1
|
Hu S, Giacopazzi S, Modlin R, Karplus K, Bernick DL, Ottemann KM. Altering under-represented DNA sequences elevates bacterial transformation efficiency. mBio 2023; 14:e0210523. [PMID: 37905805 PMCID: PMC10746208 DOI: 10.1128/mbio.02105-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 09/22/2023] [Indexed: 11/02/2023] Open
Abstract
A cornerstone of bacterial molecular biology is the ability to genetically manipulate the microbe under study. Many bacteria are difficult to manipulate genetically, a phenotype due in part to robust removal of newly acquired DNA, for example, by restriction-modification (R-M) systems. Here, we report approaches that dramatically improve bacterial transformation efficiency, piloted using a microbe that is challenging to transform due to expression of many R-M systems, Helicobacter pylori. Initially, we identified conditions that dampened expression of several R-M systems and concomitantly enhanced transformation efficiency. We then identified an approach that would broadly protect newly acquired DNA. We computationally predicted under-represented short DNA sequences in the H. pylori genome, with the idea that these sequences reflect targets of sequence-based surveillance such as R-M systems. We then used this information to modify and eliminate such sites in antibiotic resistance cassettes, creating a "stealth" version. Modifying antibiotic resistance cassettes in this way resulted in significantly higher transformation efficiency compared to non-modified cassettes, a response that was genomic loci independent. Our results suggest that avoiding R-M systems, via modification of under-represented DNA sequences or transformation conditions, is a powerful method to enhance DNA transformation. Our approach to identify under-represented sequences is applicable to any microbe with a sequenced genome.IMPORTANCEManipulating the genomes of bacteria is critical to many fields. Such manipulations are made by genetic engineering, which often requires new pieces of DNA to be added to the genome. Bacteria have robust systems for identifying and degrading new DNA, some of which rely on restriction enzymes. These enzymes cut DNA at specific sequences. We identified a set of DNA sequences that are missing normally from a bacterium's genome, more than would be expected by chance. Eliminating these sequences from a new piece of DNA allowed it to be incorporated into the bacterial genome at a higher frequency than new DNA containing the sequences. Removing such sequences appears to allow the new DNA to fly under the bacterial radar in "stealth" mode. This transformation improvement approach is straightforward to apply and likely broadly applicable.
Collapse
Affiliation(s)
- Shuai Hu
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
| | - Stefani Giacopazzi
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
| | - Ryan Modlin
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
- Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA
| | - Kevin Karplus
- Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA
| | - David L. Bernick
- Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA
| | - Karen M. Ottemann
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
| |
Collapse
|
2
|
Vesel N, Iseli C, Guex N, Lemopoulos A, Blokesch M. DNA modifications impact natural transformation of Acinetobacter baumannii. Nucleic Acids Res 2023; 51:5661-5677. [PMID: 37178001 PMCID: PMC10287943 DOI: 10.1093/nar/gkad377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/22/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Acinetobacter baumannii is a dangerous nosocomial pathogen, especially due to its ability to rapidly acquire new genetic traits, including antibiotic resistance genes (ARG). In A. baumannii, natural competence for transformation, one of the primary modes of horizontal gene transfer (HGT), is thought to contribute to ARG acquisition and has therefore been intensively studied. However, knowledge regarding the potential role of epigenetic DNA modification(s) on this process remains lacking. Here, we demonstrate that the methylome pattern of diverse A. baumannii strains differs substantially and that these epigenetic marks influence the fate of transforming DNA. Specifically, we describe a methylome-dependent phenomenon that impacts intra- and inter-species DNA exchange by the competent A. baumannii strain A118. We go on to identify and characterize an A118-specific restriction-modification (RM) system that impairs transformation when the incoming DNA lacks a specific methylation signature. Collectively, our work contributes towards a more holistic understanding of HGT in this organism and may also aid future endeavors towards tackling the spread of novel ARGs. In particular, our results suggest that DNA exchanges between bacteria that share similar epigenomes are favored and could therefore guide future research into identifying the reservoir(s) of dangerous genetic traits for this multi-drug resistant pathogen.
