alleles methylate a different DNA target, and each controls a different set of genes. However, the role of ModA phasevarions in regulating adherence of NTHi to the host airway is not well understood. This study therefore sought to investigate the role of four of the most prevalent ModA phasevarions in the regulation of adherence of NTHi to multiple substrates of the airway. Four clinical isolates of NTHi with unique modA alleles were tested in this study. The adherence of NTHi to mucus, middle ear epithelial cells, and vitronectin was regulated in a substrate-specific manner that was dependent on the ModA allele encoded. The adhesins Protein E and P4 were found to contribute to the ModA-regulated adherence of NTHi to distinct substrates. A better understanding of substrate-specific regulation of NTHi adherence by ModA phasevarions will allow identification of NTHi populations present at the site of disease within the airway and facilitate more directed development of vaccines and therapeutics. IMPORTANCE Nontypeable Haemophilus influenzae (NTHi) is a predominant pathogen of the human airway that causes respiratory infections such as otitis media (OM) and exacerbations in the lungs of patients suffering from chronic obstructive pulmonary disease (COPD). Due to the lack of a licensed vaccine against NTHi and the emergence of antibiotic-resistant strains, it is extremely challenging to target NTHi for treatment. NTHi adhesins are considered potential candidates for vaccines or other therapeutic approaches. The ModA phasevarions of NTHi play a role in the rapid adaptation of the pathogen to different environmental stress conditions. This study addressed the role of ModA phasevarions in the regulation of adherence of NTHi to specific host substrates found within the respiratory tract. The findings of this study improve our understanding of regulation of adherence of NTHi to the airway, which may further be used to enhance the potential of adhesins as vaccine antigens and therapeutic targets against NTHi.
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Affiliation(s)
- Preeti Garai
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - John M. Atack
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
- School of Environment and Science, Griffith University, Gold Coast, Queensland, Australia
| | - Brandon M. Wills
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Michael P. Jennings
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Lauren O. Bakaletz
- Abigail Wexner Research Institute, Center for Microbial Pathogenesis, Nationwide Children’s Hospital, Columbus, Ohio, USA
- College of Medicine, Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Kenneth L. Brockman
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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7
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Agnew HN, Atack JM, Fernando AR, Waters SN, van der Linden M, Smith E, Abell AD, Brazel EB, Paton JC, Trappetti C. Uncovering the link between the SpnIII restriction modification system and LuxS in Streptococcus pneumoniae meningitis isolates. Front Cell Infect Microbiol 2023; 13:1177857. [PMID: 37197203 PMCID: PMC10184825 DOI: 10.3389/fcimb.2023.1177857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/17/2023] [Indexed: 05/19/2023] Open
Abstract
Streptococcus pneumoniae is capable of randomly switching their genomic DNA methylation pattern between six distinct bacterial subpopulations (A-F) via recombination of a type 1 restriction-modification locus, spnIII. These pneumococcal subpopulations exhibit phenotypic changes which favor carriage or invasive disease. In particular, the spnIIIB allele has been associated with increased nasopharyngeal carriage and the downregulation of the luxS gene. The LuxS/AI-2 QS system represent a universal language for bacteria and has been linked to virulence and biofilm formation in S. pneumoniae. In this work, we have explored the link between spnIII alleles, the luxS gene and virulence in two clinical pneumococcal isolates from the blood and cerebrospinal fluid (CSF) of one pediatric meningitis patient. The blood and CSF strains showed different virulence profiles in mice. Analysis of the spnIII system of these strains recovered from the murine nasopharynx showed that the system switched to different alleles commensurate with the initial source of the isolate. Of note, the blood strain showed high expression of spnIIIB allele, previously linked with less LuxS protein production. Importantly, strains with deleted luxS displayed different phenotypic profiles compared to the wildtype, but similar to the strains recovered from the nasopharynx of infected mice. This study used clinically relevant S. pneumoniae strains to demonstrate that the regulatory network between luxS and the type 1 restriction-modification system play a key role in infections and may support different adaptation to specific host niches.
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Affiliation(s)
- Hannah N. Agnew
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
| | - John M. Atack
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
- School of Environment and Science, Griffith University, Gold Coast, QLD, Australia
| | - Ann R.D. Fernando
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
| | - Sophie N. Waters
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
| | - Mark van der Linden
- German National Reference Center for Streptococci, University Hospital Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen, Aachen, Germany
| | - Erin Smith
- School of Physical Sciences, Faculty of Sciences, Engineering and Technology, University of Adelaide, Adelaide, SA, Australia
| | - Andrew D. Abell
- School of Physical Sciences, Faculty of Sciences, Engineering and Technology, University of Adelaide, Adelaide, SA, Australia
| | - Erin B. Brazel
- 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
- *Correspondence: Claudia Trappetti, ; James C. Paton,
| | - Claudia Trappetti
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
- *Correspondence: Claudia Trappetti, ; James C. Paton,
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8
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Semashko TA, Arzamasov AA, Evsyutina DV, Garanina IA, Matyushkina DS, Ladygina VG, Pobeguts OV, Fisunov GY, Govorun VM. Role of DNA modifications in Mycoplasma gallisepticum. PLoS One 2022; 17:e0277819. [PMID: 36413541 PMCID: PMC9681074 DOI: 10.1371/journal.pone.0277819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 11/03/2022] [Indexed: 11/23/2022] Open
Abstract
The epigenetics of bacteria, and bacteria with a reduced genome in particular, is of great interest, but is still poorly understood. Mycoplasma gallisepticum, a representative of the class Mollicutes, is an excellent model of a minimal cell because of its reduced genome size, lack of a cell wall, and primitive cell organization. In this study we investigated DNA modifications of the model object Mycoplasma gallisepticum and their roles. We identified DNA modifications and methylation motifs in M. gallisepticum S6 at the genome level using single molecule real time (SMRT) sequencing. Only the ANCNNNNCCT methylation motif was found in the M. gallisepticum S6 genome. The studied bacteria have one functional system for DNA modifications, the Type I restriction-modification (RM) system, MgaS6I. We characterized its activity, affinity, protection and epigenetic functions. We demonstrated the protective effects of this RM system. A common epigenetic signal for bacteria is the m6A modification we found, which can cause changes in DNA-protein interactions and affect the cell phenotype. Native methylation sites are underrepresented in promoter regions and located only near the -35 box of the promoter, which does not have a significant effect on gene expression in mycoplasmas. To study the epigenetics effect of m6A for genome-reduced bacteria, we constructed a series of M. gallisepticum strains expressing EGFP under promoters with the methylation motifs in their different elements. We demonstrated that m6A modifications of the promoter located only in the -10-box affected gene expression and downregulated the expression of the corresponding gene.
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Affiliation(s)
- Tatiana A. Semashko
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russian Federation
- Research Institute for Systems Biology and Medicine, Moscow, Russian Federation
- * E-mail:
| | - Alexander A. Arzamasov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Daria V. Evsyutina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russian Federation
- Research Institute for Systems Biology and Medicine, Moscow, Russian Federation
| | - Irina A. Garanina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Daria S. Matyushkina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russian Federation
- Research Institute for Systems Biology and Medicine, Moscow, Russian Federation
| | - Valentina G. Ladygina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Olga V. Pobeguts
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Gleb Y. Fisunov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russian Federation
- Research Institute for Systems Biology and Medicine, Moscow, Russian Federation
| | - Vadim M. Govorun
- Research Institute for Systems Biology and Medicine, Moscow, Russian Federation
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9
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Adamczyk-Poplawska M, Bacal P, Mrozek A, Matczynska N, Piekarowicz A, Kwiatek A. Phase-variable Type I methyltransferase M.NgoAV from Neisseria gonorrhoeae FA1090 regulates phasevarion expression and gonococcal phenotype. Front Microbiol 2022; 13:917639. [PMID: 36267167 PMCID: PMC9577141 DOI: 10.3389/fmicb.2022.917639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
The restriction-modification (RM) systems are compared to a primitive, innate, prokaryotic immune system, controlling the invasion by foreign DNA, composed of methyltransferase (MTase) and restriction endonuclease. The biological significance of RM systems extends beyond their defensive function, but the data on the regulatory role of Type I MTases are limited. We have previously characterized molecularly a non-canonical Type I RM system, NgoAV, with phase-variable specificity, encoded by Neisseria gonorrhoeae FA1090. In the current work, we have investigated the impact of methyltransferase NgoAV (M.NgoAV) activity on gonococcal phenotype and on epigenetic control of gene expression. For this purpose, we have constructed and studied genetic variants (concerning activity and specificity) within M.NgoAV locus. Deletion of M.NgoAV or switch of its specificity had an impact on phenotype of N. gonorrhoeae. Biofilm formation and planktonic growth, the resistance to antibiotics, which target bacterial peptidoglycan or other antimicrobials, and invasion of human epithelial host cells were affected. The expression of genes was deregulated in gonococcal cells with knockout M.NgoAV gene and the variant with new specificity. For the first time, the existence of a phasevarion (phase-variable regulon), directed by phase-variable Type I MTase, is demonstrated.