Collapse
Affiliation(s)
- Nina Vesel
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Christian Iseli
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Bioinformatics Competence Center, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Bioinformatics Competence Center, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Alexandre Lemopoulos
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| |
Collapse
|
3
|
Kong Y, Cao L, Deikus G, Fan Y, Mead EA, Lai W, Zhang Y, Yong R, Sebra R, Wang H, Zhang XS, Fang G. Critical assessment of DNA adenine methylation in eukaryotes using quantitative deconvolution. Science 2022; 375:515-522. [PMID: 35113693 DOI: 10.1126/science.abe7489] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The discovery of N6-methyldeoxyadenine (6mA) across eukaryotes led to a search for additional epigenetic mechanisms. However, some studies have highlighted confounding factors that challenge the prevalence of 6mA in eukaryotes. We developed a metagenomic method to quantitatively deconvolve 6mA events from a genomic DNA sample into species of interest, genomic regions, and sources of contamination. Applying this method, we observed high-resolution 6mA deposition in two protozoa. We found that commensal or soil bacteria explained the vast majority of 6mA in insect and plant samples. We found no evidence of high abundance of 6mA in Drosophila, Arabidopsis, or humans. Plasmids used for genetic manipulation, even those from Dam methyltransferase mutant Escherichia coli, could carry abundant 6mA, confounding the evaluation of candidate 6mA methyltransferases and demethylases. On the basis of this work, we advocate for a reassessment of 6mA in eukaryotes.
Collapse
Affiliation(s)
- Yimeng Kong
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lei Cao
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yu Fan
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Edward A Mead
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Weiyi Lai
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yizhou Zhang
- Department of Neurosurgery and Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Raymund Yong
- Department of Neurosurgery and Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Sema4, a Mount Sinai Venture, Stamford, CT 06902, USA
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xue-Song Zhang
- Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, NJ 08854, 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 10029, USA
| |
Collapse
|
4
|
Huang M, Liu M, Huang L, Wang M, Jia R, Zhu D, Chen S, Zhao X, Zhang S, Gao Q, Zhang L, Cheng A. The activation and limitation of the bacterial natural transformation system: The function in genome evolution and stability. Microbiol Res 2021; 252:126856. [PMID: 34454311 DOI: 10.1016/j.micres.2021.126856] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/19/2021] [Accepted: 08/22/2021] [Indexed: 12/26/2022]
Abstract
Bacteria can take up exogenous naked DNA and integrate it into their genomes, which has been regarded as a main contributor to bacterial evolution. The competent status of bacteria is influenced by environmental cues and by the immune systems of bacteria. Here, we review recent advances in understanding the working mechanisms underlying activation of the natural transformation system and limitations thereof. Environmental stresses including the presence of antimicrobials can activate the natural transformation system. However, bacterial enzymes (nucleases), non-coding RNAs, specific DNA sequences, the restriction-modification (R-M) systems, CRISPR-Cas systems and prokaryotic Argonaute proteins (Agos) are have been found to be involved in the limitation of the natural transformation system. Together, this review represents an opportunity to gain insight into bacterial genome stability and evolution.
Collapse
Affiliation(s)
- Mi Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Li Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Dekang Zhu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Ling Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China.
| |
Collapse
|
5
|
Huang L, Liu M, Zhu D, Xie L, Huang M, Xiang C, Biville F, Jia R, Chen S, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Ou X, Mao S, Gao Q, Sun D, Tian B, Wang M, Cheng A. Natural Transformation of Riemerella columbina and Its Determinants. Front Microbiol 2021; 12:634895. [PMID: 33746928 PMCID: PMC7965970 DOI: 10.3389/fmicb.2021.634895] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 02/12/2021] [Indexed: 12/17/2022] Open
Abstract
In a previous study, it was shown that Riemerella anatipestifer, a member of Flavobacteriaceae, is naturally competent. However, whether natural competence is universal in Flavobacteriaceae remains unknown. In this study, it was shown for the first time that Riemerella columbina was naturally competent in the laboratory condition; however, Flavobacterium johnsoniae was not naturally competent under the same conditions. The competence of R. columbina was maintained throughout the growth phases, and the transformation frequency was highest during the logarithmic phase. A competition assay revealed that R. columbina preferentially took up its own genomic DNA over heterologous DNA. The natural transformation frequency of R. columbina was significantly increased in GCB medium without peptone or phosphate. Furthermore, natural transformation of R. columbina was inhibited by 0.5 mM EDTA, but could be restored by the addition of CaCl2, MgCl2, ZnCl2, and MnCl2, suggesting that these divalent cations promote the natural transformation of R. columbina. Overall, this study revealed that natural competence is not universal in Flavobacteriaceae members and triggering of competence differs from species to species.
Collapse
Affiliation(s)
- Li Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Dekang Zhu
- Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Li Xie
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Mi Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Chen Xiang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Francis Biville
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| |
Collapse
|
6
|
Liu M, Huang M, Wang M, Zhu D, Jia R, Chen S, Zhang L, Pan L, Cheng A. The Clustered Regularly Interspaced Short Palindromic Repeat System and Argonaute: An Emerging Bacterial Immunity System for Defense Against Natural Transformation? Front Microbiol 2020; 11:593301. [PMID: 33193265 PMCID: PMC7642515 DOI: 10.3389/fmicb.2020.593301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/23/2020] [Indexed: 12/21/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR) systems and prokaryotic Argonaute proteins (Agos) have been shown to defend bacterial and archaeal cells against invading nucleic acids. Indeed, they are important elements for inhibiting horizontal gene transfer between bacterial and archaeal cells. The CRISPR system employs an RNA-guide complex to target invading DNA or RNA, while Agos target DNA using single stranded DNA or RNA as guides. Thus, the CRISPR and Agos systems defend against exogenous nucleic acids by different mechanisms. It is not fully understood how antagonization of these systems occurs during natural transformation, wherein exogenous DNA enters a host cell as single stranded DNA and is then integrated into the host genome. In this review, we discuss the functions and mechanisms of the CRISPR system and Agos in cellular defense against natural transformation.
Collapse
Affiliation(s)
- Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mi Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhang
- Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Leichang Pan
- Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| |
Collapse
|
7
|
Dawson EM, Dunne KA, Richardson EJ, Praszkier J, Alfawaz D, Woelfel S, De Paoli A, Chaudhry H, Henderson IR, Ferrero RL, Rossiter AE. Complete genome sequence of Helicobacter pylori B128 7.13 and a single-step method for the generation of unmarked mutations. Helicobacter 2019; 24:e12587. [PMID: 31062466 PMCID: PMC6618122 DOI: 10.1111/hel.12587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/14/2019] [Accepted: 02/16/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND Helicobacter pylori represents an interesting model of bacterial pathogenesis given that most infections are asymptomatic, while a minority of infections cause severe gastric disease. H pylori strain B128 7.13 is used extensively to understand H pylori pathophysiology. Due to extensive restriction-modification systems, the fact that only some H pylori strains are naturally transformable, the inability of common plasmid and transposon vectors to replicate in this bacterium, as well as the limited number of antibiotic cassettes that are functional in H pylori, there are relatively few genetic tools for the mutagenesis of this bacterium. MATERIALS AND METHODS Here, we use PacBio and Illumina sequencing to reveal the complete genome sequence of H pylori B128 7.13. Furthermore, we describe a system to generate markerless and scarless mutations on the H pylori chromosome using the counter-selection marker, galactokinase from Escherichia coli. RESULTS We show that this mutagenesis strategy can be used to generate in-frame insertions, gene deletions, and multiple independent mutations in B128 7.13. Using the closed genome as a reference, we also report the absence of second site chromosomal mutations and/or rearrangements in our mutagenized strains. We compare the genome sequence of H pylori B128 7.13 with a closely related strain, H pylori B8, and reveal one notable region of difference, which is a 1430 bp insertion encoding a H pylori-specific DUF874 family protein of unknown function. CONCLUSIONS This article reports the closed genome of the important H pylori B128 7.13 strain and a mutagenesis method that can be adopted by researchers as an alternative strategy to generate isogenic mutants of H pylori in order to further our understanding of this bacterium.