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Affiliation(s)
- Monika Adamczyk-Poplawska
- Department of Molecular Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- *Correspondence: Monika Adamczyk-Poplawska,
| | - Pawel Bacal
- Institute of Paleobiology, Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Mrozek
- Department of Molecular Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Natalia Matczynska
- Department of Molecular Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Andrzej Piekarowicz
- Department of Molecular Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Agnieszka Kwiatek
- Department of Molecular Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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10
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Seong HJ, Roux S, Hwang CY, Sul WJ. Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics. MICROBIOME 2022; 10:157. [PMID: 36167684 PMCID: PMC9516812 DOI: 10.1186/s40168-022-01340-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 07/28/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND DNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in culturable microorganisms, resulting in a limited understanding of DNA methylation from a microbial ecology perspective. Here, we analyze the distribution patterns of several microbial epigenetics marks in the ocean microbiome through genome-centric metagenomics across all domains of life. RESULTS We reconstructed 15,056 viral, 252 prokaryotic, 56 giant viral, and 6 eukaryotic metagenome-assembled genomes from northwest Pacific Ocean seawater samples using short- and long-read sequencing approaches. These metagenome-derived genomes mostly represented novel taxa, and recruited a majority of reads. Thanks to single-molecule real-time (SMRT) sequencing technology, base modification could also be detected for these genomes. This showed that DNA methylation can readily be detected across dominant oceanic bacterial, archaeal, and viral populations, and microbial epigenetic changes correlate with population differentiation. Furthermore, our genome-wide epigenetic analysis of Pelagibacter suggests that GANTC, a DNA methyltransferase target motif, is related to the cell cycle and is affected by environmental conditions. Yet, the presence of this motif also partitions the phylogeny of the Pelagibacter phages, possibly hinting at a competitive co-evolutionary history and multiple effects of a single methylation mark. CONCLUSIONS Overall, this study elucidates that DNA methylation patterns are associated with ecological changes and virus-host dynamics in the ocean microbiome. Video Abstract.
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Affiliation(s)
- Hoon Je Seong
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Chung Yeon Hwang
- School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul, Republic of Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea
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11
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Epigenetic-Mediated Antimicrobial Resistance: Host versus Pathogen Epigenetic Alterations. Antibiotics (Basel) 2022; 11:antibiotics11060809. [PMID: 35740215 PMCID: PMC9220109 DOI: 10.3390/antibiotics11060809] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 02/04/2023] Open
Abstract
Since the discovery of antibiotics, humans have been benefiting from them by decreasing the morbidity and mortality associated with bacterial infections. However, in the past few decades, misuse of antibiotics has led to the emergence of bacterial infections resistant to multiple drugs, a significant health concern. Bacteria exposed to inappropriate levels of antibiotics lead to several genetic changes, enabling them to survive in the host and become more resistant. Despite the understanding and targeting of genetic-based biochemical changes in the bacteria, the increasing levels of antibiotic resistance are not under control. Many reports hint at the role of epigenetic modifications in the bacterial genome and host epigenetic reprogramming due to interaction with resistant pathogens. Epigenetic changes, such as the DNA-methylation-based regulation of bacterial mutation rates or bacteria-induced histone modification in human epithelial cells, facilitate its long-term survival. In this review article, epigenetic changes leading to the development of antibiotic resistance in clinically relevant bacteria are discussed. Additionally, recent lines of evidence focusing on human host epigenetic changes due to the human–pathogen interactions are presented. As genetic mechanisms cannot explain the transient nature of antimicrobial resistance, we believe that epigenetics may provide new frontiers in antimicrobial discovery.
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12
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Filipi K, Rahman WU, Osickova A, Osicka R. Kingella kingae RtxA Cytotoxin in the Context of Other RTX Toxins. Microorganisms 2022; 10:518. [PMID: 35336094 PMCID: PMC8953716 DOI: 10.3390/microorganisms10030518] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/04/2022] Open
Abstract
The Gram-negative bacterium Kingella kingae is part of the commensal oropharyngeal flora of young children. As detection methods have improved, K. kingae has been increasingly recognized as an emerging invasive pathogen that frequently causes skeletal system infections, bacteremia, and severe forms of infective endocarditis. K. kingae secretes an RtxA cytotoxin, which is involved in the development of clinical infection and belongs to an ever-growing family of cytolytic RTX (Repeats in ToXin) toxins secreted by Gram-negative pathogens. All RTX cytolysins share several characteristic structural features: (i) a hydrophobic pore-forming domain in the N-terminal part of the molecule; (ii) an acylated segment where the activation of the inactive protoxin to the toxin occurs by a co-expressed toxin-activating acyltransferase; (iii) a typical calcium-binding RTX domain in the C-terminal portion of the molecule with the characteristic glycine- and aspartate-rich nonapeptide repeats; and (iv) a C-proximal secretion signal recognized by the type I secretion system. RTX toxins, including RtxA from K. kingae, have been shown to act as highly efficient 'contact weapons' that penetrate and permeabilize host cell membranes and thus contribute to the pathogenesis of bacterial infections. RtxA was discovered relatively recently and the knowledge of its biological role remains limited. This review describes the structure and function of RtxA in the context of the most studied RTX toxins, the knowledge of which may contribute to a better understanding of the action of RtxA in the pathogenesis of K. kingae infections.
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Affiliation(s)
| | | | | | - Radim Osicka
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; (K.F.); (W.U.R.); (A.O.)
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13
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Capparelli R, Iannelli D. Epigenetics and Helicobacter pylori. Int J Mol Sci 2022; 23:ijms23031759. [PMID: 35163679 PMCID: PMC8836069 DOI: 10.3390/ijms23031759] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/21/2022] [Accepted: 02/01/2022] [Indexed: 02/06/2023] Open
Abstract
Epigenetics regulates gene expression, cell type development during differentiation, and the cell response to environmental stimuli. To survive, bacteria need to evade the host immune response. Bacteria, including Helicobacter pylori (Hp), reach this target epigenetically, altering the chromatin of the host cells, in addition to several more approaches, such as DNA mutation and recombination. This review shows that Hp prevalently silences the genes of the human gastric mucosa by DNA methylation. Epigenetics includes different mechanisms. However, DNA methylation persists after DNA replication and therefore is frequently associated with the inheritance of repressed genes. Chromatin modification can be transmitted to daughter cells leading to heritable changes in gene expression. Aberrant epigenetic alteration of the gastric mucosa DNA remains the principal cause of gastric cancer. Numerous methylated genes have been found in cancer as well as in precancerous lesions of Hp-infected patients. These methylated genes inactivate tumor-suppressor genes. It is time for us to complain about our genetic and epigenetic makeups for our diseases.
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14
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Wilkinson DJ, Dickins B, Robinson K, Winter JA. Genomic diversity of Helicobacter pylori populations from different regions of the human stomach. Gut Microbes 2022; 14:2152306. [PMID: 36469575 PMCID: PMC9728471 DOI: 10.1080/19490976.2022.2152306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Individuals infected with Helicobacter pylori harbor unique and diverse populations of quasispecies, but diversity between and within different regions of the human stomach and the process of bacterial adaptation to each location are not yet well understood. We applied whole-genome deep sequencing to characterize the within- and between-stomach region genetic diversity of H. pylori populations from paired antrum and corpus biopsies of 15 patients, along with single biopsies from one region of an additional 3 patients, by scanning allelic diversity. We combined population deep sequencing with more conventional sequencing of multiple H. pylori single colony isolates from individual biopsies to generate a unique dataset. Single colony isolates were used to validate the scanning allelic diversity pipelines. We detected extensive population allelic diversity within the different regions of each patient's stomach. Diversity was most commonly found within non-coding, hypothetical, outer membrane, restriction modification system, virulence, lipopolysaccharide biosynthesis, efflux systems, and chemotaxis-associated genes. Antrum and corpus populations from the same patient grouped together phylogenetically, indicating that most patients were initially infected with a single strain, which then diversified. Single colonies from the antrum and corpus of the same patients grouped into distinct clades, suggesting mechanisms for within-location adaptation across multiple H. pylori isolates from different patients. The comparisons made available by combined sequencing and analysis of isolates and populations enabled comprehensive analysis of the genetic changes associated with H. pylori diversification and stomach region adaptation.
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Affiliation(s)
- Daniel James Wilkinson
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
- School of Science and Technology, Nottingham Trent University, UK
| | - Benjamin Dickins
- School of Science and Technology, Nottingham Trent University, UK
| | - Karen Robinson
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Jody Anne Winter
- School of Science and Technology, Nottingham Trent University, UK
- CONTACT Jody Anne Winter School of Science and Technology, Nottingham Trent University Clifton Campus, Clifton Lane, NottinghamNG118NS, UK
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15
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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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16
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Meng B, Epp N, Wijaya W, Mrázek J, Hoover TR. Methylation Motifs in Promoter Sequences May Contribute to the Maintenance of a Conserved m5C Methyltransferase in Helicobacter pylori. Microorganisms 2021; 9:microorganisms9122474. [PMID: 34946076 PMCID: PMC8706393 DOI: 10.3390/microorganisms9122474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 01/22/2023] Open
Abstract
DNA methylomes of Helicobacter pylori strains are complex due to the large number of DNA methyltransferases (MTases) they possess. H. pylori J99 M.Hpy99III is a 5-methylcytosine (m5C) MTase that converts GCGC motifs to Gm5CGC. Homologs of M.Hpy99III are found in essentially all H. pylori strains. Most of these homologs are orphan MTases that lack a cognate restriction endonuclease, and their retention in H. pylori strains suggest they have roles in gene regulation. To address this hypothesis, green fluorescent protein (GFP) reporter genes were constructed with six putative promoters that had a GCGC motif in the extended −10 region, and the expression of the reporter genes was compared in wild-type H. pylori G27 and a mutant lacking the M.Hpy99III homolog (M.HpyGIII). The expression of three of the GFP reporter genes was decreased significantly in the mutant lacking M.HpyGIII. In addition, the growth rate of the H. pylori G27 mutant lacking M.HpyGIII was reduced markedly compared to that of the wild type. These findings suggest that the methylation of the GCGC motif in many H. pylori GCGC-containing promoters is required for the robust expression of genes controlled by these promoters, which may account for the universal retention of M.Hpy99III homologs in H. pylori strains.
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Affiliation(s)
- Bowen Meng
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA; (B.M.); (N.E.); (W.W.)
| | - Naomi Epp
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA; (B.M.); (N.E.); (W.W.)
| | - Winsen Wijaya
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA; (B.M.); (N.E.); (W.W.)
| | - Jan Mrázek
- Department of Microbiology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA;
| | - Timothy R. Hoover
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA; (B.M.); (N.E.); (W.W.)
- Correspondence: ; Tel.: +1-706-542-2675
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17
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Ailloud F, Estibariz I, Suerbaum S. Evolved to vary: genome and epigenome variation in the human pathogen Helicobacter pylori. FEMS Microbiol Rev 2021; 45:5900976. [PMID: 32880636 DOI: 10.1093/femsre/fuaa042] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/31/2020] [Indexed: 12/24/2022] Open
Abstract
Helicobacter pylori is a Gram-negative, spiral shaped bacterium that selectively and chronically infects the gastric mucosa of humans. The clinical course of this infection can range from lifelong asymptomatic infection to severe disease, including peptic ulcers or gastric cancer. The high mutation rate and natural competence typical of this species are responsible for massive inter-strain genetic variation exceeding that observed in all other bacterial human pathogens. The adaptive value of such a plastic genome is thought to derive from a rapid exploration of the fitness landscape resulting in fast adaptation to the changing conditions of the gastric environment. Nevertheless, diversity is also lost through recurrent bottlenecks and H. pylori's lifestyle is thus a perpetual race to maintain an appropriate pool of standing genetic variation able to withstand selection events. Another aspect of H. pylori's diversity is a large and variable repertoire of restriction-modification systems. While not yet completely understood, methylome evolution could generate enough transcriptomic variation to provide another intricate layer of adaptive potential. This review provides an up to date synopsis of this rapidly emerging area of H. pylori research that has been enabled by the ever-increasing throughput of Omics technologies and a multitude of other technological advances.
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Affiliation(s)
- Florent Ailloud
- Max von Pettenkofer Institute, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 München, Germany
| | - Iratxe Estibariz
- Max von Pettenkofer Institute, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 München, Germany
| | - Sebastian Suerbaum
- Max von Pettenkofer Institute, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 München, Germany.,DZIF Deutsches Zentrum für Infektionsforschung, Partner Site Munich, Pettenkoferstr. 9a, 80336 München, Germany.,National Reference Center for Helicobacter pylori, Pettenkoferstr. 9a, 80336 München, Germany
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18
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Mehershahi KS, Chen SL. DNA methylation by three Type I restriction modification systems of Escherichia coli does not influence gene regulation of the host bacterium. Nucleic Acids Res 2021; 49:7375-7388. [PMID: 34181709 PMCID: PMC8287963 DOI: 10.1093/nar/gkab530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/01/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is a common epigenetic mark that influences transcriptional regulation, and therefore cellular phenotype, across all domains of life. In particular, both orphan methyltransferases and those from phasevariable restriction modification systems (RMSs) have been co-opted to regulate virulence epigenetically in many bacteria. We now show that three distinct non-phasevariable Type I RMSs in Escherichia coli have no measurable impact on gene expression, in vivo virulence, or any of 1190 in vitro growth phenotypes. We demonstrated this using both Type I RMS knockout mutants as well as heterologous installation of Type I RMSs into two E. coli strains. These data provide three clear and currently rare examples of restriction modification systems that have no impact on their host organism’s gene regulation. This leads to the possibility that other such nonregulatory methylation systems may exist, broadening our view of the potential role that RMSs may play in bacterial evolution.
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Affiliation(s)
- Kurosh S Mehershahi
- NUHS Infectious Diseases Translational Research Programme, Department of Medicine, Division of Infectious Diseases, Yong Loo Lin School of Medicine, Singapore 119228
| | - Swaine L Chen
- NUHS Infectious Diseases Translational Research Programme, Department of Medicine, Division of Infectious Diseases, Yong Loo Lin School of Medicine, Singapore 119228.,Laboratory of Bacterial Genomics, Genome Institute of Singapore, Singapore 138672
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19
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Gupta A, Alland D. Reversible gene silencing through frameshift indels and frameshift scars provide adaptive plasticity for Mycobacterium tuberculosis. Nat Commun 2021; 12:4702. [PMID: 34349104 PMCID: PMC8339072 DOI: 10.1038/s41467-021-25055-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 07/16/2021] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium tuberculosis can adapt to changing environments by non-heritable mechanisms. Frame-shifting insertions and deletions (indels) may also participate in adaptation through gene disruption, which could be reversed by secondary introduction of a frame-restoring indel. We present ScarTrek, a program that scans genomic data for indels, including those that together disrupt and restore a gene's reading frame, producing "frame-shift scars" suggestive of reversible gene inactivation. We use ScarTrek to analyze 5977 clinical M. tuberculosis isolates. We show that indel frequency inversely correlates with genomic linguistic complexity and varies with gene-position and gene-essentiality. Using ScarTrek, we detect 74 unique frame-shift scars in 48 genes, with a 3.74% population-level incidence of unique scar events. We find multiple scars in the ESX-1 gene cluster. Six scars show evidence of convergent evolution while the rest shared a common ancestor. Our results suggest that sequential indels are a mechanism for reversible gene silencing and adaptation in M. tuberculosis.
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Affiliation(s)
- Aditi Gupta
- Center for Emerging Pathogens, New Jersey Medical School, Rutgers University, Newark, NJ, USA.
| | - David Alland
- Center for Emerging Pathogens, New Jersey Medical School, Rutgers University, Newark, NJ, USA.
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20
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Anton BP, Roberts RJ. Beyond Restriction Modification: Epigenomic Roles of DNA Methylation in Prokaryotes. Annu Rev Microbiol 2021; 75:129-149. [PMID: 34314594 DOI: 10.1146/annurev-micro-040521-035040] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The amount of bacterial and archaeal genome sequence and methylome data has greatly increased over the last decade, enabling new insights into the functional roles of DNA methylation in these organisms. Methyltransferases (MTases), the enzymes responsible for DNA methylation, are exchanged between prokaryotes through horizontal gene transfer and can function either as part of restriction-modification systems or in apparent isolation as single (orphan) genes. The patterns of DNA methylation they confer on the host chromosome can have significant effects on gene expression, DNA replication, and other cellular processes. Some processes require very stable patterns of methylation, resulting in conservation of persistent MTases in a particular lineage. Other processes require patterns that are more dynamic yet more predictable than what is afforded by horizontal gene transfer and gene loss, resulting in phase-variable or recombination-driven MTase alleles. In this review, we discuss what is currently known about the functions of DNA methylation in prokaryotes in light of these evolutionary patterns. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Brian P Anton
- New England Biolabs, Ipswich, Massachusetts 01938, USA; ,
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21
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Streptococcus suis Encodes Multiple Allelic Variants of a Phase-Variable Type III DNA Methyltransferase, ModS, That Control Distinct Phasevarions. mSphere 2021; 6:6/3/e00069-21. [PMID: 33980672 PMCID: PMC8125046 DOI: 10.1128/msphere.00069-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptococcus suis is a causative agent of meningitis, polyarthritis, and polyserositis in swine, and it is a major cause of zoonotic meningitis in humans. Here, we investigate epigenetic gene regulation in S. suis by multiple phasevarions controlled by the phase-variable type III DNA methyltransferase ModS. Streptococcus suis is a significant cause of bacterial meningitis in humans, particularly in Southeast Asia, and is a leading cause of respiratory and invasive disease in pigs. Phase-variable DNA methyltransferases, associated with restriction-modification (R-M) systems, are a source of epigenetic gene regulation, controlling the expression of multiple genes. These systems are known as phasevarions (phase-variable regulons) and have been characterized in many host-adapted bacterial pathogens. We recently described the presence of a Type III DNA methyltransferase in S. suis, ModS, which contains a simple sequence repeat (SSR) tract within the open reading frame of the modS gene and which differed in length between individual strains. We also observed that multiple allelic variants of the modS gene were present in a population of S. suis isolates. Here, we demonstrate that a biphasic ON-OFF switching of expression occurs in the two most common ModS alleles, ModS1 and ModS2, and that switching is dependent on SSR tract length. Furthermore, we show using single-molecule real-time (SMRT) sequencing that ModS1 and ModS2 are active methyltransferases in S. suis. ON-OFF switching of each ModS allele results in the regulation of distinct phasevarions, with the ModS2 phasevarion impacting growth patterns and antibiotic resistance. This is the first demonstration of a phase-variable Type III DNA methyltransferase in a Gram-positive organism that controls a phasevarion. Characterizing the phenotypic effects of phasevarions in S. suis is key to understanding pathogenesis and the development of future vaccines. IMPORTANCEStreptococcus suis is a causative agent of meningitis, polyarthritis, and polyserositis in swine, and it is a major cause of zoonotic meningitis in humans. Here, we investigate epigenetic gene regulation in S. suis by multiple phasevarions controlled by the phase-variable Type III DNA methyltransferase ModS. This is the first characterized example of a Type III R-M system regulating a phasevarion in a Gram-positive organism. We demonstrate that biphasic ON-OFF switching of ModS expression results in differences in bacterial growth and antibiotic resistance. Understanding the effects of ModS phase variation is required to determine the stably expressed antigenic repertoire of S. suis, which will direct and inform the development of antimicrobial treatments and vaccines against this important pathogen.