Collapse
Affiliation(s)
- Emma M. Dawson
- Institute of Microbiology and Infection College of Medical and Dental SciencesUniversity of BirminghamBirminghamUK
| | - Karl A. Dunne
- Institute of Microbiology and Infection College of Medical and Dental SciencesUniversity of BirminghamBirminghamUK
| | - Emily J. Richardson
- Institute of Microbiology and Infection College of Medical and Dental SciencesUniversity of BirminghamBirminghamUK
| | - Judyta Praszkier
- Hudson Institute for Medical Research, MonashMelbourneVictoriaAustralia
| | - Dana Alfawaz
- Institute of Microbiology and Infection College of Medical and Dental SciencesUniversity of BirminghamBirminghamUK
| | - Simon Woelfel
- Institute of Microbiology and Infection College of Medical and Dental SciencesUniversity of BirminghamBirminghamUK
| | - Amanda De Paoli
- Hudson Institute for Medical Research, MonashMelbourneVictoriaAustralia
| | - Hassan Chaudhry
- Hudson Institute for Medical Research, MonashMelbourneVictoriaAustralia
| | - Ian R. Henderson
- Institute of Microbiology and Infection College of Medical and Dental SciencesUniversity of BirminghamBirminghamUK
| | - Richard L. Ferrero
- Hudson Institute for Medical Research, MonashMelbourneVictoriaAustralia,Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourneVictoriaAustralia
| | - Amanda E. Rossiter
- Institute of Microbiology and Infection College of Medical and Dental SciencesUniversity of BirminghamBirminghamUK
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Joshi S, Fedoseyenko D, Mahanta N, Ducati RG, Feng M, Schramm VL, Begley TP. Antibacterial Strategy against H. pylori: Inhibition of the Radical SAM Enzyme MqnE in Menaquinone Biosynthesis. ACS Med Chem Lett 2019; 10:363-366. [PMID: 30891141 PMCID: PMC6421580 DOI: 10.1021/acsmedchemlett.8b00649] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/15/2019] [Indexed: 12/13/2022] Open
Abstract
Aminofutalosine synthase (MqnE) catalyzes an important rearrangement reaction in menaquinone biosynthesis by the futalosine pathway. In this Letter, we report the identification of previously unreported inhibitors of MqnE using a mechanism-guided approach. The best inhibitor shows efficient inhibitory activity against H. pylori (IC50 = 1.8 ± 0.4 μM) and identifies MqnE as a promising target for antibiotic development.
Collapse
Affiliation(s)
- Sumedh Joshi
- Department
of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Dmytro Fedoseyenko
- Department
of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Nilkamal Mahanta
- Department
of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Rodrigo G. Ducati
- Department
of Biochemistry, Albert Einstein College
of Medicine, Bronx, New York 10461, United States
| | - Mu Feng
- Department
of Biochemistry, Albert Einstein College
of Medicine, Bronx, New York 10461, United States
| | - Vern L. Schramm
- Department
of Biochemistry, Albert Einstein College
of Medicine, Bronx, New York 10461, United States
| | - Tadhg P. Begley
- Department
of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| |
Collapse
|
10
|
Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation. Nat Biotechnol 2017; 36:61-69. [PMID: 29227468 PMCID: PMC5762413 DOI: 10.1038/nbt.4037] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/13/2017] [Indexed: 02/04/2023]
Abstract
Shotgun metagenomics methods enable characterization of microbial communities in human microbiome and environmental samples. Assembly of metagenome sequences does not output whole genomes, so computational binning methods have been developed to cluster sequences into genome ‘bins’. These methods exploit sequence composition, species abundance, or chromosome organization but cannot fully distinguish closely related species and strains. We present a binning method that incorporates bacterial DNA methylation signatures, which are detected using single-molecule real-time sequencing. Our method takes advantage of these endogenous epigenetic barcodes to resolve individual reads and assembled contigs into species- and strain-level bins. We validated our method using synthetic and real microbiome sequences. In addition to genome binning, we show that our method links plasmids and other mobile genetic elements to their host species in a real microbiome sample. Incorporation of DNA methylation information into shotgun metagenomics analyses will complement existing methods to enable more accurate sequence binning.