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22
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Transcriptional Profile of Helicobacter pylori Virulence Genes in Patients with Gastritis and Gastric Cancer. ACTA ACUST UNITED AC 2021; 2021:1309519. [PMID: 33628350 PMCID: PMC7889378 DOI: 10.1155/2021/1309519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 01/01/2021] [Accepted: 02/01/2021] [Indexed: 12/14/2022]
Abstract
Introduction Numerous molecular epidemiology studies have been performed about the frequency of Helicobacter pylori virulence genes in patients with H. pylori infection so far. This study was conducted to detect transcriptional profile by cDNA of H. pylori virulence genes in gastric biopsy samples of gastritis and gastric carcinoma patients. Materials and Methods In a case-control study, based on the prevalence of gastritis and gastric cancer in Sanandaj city during 2018 and 2019, 23 and 11 gastric antral biopsy samples with H. pylori infection were collected from gastritis and gastric carcinoma patients by the consecutive and available sampling method. Pathological characters, including tumor grades and tumor areas for gastric carcinoma biopsy samples prepared from gastric cancer areas, were determined by the pathologist. Total RNA of gastric antral biopsy samples was extracted, and their cDNA was synthesized by TaKaRa kit. H. pylori virulence genes' cDNA using specific primers and PCR was detected. This study's results were analyzed by SPSS version 25 and statics chi-square tests for determination of relationship and correlation between cDNAs of H. pylori transcriptional profile and clinical outcomes of H. pylori infection, including gastritis, gastric carcinoma, tumor grades, and tumor area. Results The positive statistical correlations were observed between transcripts of cagA, cagA-EPIYAC, cagE, and cagY genes and H. pylori infection clinical outcomes (P < 0.05). Conclusion Detection of the H. pylori virulence genes' cDNA in gastric biopsy samples can help provide the prognosis of clinical outcomes.
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23
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Prokaryotic DNA methylation and its functional roles. J Microbiol 2021; 59:242-248. [DOI: 10.1007/s12275-021-0674-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/31/2022]
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24
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Robledo-Avila FH, Ruiz-Rosado JDD, Partida-Sanchez S, Brockman KL. A Bacterial Epigenetic Switch in Non-typeable Haemophilus influenzae Modifies Host Immune Response During Otitis Media. Front Cell Infect Microbiol 2020; 10:512743. [PMID: 33194779 PMCID: PMC7644868 DOI: 10.3389/fcimb.2020.512743] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 09/15/2020] [Indexed: 01/15/2023] Open
Abstract
Non-typeable Haemophilus influenzae (NTHi) causes multiple diseases of the human airway and is a predominant bacterial pathogen of acute otitis media and otitis media in which treatment fails. NTHi utilizes a system of phase variable epigenetic regulation, termed the phasevarion, to facilitate adaptation and survival within multiple sites of the human host. The NTHi phasevarion influences numerous disease-relevant phenotypes such as biofilm formation, antibiotic resistance, and opsonization. We have previously identified an advantageous selection for a specific phasevarion status, which significantly affects severity and chronicity of experimental otitis media. In this study, we utilized pure cultures of NTHi variants in which modA was either locked ON or locked OFF, and thus modA was unable to phase vary. These locked variants were used to assess the progression of experimental otitis media and define the specific immune response induced by each subpopulation. Although the initial disease caused by each subpopulation was similar, the immune response elicited by each subpopulation was unique. The modA2 OFF variant induced significantly greater activation of macrophages both in vitro and within the middle ear during disease. In contrast, the modA2 ON variant induced a greater neutrophil extracellular trap response, which led to greater killing of the modA2 ON variant. These data suggest that not only does the NTHi phasevarion facilitate adaptation, but also allows the bacteria to alter immune responses during disease. Understanding these complex bacterial-host interactions and the regulation of bacterial factors responsible is critical to the development of better diagnostic, treatment, and preventative strategies for these bacterial pathogens.
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Affiliation(s)
- Frank H Robledo-Avila
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, United States
| | - Juan de Dios Ruiz-Rosado
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.,Department of Biochemistry and Immunology, National Technological Institute of Oaxaca, Oaxaca, Mexico
| | - Santiago Partida-Sanchez
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Kenneth L Brockman
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH, United States.,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
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25
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Nye TM, Fernandez NL, Simmons LA. A positive perspective on DNA methylation: regulatory functions of DNA methylation outside of host defense in Gram-positive bacteria. Crit Rev Biochem Mol Biol 2020; 55:576-591. [PMID: 33059472 DOI: 10.1080/10409238.2020.1828257] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The presence of post-replicative DNA methylation is pervasive among both prokaryotic and eukaryotic organisms. In bacteria, the study of DNA methylation has largely been in the context of restriction-modification systems, where DNA methylation serves to safeguard the chromosome against restriction endonuclease cleavage intended for invading DNA. There has been a growing recognition that the methyltransferase component of restriction-modification systems can also regulate gene expression, with important contributions to virulence factor gene expression in bacterial pathogens. Outside of restriction-modification systems, DNA methylation from orphan methyltransferases, which lack cognate restriction endonucleases, has been shown to regulate important processes, including DNA replication, DNA mismatch repair, and the regulation of gene expression. The majority of research and review articles have been focused on DNA methylation in the context of Gram-negative bacteria, with emphasis toward Escherichia coli, Caulobacter crescentus, and related Proteobacteria. Here we summarize the epigenetic functions of DNA methylation outside of host defense in Gram-positive bacteria, with a focus on the regulatory effects of both phase variable methyltransferases and DNA methyltransferases from traditional restriction-modification systems.
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Affiliation(s)
- Taylor M Nye
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Nicolas L Fernandez
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lyle A Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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26
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Promiscuous DNA cleavage by HpyAII endonuclease is modulated by the HNH catalytic residues. Biosci Rep 2020; 40:226299. [PMID: 32880391 PMCID: PMC7494987 DOI: 10.1042/bsr20201633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/21/2020] [Accepted: 09/02/2020] [Indexed: 11/17/2022] Open
Abstract
Helicobacter pylori is a carcinogenic bacterium that is responsible for 5.5% of all human gastric cancers. H. pylori codes for an unusually large number of restriction-modification (R-M) systems and several of them are strain-specific and phase-variable. HpyAII is a novel Type IIs phase-variable restriction endonuclease present in 26695 strain of H. pylori. We show that HpyAII prefers two-site substrates over one-site substrates for maximal cleavage activity. HpyAII is less stringent in metal ion requirement and shows higher cleavage activity with Ni2+ over Mg2+. Mutational analysis of the putative residues of the HNH motif of HpyAII confirms that the protein has an active HNH site for the cleavage of DNA. However, mutation of the first Histidine residue of the HNH motif to Alanine does not abolish the enzymatic activity, but instead causes loss of fidelity compared with wildtype HpyAII. Previous studies have shown that mutation of the first Histidine residue of the HNH motif of all other known HNH motif motif-containing enzymes completely abolishes enzymatic activity. We found, in the case of HpyAII, mutation of an active site residue leads to the loss of endonuclease fidelity. The present study provides further insights into the evolution of restriction enzymes.
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Oliver MB, Swords WE. Comparative Analysis of Streptococcus pneumoniae Type I Restriction-Modification Loci: Variation in hsdS Gene Target Recognition Domains. Pathogens 2020; 9:pathogens9090712. [PMID: 32872494 PMCID: PMC7557576 DOI: 10.3390/pathogens9090712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 11/17/2022] Open
Abstract
Streptococcus pneumoniae (pneumococcus) is a respiratory commensal pathogen that causes a range of infections, particularly in young children and the elderly. Pneumococci undergo spontaneous phase variation in colony opacity phenotype, in which DNA rearrangements within the Type I restriction-modification (R-M) system specificity gene hsdS can potentially generate up to six different hsdS alleles with differential DNA methylation activity, resulting in changes in gene expression. To gain a broader perspective of this system, we performed bioinformatic analyses of Type I R-M loci from 18 published pneumococcal genomes, and one R-M locus sequenced for this study, to compare genetic content, organization, and homology. All 19 loci encoded the genes hsdR, hsdM, hsdS, and at least one hsdS pseudogene, but differed in gene order, gene orientation, and hsdS target recognition domain (TRD) content. We determined the coding sequences of 87 hsdS TRDs and excluded seven from further analysis due to the presence of premature stop codons. Comparative analyses revealed that the TRD 1.1, 1.2, and 2.1 protein sequences had single amino acid substitutions, and TRD 2.2 and 2.3 each had seven differences. The results of this study indicate that variability exists among the gene content and arrangements within Type I R-M loci may provide an additional level of divergence between pneumococcal strains, such that phase variation-mediated control of virulence factors may vary significantly between individual strains. These findings are consistent with presently available transcript profile data.
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Affiliation(s)
- Melissa B. Oliver
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine University of Alabama at Birmingham, Birmingham, 35294 AL, USA;
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, 35294 AL, USA
| | - W. Edward Swords
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine University of Alabama at Birmingham, Birmingham, 35294 AL, USA;
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, 35294 AL, USA
- Correspondence:
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In Vivo Genome and Methylome Adaptation of cag-Negative Helicobacter pylori during Experimental Human Infection. mBio 2020; 11:mBio.01803-20. [PMID: 32843556 PMCID: PMC7448279 DOI: 10.1128/mbio.01803-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Exceptional genetic diversity and variability are hallmarks of Helicobacter pylori, but the biological role of this plasticity remains incompletely understood. Here, we had the rare opportunity to investigate the molecular evolution during the first weeks of H. pylori infection by comparing the genomes and epigenomes of H. pylori strain BCS 100 used to challenge human volunteers in a vaccine trial with those of bacteria reisolated from the volunteers 10 weeks after the challenge. The data provide molecular insights into the process of establishment of this highly versatile pathogen in 10 different human individual hosts, showing, for example, selection for changes in host-interaction molecules as well as changes in epigenetic methylation patterns. The data provide important clues to the early adaptation of H. pylori to new host niches after transmission, which we believe is vital to understand its success as a chronic pathogen and develop more efficient treatments and vaccines. Multiple studies have demonstrated rapid bacterial genome evolution during chronic infection with Helicobacter pylori. In contrast, little was known about genetic changes during the first stages of infection, when selective pressure is likely to be highest. Using single-molecule, real-time (SMRT) and Illumina sequencing technologies, we analyzed genome and methylome evolution during the first 10 weeks of infection by comparing the cag pathogenicity island (cagPAI)-negative H. pylori challenge strain BCS 100 with pairs of H. pylori reisolates from gastric antrum and corpus biopsy specimens of 10 human volunteers who had been infected with this strain as part of a vaccine trial. Most genetic changes detected in the reisolates affected genes with a surface-related role or a predicted function in peptide uptake. Apart from phenotypic changes of the bacterial envelope, a duplication of the catalase gene was observed in one reisolate, which resulted in higher catalase activity and improved survival under oxidative stress conditions. The methylomes also varied in some of the reisolates, mostly by activity switching of phase-variable methyltransferase (MTase) genes. The observed in vivo mutation spectrum was remarkable for a very high proportion of nonsynonymous mutations. Although the data showed substantial within-strain genome diversity in the challenge strain, most antrum and corpus reisolates from the same volunteers were highly similar to each other, indicating that the challenge infection represents a major selective bottleneck shaping the transmitted population. Our findings suggest rapid in vivo selection of H. pylori during early-phase infection providing adaptation to different individuals by common mechanisms of genetic and epigenetic alterations.
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29
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Systematic Analysis of REBASE Identifies Numerous Type I Restriction-Modification Systems with Duplicated, Distinct hsdS Specificity Genes That Can Switch System Specificity by Recombination. mSystems 2020; 5:5/4/e00497-20. [PMID: 32723795 PMCID: PMC7394358 DOI: 10.1128/msystems.00497-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Many bacterial species contain DNA methyltransferases that have random on/off switching of expression. These systems, called phasevarions (phase-variable regulons), control the expression of multiple genes by global methylation changes. In every previously characterized phasevarion, genes involved in pathobiology, antibiotic resistance, and potential vaccine candidates are randomly varied in their expression, commensurate with methyltransferase switching. Our systematic study to determine the extent of phasevarions controlled by invertible Type I R-M systems will provide valuable information for understanding how bacteria regulate genes and is key to the study of physiology, virulence, and vaccine development; therefore, it is critical to identify and characterize phase-variable methyltransferases controlling phasevarions. N6-Adenine DNA methyltransferases associated with some Type I and Type III restriction-modification (R-M) systems are able to undergo phase variation, randomly switching expression ON or OFF by varying the length of locus-encoded simple sequence repeats (SSRs). This variation of methyltransferase expression results in genome-wide methylation differences and global changes in gene expression. These epigenetic regulatory systems are called phasevarions, phase-variable regulons, and are widespread in bacteria. A distinct switching system has also been described in Type I R-M systems, based on recombination-driven changes in hsdS genes, which dictate the DNA target site. In order to determine the prevalence of recombination-driven phasevarions, we generated a program called RecombinationRepeatSearch to interrogate REBASE and identify the presence and number of inverted repeats of hsdS downstream of Type I R-M loci. We report that 3.9% of Type I R-M systems have duplicated variable hsdS genes containing inverted repeats capable of phase variation. We report the presence of these systems in the major pathogens Enterococcus faecalis and Listeria monocytogenes, which could have important implications for pathogenesis and vaccine development. These data suggest that in addition to SSR-driven phasevarions, many bacteria have independently evolved phase-variable Type I R-M systems via recombination between multiple, variable hsdS genes. IMPORTANCE Many bacterial species contain DNA methyltransferases that have random on/off switching of expression. These systems, called phasevarions (phase-variable regulons), control the expression of multiple genes by global methylation changes. In every previously characterized phasevarion, genes involved in pathobiology, antibiotic resistance, and potential vaccine candidates are randomly varied in their expression, commensurate with methyltransferase switching. Our systematic study to determine the extent of phasevarions controlled by invertible Type I R-M systems will provide valuable information for understanding how bacteria regulate genes and is key to the study of physiology, virulence, and vaccine development; therefore, it is critical to identify and characterize phase-variable methyltransferases controlling phasevarions.
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30
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Seib KL, Srikhanta YN, Atack JM, Jennings MP. Epigenetic Regulation of Virulence and Immunoevasion by Phase-Variable Restriction-Modification Systems in Bacterial Pathogens. Annu Rev Microbiol 2020; 74:655-671. [PMID: 32689914 DOI: 10.1146/annurev-micro-090817-062346] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human-adapted bacterial pathogens use a mechanism called phase variation to randomly switch the expression of individual genes to generate a phenotypically diverse population to adapt to challenges within and between human hosts. There are increasing reports of restriction-modification systems that exhibit phase-variable expression. The outcome of phase variation of these systems is global changes in DNA methylation. Analysis of phase-variable Type I and Type III restriction-modification systems in multiple human-adapted bacterial pathogens has demonstrated that global changes in methylation regulate the expression of multiple genes. These systems are called phasevarions (phase-variable regulons). Phasevarion switching alters virulence phenotypes and facilitates evasion of host immune responses. This review describes the characteristics of phasevarions and implications for pathogenesis and immune evasion. We present and discuss examples of phasevarion systems in the major human pathogens Haemophilus influenzae, Neisseria meningitidis, Neisseria gonorrhoeae, Helicobacter pylori, Moraxella catarrhalis, and Streptococcus pneumoniae.
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Affiliation(s)
- Kate L Seib
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia; ,
| | - Yogitha N Srikhanta
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - John M Atack
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia; ,
| | - Michael P Jennings
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia; ,
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31
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Yano H, Alam MZ, Rimbara E, Shibata TF, Fukuyo M, Furuta Y, Nishiyama T, Shigenobu S, Hasebe M, Toyoda A, Suzuki Y, Sugano S, Shibayama K, Kobayashi I. Networking and Specificity-Changing DNA Methyltransferases in Helicobacter pylori. Front Microbiol 2020; 11:1628. [PMID: 32765461 PMCID: PMC7379913 DOI: 10.3389/fmicb.2020.01628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
Epigenetic DNA base methylation plays important roles in gene expression regulation. We here describe a gene expression regulation network consisting of many DNA methyltransferases each frequently changing its target sequence-specificity. Our object Helicobacter pylori, a bacterium responsible for most incidence of stomach cancer, carries a large and variable repertoire of sequence-specific DNA methyltransferases. By creating a dozen of single-gene knockout strains for the methyltransferases, we revealed that they form a network controlling methylome, transcriptome and adaptive phenotype sets. The methyltransferases interact with each other in a hierarchical way, sometimes regulated positively by one methyltransferase but negatively with another. Motility, oxidative stress tolerance and DNA damage repair are likewise regulated by multiple methyltransferases. Their regulation sometimes involves translation start and stop codons suggesting coupling of methylation, transcription and translation. The methyltransferases frequently change their sequence-specificity through gene conversion of their target recognition domain and switch their target sets to remodel the network. The emerging picture of a metamorphosing gene regulation network, or firework, consisting of epigenetic systems ever-changing their specificity in search for adaptation, provides a new paradigm in understanding global gene regulation and adaptive evolution.
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Affiliation(s)
- Hirokazu Yano
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.,Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Md Zobaidul Alam
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Emiko Rimbara
- Department of Bacteriology II, National Institute of Infectious Diseases (NIID), Musashimurayama, Japan
| | | | | | - Yoshikazu Furuta
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.,Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | | | - Mitsuyasu Hasebe
- National Institute for Basic Biology (NIBB), Okazaki, Japan.,Department of Basic Biology, School of Life Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Sumio Sugano
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.,Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Keigo Shibayama
- Department of Bacteriology II, National Institute of Infectious Diseases (NIID), Musashimurayama, Japan
| | - Ichizo Kobayashi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.,Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Department of Infectious Diseases, School of Medicine, Kyorin University, Mitaka, Japan.,Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France.,Research Center for Micro-Nano Technology, Hosei University, Koganei, Japan
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32
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Antibiotic Resistance and Epigenetics: More to It than Meets the Eye. Antimicrob Agents Chemother 2020; 64:AAC.02225-19. [PMID: 31740560 DOI: 10.1128/aac.02225-19] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The discovery of antibiotics in the last century is considered one of the most important achievements in the history of medicine. Antibiotic usage has significantly reduced morbidity and mortality associated with bacterial infections. However, inappropriate use of antibiotics has led to emergence of antibiotic resistance at an alarming rate. Antibiotic resistance is regarded as a major health care challenge of this century. Despite extensive research, well-documented biochemical mechanisms and genetic changes fail to fully explain mechanisms underlying antibiotic resistance. Several recent reports suggest a key role for epigenetics in the development of antibiotic resistance in bacteria. The intrinsic heterogeneity as well as transient nature of epigenetic inheritance provides a plausible backdrop for high-paced emergence of drug resistance in bacteria. The methylation of adenines and cytosines can influence mutation rates in bacterial genomes, thus modulating antibiotic susceptibility. In this review, we discuss a plethora of recently discovered epigenetic mechanisms and their emerging roles in antibiotic resistance. We also highlight specific epigenetic mechanisms that merit further investigation for their role in antibiotic resistance.
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33
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Narayanan N, Banerjee A, Jain D, Kulkarni DS, Sharma R, Nirwal S, Rao DN, Nair DT. Tetramerization at Low pH Licenses DNA Methylation Activity of M.HpyAXI in the Presence of Acid Stress. J Mol Biol 2020; 432:324-342. [DOI: 10.1016/j.jmb.2019.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/01/2019] [Accepted: 10/01/2019] [Indexed: 11/25/2022]
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34
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Blakeway LV, Tan A, Jurcisek JA, Bakaletz LO, Atack JM, Peak IR, Seib KL. The Moraxella catarrhalis phase-variable DNA methyltransferase ModM3 is an epigenetic regulator that affects bacterial survival in an in vivo model of otitis media. BMC Microbiol 2019; 19:276. [PMID: 31818247 PMCID: PMC6902483 DOI: 10.1186/s12866-019-1660-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 11/22/2019] [Indexed: 12/23/2022] Open
Abstract
Background Moraxella catarrhalis is a leading cause of otitis media (OM) and chronic obstructive pulmonary disease (COPD). M. catarrhalis contains a Type III DNA adenine methyltransferase (ModM) that is phase-variably expressed (i.e., its expression is subject to random, reversible ON/OFF switching). ModM has six target recognition domain alleles (modM1–6), and we have previously shown that modM2 is the predominant allele, while modM3 is associated with OM. Phase-variable DNA methyltransferases mediate epigenetic regulation and modulate pathogenesis in several bacteria. ModM2 of M. catarrhalis regulates the expression of a phasevarion containing genes important for colonization and infection. Here we describe the phase-variable expression of modM3, the ModM3 methylation site and the suite of genes regulated within the ModM3 phasevarion. Results Phase-variable expression of modM3, mediated by variation in length of a 5′-(CAAC)n-3′ tetranucleotide repeat tract in the open reading frame was demonstrated in M. catarrhalis strain CCRI-195ME with GeneScan fragment length analysis and western immunoblot. We determined that ModM3 is an active N6-adenine methyltransferase that methylates the sequence 5′-ACm6ATC-3′. Methylation was detected at all 4446 5′-ACATC-3′ sites in the genome when ModM3 is expressed. RNASeq analysis identified 31 genes that are differentially expressed between modM3 ON and OFF variants, including five genes that are involved in the response to oxidative and nitrosative stress, with potential roles in biofilm formation and survival in anaerobic environments. An in vivo chinchilla (Chinchilla lanigera) model of otitis media demonstrated that transbullar challenge with the modM3 OFF variant resulted in an increased middle ear bacterial load compared to a modM3 ON variant. In addition, co-infection experiments with NTHi and M. catarrhalis modM3 ON or modM3 OFF variants revealed that phase variation of modM3 altered survival of NTHi in the middle ear during early and late stage infection. Conclusions Phase variation of ModM3 epigenetically regulates the expression of a phasevarion containing multiple genes that are potentially important in the progression of otitis media.
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Affiliation(s)
- Luke V Blakeway
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia
| | - Aimee Tan
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia
| | - Joseph A Jurcisek
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, OH, 43215, USA
| | - Lauren O Bakaletz
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, OH, 43215, USA
| | - John M Atack
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia
| | - Ian R Peak
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia.,School of Medical Science, Griffith University, Gold Coast, Queensland, 4215, Australia
| | - Kate L Seib
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia.
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35
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Atack JM, Guo C, Yang L, Zhou Y, Jennings MP. DNA sequence repeats identify numerous Type I restriction-modification systems that are potential epigenetic regulators controlling phase-variable regulons; phasevarions. FASEB J 2019; 34:1038-1051. [PMID: 31914596 PMCID: PMC7383803 DOI: 10.1096/fj.201901536rr] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 11/07/2019] [Accepted: 11/09/2019] [Indexed: 12/27/2022]
Abstract
Over recent years several examples of randomly switching methyltransferases, associated with Type III restriction‐modification (R‐M) systems, have been described in pathogenic bacteria. In every case examined, changes in simple DNA sequence repeats result in variable methyltransferase expression and result in global changes in gene expression, and differentiation of the bacterial cell into distinct phenotypes. These epigenetic regulatory systems are called phasevarions, phase‐variable regulons, and are widespread in bacteria, with 17.4% of Type III R‐M system containing simple DNA sequence repeats. A distinct, recombination‐driven random switching system has also been described in Streptococci in Type I R‐M systems that also regulate gene expression. Here, we interrogate the most extensive and well‐curated database of R‐M systems, REBASE, by searching for all possible simple DNA sequence repeats in the hsdRMS genes that encode Type I R‐M systems. We report that 7.9% of hsdS, 2% of hsdM, and of 4.3% of hsdR genes contain simple sequence repeats that are capable of mediating phase variation. Phase variation of both hsdM and hsdS genes will lead to differential methyltransferase expression or specificity, and thereby the potential to control phasevarions. These data suggest that in addition to well characterized phasevarions controlled by Type III mod genes, and the previously described Streptococcal Type I R‐M systems that switch via recombination, approximately 10% of all Type I R‐M systems surveyed herein have independently evolved the ability to randomly switch expression via simple DNA sequence repeats.
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Affiliation(s)
- John M Atack
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
| | - Chengying Guo
- College of Plant Protection, Shandong Agricultural University, Taian City, China
| | - Long Yang
- College of Plant Protection, Shandong Agricultural University, Taian City, China
| | - Yaoqi Zhou
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
| | - Michael P Jennings
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
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36
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Non-typeable Haemophilus influenzae isolates from patients with chronic obstructive pulmonary disease contain new phase-variable modA methyltransferase alleles controlling phasevarions. Sci Rep 2019; 9:15963. [PMID: 31685916 PMCID: PMC6828955 DOI: 10.1038/s41598-019-52429-6] [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: 04/08/2019] [Accepted: 10/12/2019] [Indexed: 02/07/2023] Open
Abstract
Phasevarions (phase-variable regulons) are emerging as an important area of bacterial gene regulation. Many bacterial pathogens contain phasevarions, with gene expression controlled by the phase-variable expression of DNA methyltransferases via epigenetic mechanisms. Non-typeable Haemophilus influenzae (NTHi) contains the phase-variable methyltransferase modA, of which multiple allelic variants exist (modA1-21). We have previously demonstrated 5 of 21 these modA alleles are overrepresented in NTHi strains isolated from children with middle ear infections. In this study we investigated the modA allele distribution in NTHi strains isolated from patients with chronic obstructive pulmonary disease, COPD. We demonstrate that the distribution of modA alleles in a large panel of COPD isolates is different to the distribution seen in middle ear infections, suggesting different modA alleles may provide distinct advantages in the differing niches of the middle ear and COPD airways. We also identified two new phase-variable modA alleles – modA15 and modA18 – and demonstrate that these alleles methylate distinct DNA sequences and control unique phasevarions. The modA15 and modA18 alleles have only been observed in COPD isolates, indicating that these two alleles may be markers for isolates likely to cause exacerbations of COPD.
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37
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Sánchez-Busó L, Golparian D, Parkhill J, Unemo M, Harris SR. Genetic variation regulates the activation and specificity of Restriction-Modification systems in Neisseria gonorrhoeae. Sci Rep 2019; 9:14685. [PMID: 31605008 PMCID: PMC6789123 DOI: 10.1038/s41598-019-51102-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 09/25/2019] [Indexed: 01/14/2023] Open
Abstract
Restriction-Modification systems (RMS) are one of the main mechanisms of defence against foreign DNA invasion and can have an important role in the regulation of gene expression. The obligate human pathogen Neisseria gonorrhoeae carries one of the highest loads of RMS in its genome; between 13 to 15 of the three main types. Previous work has described their organization in the reference genome FA1090 and has inferred the associated methylated motifs. Here, we studied the structure of RMS and target methylated motifs in 25 gonococcal strains sequenced with Single Molecule Real-Time (SMRT) technology, which provides data on DNA modification. The results showed a variable picture of active RMS in different strains, with phase variation switching the activity of Type III RMS, and both the activity and specificity of a Type I RMS. Interestingly, the Dam methylase was found in place of the NgoAXI endonuclease in two of the strains, despite being previously thought to be absent in the gonococcus. We also identified the real methylation target of NgoAXII as 5′-GCAGA-3′, different from that previously described. Results from this work give further insights into the diversity and dynamics of RMS and methylation patterns in N. gonorrhoeae.
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Affiliation(s)
- Leonor Sánchez-Busó
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK. .,Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, National Reference Laboratory for Sexually Transmitted Infections, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, National Reference Laboratory for Sexually Transmitted Infections, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Simon R Harris
- Microbiotica Ltd, Biodata Innovation Centre, Wellcome Genome Campus, Hinxton, Cambridge, UK.
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38
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Phase-variable bacterial loci: how bacteria gamble to maximise fitness in changing environments. Biochem Soc Trans 2019; 47:1131-1141. [PMID: 31341035 DOI: 10.1042/bst20180633] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/02/2019] [Accepted: 07/05/2019] [Indexed: 12/19/2022]
Abstract
Phase-variation of genes is defined as the rapid and reversible switching of expression - either ON-OFF switching or the expression of multiple allelic variants. Switching of expression can be achieved by a number of different mechanisms. Phase-variable genes typically encode bacterial surface structures, such as adhesins, pili, and lipooligosaccharide, and provide an extra contingency strategy in small-genome pathogens that may lack the plethora of 'sense-and-respond' gene regulation systems found in other organisms. Many bacterial pathogens also encode phase-variable DNA methyltransferases that control the expression of multiple genes in systems called phasevarions (phase-variable regulons). The presence of phase-variable genes allows a population of bacteria to generate a number of phenotypic variants, some of which may be better suited to either colonising certain host niches, surviving a particular environmental condition and/or evading an immune response. The presence of phase-variable genes complicates the determination of an organism's stably expressed antigenic repertoire; many phase-variable genes are highly immunogenic, and so would be ideal vaccine candidates, but unstable expression due to phase-variation may allow vaccine escape. This review will summarise our current understanding of phase-variable genes that switch expression by a variety of mechanisms, and describe their role in disease and pathobiology.
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Kumar S, Karmakar BC, Nagarajan D, Mukhopadhyay AK, Morgan RD, Rao DN. N4-cytosine DNA methylation regulates transcription and pathogenesis in Helicobacter pylori. Nucleic Acids Res 2019; 46:3429-3445. [PMID: 29481677 PMCID: PMC5909468 DOI: 10.1093/nar/gky126] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 02/13/2018] [Indexed: 01/08/2023] Open
Abstract
Many bacterial genomes exclusively display an N4-methyl cytosine base (m4C), whose physiological significance is not yet clear. Helicobacter pylori is a carcinogenic bacterium and the leading cause of gastric cancer in humans. Helicobacter pylori strain 26695 harbors a single m4C cytosine methyltransferase, M2.HpyAII which recognizes 5′ TCTTC 3′ sequence and methylates the first cytosine residue. To understand the role of m4C modification, M2.hpyAII deletion strain was constructed. Deletion strain displayed lower adherence to host AGS cells and reduced potential to induce inflammation and apoptosis. M2.hpyAII gene deletion strain exhibited reduced capacity for natural transformation, which was rescued in the complemented strain carrying an active copy of M2.hpyAII gene in the genome. Genome-wide gene expression and proteomic analysis were carried out to discern the possible reasons behind the altered phenotype of the M2.hpyAII gene deletion strain. Upon the loss of m4C modification a total of 102 genes belonging to virulence, ribosome assembly and cellular components were differentially expressed. The present study adds a functional role for the presence of m4C modification in H. pylori and provides the first evidence that m4C signal acts as a global epigenetic regulator in H. pylori.
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Affiliation(s)
- Sumith Kumar
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Bipul C Karmakar
- Division of Bacteriology, National Institute for Cholera and Enteric Diseases, Kolkata 700010, India
| | - Deepesh Nagarajan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Asish K Mukhopadhyay
- Division of Bacteriology, National Institute for Cholera and Enteric Diseases, Kolkata 700010, India
| | | | - Desirazu N Rao
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
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40
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Atack JM, Yang Y, Seib KL, Zhou Y, Jennings MP. A survey of Type III restriction-modification systems reveals numerous, novel epigenetic regulators controlling phase-variable regulons; phasevarions. Nucleic Acids Res 2019; 46:3532-3542. [PMID: 29554328 PMCID: PMC5909438 DOI: 10.1093/nar/gky192] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/10/2018] [Indexed: 12/21/2022] Open
Abstract
Many bacteria utilize simple DNA sequence repeats as a mechanism to randomly switch genes on and off. This process is called phase variation. Several phase-variable N6-adenine DNA-methyltransferases from Type III restriction-modification systems have been reported in bacterial pathogens. Random switching of DNA methyltransferases changes the global DNA methylation pattern, leading to changes in gene expression. These epigenetic regulatory systems are called phasevarions — phase-variable regulons. The extent of these phase-variable genes in the bacterial kingdom is unknown. Here, we interrogated a database of restriction-modification systems, REBASE, by searching for all simple DNA sequence repeats in mod genes that encode Type III N6-adenine DNA-methyltransferases. We report that 17.4% of Type III mod genes (662/3805) contain simple sequence repeats. Of these, only one-fifth have been previously identified. The newly discovered examples are widely distributed and include many examples in opportunistic pathogens as well as in environmental species. In many cases, multiple phasevarions exist in one genome, with examples of up to 4 independent phasevarions in some species. We found several new types of phase-variable mod genes, including the first example of a phase-variable methyltransferase in pathogenic Escherichia coli. Phasevarions are a common epigenetic regulation contingency strategy used by both pathogenic and non-pathogenic bacteria.
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Affiliation(s)
- John M Atack
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Yuedong Yang
- School of Data and Computer Science, Sun Yat-Sen University, Guangzhou 510006, China
| | - Kate L Seib
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Yaoqi Zhou
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Michael P Jennings
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
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41
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Phillips ZN, Husna AU, Jennings MP, Seib KL, Atack JM. Phasevarions of bacterial pathogens - phase-variable epigenetic regulators evolving from restriction-modification systems. MICROBIOLOGY-SGM 2019; 165:917-928. [PMID: 30994440 DOI: 10.1099/mic.0.000805] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Phase-variable DNA methyltransferases control the expression of multiple genes via epigenetic mechanisms in a wide variety of bacterial species. These systems are called phasevarions, for phase-variable regulons. Phasevarions regulate genes involved in pathogenesis, host adaptation and antibiotic resistance. Many human-adapted bacterial pathogens contain phasevarions. These include leading causes of morbidity and mortality worldwide, such as non-typeable Haemophilus influenzae, Streptococcus pneumoniae and Neisseria spp. Phase-variable methyltransferases and phasevarions have also been discovered in environmental organisms and veterinary pathogens. The existence of many different examples suggests that phasevarions have evolved multiple times as a contingency strategy in the bacterial domain, controlling phenotypes that are important in adapting to environmental change. Many of the organisms that contain phasevarions have existing or emerging drug resistance. Vaccines may therefore represent the best and most cost-effective tool to prevent disease caused by these organisms. However, many phasevarions also control the expression of current and putative vaccine candidates; variable expression of antigens could lead to immune evasion, meaning that vaccines designed using these targets become ineffective. It is therefore essential to characterize phasevarions in order to determine an organism's stably expressed antigenic repertoire, and rationally design broadly effective vaccines.
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Affiliation(s)
- Zachary N Phillips
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Asma-Ul Husna
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Michael P Jennings
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Kate L Seib
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - John M Atack
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
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42
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Estibariz I, Overmann A, Ailloud F, Krebes J, Josenhans C, Suerbaum S. The core genome m5C methyltransferase JHP1050 (M.Hpy99III) plays an important role in orchestrating gene expression in Helicobacter pylori. Nucleic Acids Res 2019; 47:2336-2348. [PMID: 30624738 PMCID: PMC6412003 DOI: 10.1093/nar/gky1307] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 12/18/2018] [Accepted: 12/21/2018] [Indexed: 12/20/2022] Open
Abstract
Helicobacter pylori encodes a large number of restriction-modification (R-M) systems despite its small genome. R-M systems have been described as 'primitive immune systems' in bacteria, but the role of methylation in bacterial gene regulation and other processes is increasingly accepted. Every H. pylori strain harbours a unique set of R-M systems resulting in a highly diverse methylome. We identified a highly conserved GCGC-specific m5C MTase (JHP1050) that was predicted to be active in all of 459 H. pylori genome sequences analyzed. Transcriptome analysis of two H. pylori strains and their respective MTase mutants showed that inactivation of the MTase led to changes in the expression of 225 genes in strain J99, and 29 genes in strain BCM-300. Ten genes were differentially expressed in both mutated strains. Combining bioinformatic analysis and site-directed mutagenesis, we demonstrated that motifs overlapping the promoter influence the expression of genes directly, while methylation of other motifs might cause secondary effects. Thus, m5C methylation modifies the transcription of multiple genes, affecting important phenotypic traits that include adherence to host cells, natural competence for DNA uptake, bacterial cell shape, and susceptibility to copper.
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Affiliation(s)
- Iratxe Estibariz
- Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, München, Germany
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Munich Site, Munich, Germany
| | - Annemarie Overmann
- Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, München, Germany
| | - Florent Ailloud
- Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, München, Germany
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Munich Site, Munich, Germany
| | - Juliane Krebes
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Christine Josenhans
- Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, München, Germany
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Munich Site, Munich, Germany
| | - Sebastian Suerbaum
- Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, München, Germany
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Munich Site, Munich, Germany
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43
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Beaulaurier J, Schadt EE, Fang G. Deciphering bacterial epigenomes using modern sequencing technologies. Nat Rev Genet 2019; 20:157-172. [PMID: 30546107 PMCID: PMC6555402 DOI: 10.1038/s41576-018-0081-3] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Prokaryotic DNA contains three types of methylation: N6-methyladenine, N4-methylcytosine and 5-methylcytosine. The lack of tools to analyse the frequency and distribution of methylated residues in bacterial genomes has prevented a full understanding of their functions. Now, advances in DNA sequencing technology, including single-molecule, real-time sequencing and nanopore-based sequencing, have provided new opportunities for systematic detection of all three forms of methylated DNA at a genome-wide scale and offer unprecedented opportunities for achieving a more complete understanding of bacterial epigenomes. Indeed, as the number of mapped bacterial methylomes approaches 2,000, increasing evidence supports roles for methylation in regulation of gene expression, virulence and pathogen-host interactions.
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Affiliation(s)
- John Beaulaurier
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Abstract
ABSTRACT
Streptococcus pneumoniae
undergoes phase variation or spontaneous, reversible phenotypic variation in colony opacity, encapsulation, and pilus expression. The variation in colony opacity appears to occur in all strains, whereas the switches in the production of the capsule and pilus have been observed in several strains. This chapter elaborates on the variation in colony opacity since this phenomenon has been extensively characterized.
S. pneumoniae
produces opaque and transparent colonies on the translucent agar medium. The different colony phases are fundamentally distinct phenotypes in their metabolism and multiple characteristics, as exemplified by cell surface features and phenotypes in colonization and virulence. Opaque variants, which express more capsular polysaccharides and fewer teichoic acids, are more virulent in animal models of sepsis but colonize the nasopharynx poorly. In contrast, transparent variants, with fewer capsular polysaccharides and more teichoic acid, colonize the nasopharynx in animal models more efficiently but are relatively avirulent. Lastly, pneumococcal opacity variants are generated by differential methylation of the genome DNA variation. The reversible switch in the methylation pattern is caused by DNA inversions in three homologous
hsdS
genes of the colony opacity determinant (
cod
) or SpnD39III locus, a conserved type I restriction-modification (RM) system. The
hsdS
gene encodes the sequence recognition subunit of the type I RM DNA methyltransferase. The combination of DNA inversion and differential methylation, a complex mechanism of phase variation, generates a mixed population that may allow for the selection of organisms
in vivo
with characteristics permissive for either carriage or systemic infection.
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45
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Atack JM, Weinert LA, Tucker AW, Husna AU, Wileman TM, F. Hadjirin N, Hoa NT, Parkhill J, Maskell DJ, Blackall PJ, Jennings MP. Streptococcus suis contains multiple phase-variable methyltransferases that show a discrete lineage distribution. Nucleic Acids Res 2018; 46:11466-11476. [PMID: 30304532 PMCID: PMC6265453 DOI: 10.1093/nar/gky913] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/20/2018] [Accepted: 10/06/2018] [Indexed: 12/22/2022] Open
Abstract
Streptococcus suis is a major pathogen of swine, responsible for a number of chronic and acute infections, and is also emerging as a major zoonotic pathogen, particularly in South-East Asia. Our study of a diverse population of S. suis shows that this organism contains both Type I and Type III phase-variable methyltransferases. In all previous examples, phase-variation of methyltransferases results in genome wide methylation differences, and results in differential regulation of multiple genes, a system known as the phasevarion (phase-variable regulon). We hypothesized that each variant in the Type I and Type III systems encoded a methyltransferase with a unique specificity, and could therefore control a distinct phasevarion, either by recombination-driven shuffling between different specificities (Type I) or by biphasic on-off switching via simple sequence repeats (Type III). Here, we present the identification of the target specificities for each Type III allelic variant from S. suis using single-molecule, real-time methylome analysis. We demonstrate phase-variation is occurring in both Type I and Type III methyltransferases, and show a distinct association between methyltransferase type and presence, and population clades. In addition, we show that the phase-variable Type I methyltransferase was likely acquired at the origin of a highly virulent zoonotic sub-population.
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Affiliation(s)
- John M Atack
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Alexander W Tucker
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Asma U Husna
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Thomas M Wileman
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Nazreen F. Hadjirin
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Ngo T Hoa
- Oxford University Clinical Research Unit (OUCRU), 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | | | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Patrick J Blackall
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Michael P Jennings
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
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46
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Epigenetic Regulation Alters Biofilm Architecture and Composition in Multiple Clinical Isolates of Nontypeable Haemophilus influenzae. mBio 2018; 9:mBio.01682-18. [PMID: 30228240 PMCID: PMC6143736 DOI: 10.1128/mbio.01682-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Upper respiratory tract infections are the number one reason for a child to visit the emergency department, and otitis media (middle ear infection) ranks third overall. Biofilms contribute significantly to the chronic nature of bacterial respiratory tract infections, including otitis media, and make these diseases particularly difficult to treat. Several mucosa-associated human pathogens utilize a mechanism of rapid adaptation termed the phasevarion, or phasevariable regulon, to resist environmental and host immune pressures. In this study, we assessed the role of the phasevarion in regulation of biofilm formation by nontypeable Haemophilus influenzae (NTHI), which causes numerous respiratory tract diseases. We found that the NTHI phasevarion regulates biofilm structure and critical biofilm matrix components under disease-specific conditions. The findings of this work could be significant in the design of improved strategies against NTHI infections, as well as diseases due to other pathogens that utilize a phasevarion. Biofilms play a critical role in the colonization, persistence, and pathogenesis of many human pathogens. Multiple mucosa-associated pathogens have evolved a mechanism of rapid adaptation, termed the phasevarion, which facilitates a coordinated regulation of numerous genes throughout the bacterial genome. This epigenetic regulation occurs via phase variation of a DNA methyltransferase, Mod. The phasevarion of nontypeable Haemophilus influenzae (NTHI) significantly affects the severity of experimental otitis media and regulates several disease-related processes. However, the role of the NTHI phasevarion in biofilm formation is unclear. The present study shows that the phasevarions of multiple NTHI clinical isolates regulate in vitro biofilm formation under disease-specific microenvironmental conditions. The impact of phasevarion regulation was greatest under alkaline conditions that mimic those known to occur in the middle ear during disease. Under alkaline conditions, NTHI strains that express the ModA2 methyltransferase formed biofilms with significantly greater biomass and less distinct architecture than those formed by a ModA2-deficient population. The biofilms formed by NTHI strains that express ModA2 also contained less extracellular DNA (eDNA) and significantly less extracellular HU, a DNABII DNA-binding protein critical for biofilm structural stability. Stable biofilm structure is critical for bacterial pathogenesis and persistence in multiple experimental models of disease. These results identify a role for the phasevarion in regulation of biofilm formation, a process integral to the chronic nature of many infections. Understanding the role of the phasevarion in biofilm formation is critical to the development of prevention and treatment strategies for these chronic diseases.
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47
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Atack JM, Tan A, Bakaletz LO, Jennings MP, Seib KL. Phasevarions of Bacterial Pathogens: Methylomics Sheds New Light on Old Enemies. Trends Microbiol 2018; 26:715-726. [PMID: 29452952 PMCID: PMC6054543 DOI: 10.1016/j.tim.2018.01.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 01/06/2018] [Accepted: 01/26/2018] [Indexed: 01/04/2023]
Abstract
A wide variety of bacterial pathogens express phase-variable DNA methyltransferases that control expression of multiple genes via epigenetic mechanisms. These randomly switching regulons - phasevarions - regulate genes involved in pathogenesis, host adaptation, and antibiotic resistance. Individual phase-variable genes can be identified in silico as they contain easily recognized features such as simple sequence repeats (SSRs) or inverted repeats (IRs) that mediate the random switching of expression. Conversely, phasevarion-controlled genes do not contain any easily identifiable features. The study of DNA methyltransferase specificity using Single-Molecule, Real-Time (SMRT) sequencing and methylome analysis has rapidly advanced the analysis of phasevarions by allowing methylomics to be combined with whole-transcriptome/proteome analysis to comprehensively characterize these systems in a number of important bacterial pathogens.
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Affiliation(s)
- John M Atack
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4222, Australia.
| | - Aimee Tan
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4222, Australia
| | - Lauren O Bakaletz
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH 43205, USA
| | - Michael P Jennings
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4222, Australia
| | - Kate L Seib
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4222, Australia.
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48
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Srikhanta YN, Gorrell RJ, Power PM, Tsyganov K, Boitano M, Clark TA, Korlach J, Hartland EL, Jennings MP, Kwok T. Methylomic and phenotypic analysis of the ModH5 phasevarion of Helicobacter pylori. Sci Rep 2017; 7:16140. [PMID: 29170397 PMCID: PMC5700931 DOI: 10.1038/s41598-017-15721-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 10/31/2017] [Indexed: 12/20/2022] Open
Abstract
The Helicobacter pylori phase variable gene modH, typified by gene HP1522 in strain 26695, encodes a N6-adenosine type III DNA methyltransferase. Our previous studies identified multiple strain-specific modH variants (modH1 – modH19) and showed that phase variation of modH5 in H. pylori P12 influenced expression of motility-associated genes and outer membrane protein gene hopG. However, the ModH5 DNA recognition motif and the mechanism by which ModH5 controls gene expression were unknown. Here, using comparative single molecule real-time sequencing, we identify the DNA site methylated by ModH5 as 5′-Gm6ACC-3′. This motif is vastly underrepresented in H. pylori genomes, but overrepresented in a number of virulence genes, including motility-associated genes, and outer membrane protein genes. Motility and the number of flagella of H. pylori P12 wild-type were significantly higher than that of isogenic modH5 OFF or ΔmodH5 mutants, indicating that phase variable switching of modH5 expression plays a role in regulating H. pylori motility phenotypes. Using the flagellin A (flaA) gene as a model, we show that ModH5 modulates flaA promoter activity in a GACC methylation-dependent manner. These findings provide novel insights into the role of ModH5 in gene regulation and how it mediates epigenetic regulation of H. pylori motility.
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Affiliation(s)
- Yogitha N Srikhanta
- Department of Microbiology, Monash University, Clayton, 3800, Victoria, Australia.,Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, 3010, Victoria, Australia.,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Victoria, Australia
| | - Rebecca J Gorrell
- Department of Microbiology, Monash University, Clayton, 3800, Victoria, Australia.,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, 3800, Victoria, Australia.,Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Victoria, Australia
| | - Peter M Power
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4222, Australia
| | - Kirill Tsyganov
- Bioinformatics Platform, Monash University, Clayton, 3800, Victoria, Australia
| | | | | | | | - Elizabeth L Hartland
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, 3010, Victoria, Australia.,Department of Molecular and Translational Science, Hudson Institute of Medical Research, Monash University, Clayton, 3800, Victoria, Australia
| | - Michael P Jennings
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4222, Australia.
| | - Terry Kwok
- Department of Microbiology, Monash University, Clayton, 3800, Victoria, Australia. .,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Victoria, Australia. .,Department of Biochemistry and Molecular Biology, Monash University, Clayton, 3800, Victoria, Australia. .,Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Victoria, Australia.
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49
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Phasevarion-Regulated Virulence in the Emerging Pediatric Pathogen Kingella kingae. Infect Immun 2017; 85:IAI.00319-17. [PMID: 28947652 DOI: 10.1128/iai.00319-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/19/2017] [Indexed: 01/18/2023] Open
Abstract
Kingella kingae is a common etiological agent of pediatric osteoarticular infections. While current research has expanded our understanding of K. kingae pathogenesis, there is a paucity of knowledge about host-pathogen interactions and virulence gene regulation. Many host-adapted bacterial pathogens contain phase variable DNA methyltransferases (mod genes), which can control expression of a regulon of genes (phasevarion) through differential methylation of the genome. Here, we identify a phase variable type III mod gene in K. kingae, suggesting that phasevarions operate in this pathogen. Phylogenetic studies revealed that there are two active modK alleles in K. kingae Proteomic analysis of secreted and surface-associated proteins, quantitative PCR, and a heat shock assay comparing the wild-type modK1 ON (i.e., in frame for expression) strain to a modK1 OFF (i.e., out of frame) strain revealed three virulence-associated genes under ModK1 control. These include the K. kingae toxin rtxA and the heat shock genes groEL and dnaK Cytokine expression analysis showed that the interleukin-8 (IL-8), IL-1β, and tumor necrosis factor responses of THP-1 macrophages were lower in the modK1 ON strain than in the modK1::kan mutant. This suggests that the ModK1 phasevarion influences the host inflammatory response and provides the first evidence of this phase variable epigenetic mechanism of gene regulation in K. kingae.
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50
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Seib KL, Jen FEC, Scott AL, Tan A, Jennings MP. Phase variation of DNA methyltransferases and the regulation of virulence and immune evasion in the pathogenic Neisseria. Pathog Dis 2017; 75:3966716. [DOI: 10.1093/femspd/ftx080] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/13/2017] [Indexed: 01/31/2023] Open
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