Collapse
|
11
|
Bubendorfer S, Krebes J, Yang I, Hage E, Schulz TF, Bahlawane C, Didelot X, Suerbaum S. Genome-wide analysis of chromosomal import patterns after natural transformation of Helicobacter pylori. Nat Commun 2016; 7:11995. [PMID: 27329939 PMCID: PMC4917963 DOI: 10.1038/ncomms11995] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/19/2016] [Indexed: 12/17/2022] Open
Abstract
Recombination plays a dominant role in the evolution of the bacterial pathogen Helicobacter pylori, but its dynamics remain incompletely understood. Here we use an in vitro transformation system combined with genome sequencing to study chromosomal integration patterns after natural transformation. A single transformation cycle results in up to 21 imports, and repeated transformations generate a maximum of 92 imports (8% sequence replacement). Import lengths show a bimodal distribution with averages of 28 and 1,645 bp. Reanalysis of paired H. pylori genomes from chronically infected people demonstrates the same bimodal import pattern in vivo. Restriction endonucleases (REases) of the recipient bacteria fail to inhibit integration of homeologous DNA, independently of methylation. In contrast, REases limit the import of heterologous DNA. We conclude that restriction-modification systems inhibit the genomic integration of novel sequences, while they pose no barrier to homeologous recombination, which reconciles the observed stability of the H. pylori gene content and its highly recombinational population structure. Uptake and integration of exogenous DNA into the bacterial genome play an important role in the evolution of the pathogen Helicobacter pylori. Here, the authors describe a bimodal pattern of chromosomal integration and show how restriction-modification systems limit the import of heterologous DNA.
Collapse
Affiliation(s)
- Sebastian Bubendorfer
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.,DZIF-German Center for Infection Research, Hannover-Braunschweig Site, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Juliane Krebes
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.,DZIF-German Center for Infection Research, Hannover-Braunschweig Site, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Ines Yang
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.,DZIF-German Center for Infection Research, Hannover-Braunschweig Site, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Elias Hage
- DZIF-German Center for Infection Research, Hannover-Braunschweig Site, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.,Institute of Virology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Thomas F Schulz
- DZIF-German Center for Infection Research, Hannover-Braunschweig Site, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.,Institute of Virology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Christelle Bahlawane
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College, Norfolk Place, London W2 1PG, UK
| | - Sebastian Suerbaum
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.,DZIF-German Center for Infection Research, Hannover-Braunschweig Site, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| |
Collapse
|
12
|
Weigele P, Raleigh EA. Biosynthesis and Function of Modified Bases in Bacteria and Their Viruses. Chem Rev 2016; 116:12655-12687. [PMID: 27319741 DOI: 10.1021/acs.chemrev.6b00114] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Naturally occurring modification of the canonical A, G, C, and T bases can be found in the DNA of cellular organisms and viruses from all domains of life. Bacterial viruses (bacteriophages) are a particularly rich but still underexploited source of such modified variant nucleotides. The modifications conserve the coding and base-pairing functions of DNA, but add regulatory and protective functions. In prokaryotes, modified bases appear primarily to be part of an arms race between bacteriophages (and other genomic parasites) and their hosts, although, as in eukaryotes, some modifications have been adapted to convey epigenetic information. The first half of this review catalogs the identification and diversity of DNA modifications found in bacteria and bacteriophages. What is known about the biogenesis, context, and function of these modifications are also described. The second part of the review places these DNA modifications in the context of the arms race between bacteria and bacteriophages. It focuses particularly on the defense and counter-defense strategies that turn on direct recognition of the presence of a modified base. Where modification has been shown to affect other DNA transactions, such as expression and chromosome segregation, that is summarized, with reference to recent reviews.
Collapse
Affiliation(s)
- Peter Weigele
- Chemical Biology, New England Biolabs , Ipswich, Massachusetts 01938, United States
| | | |
Collapse
|
13
|
Addiction of Hypertransformable Pneumococcal Isolates to Natural Transformation for In Vivo Fitness and Virulence. Infect Immun 2016; 84:1887-1901. [PMID: 27068094 DOI: 10.1128/iai.00097-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/06/2016] [Indexed: 12/25/2022] Open
Abstract
Natural genetic transformation of Streptococcus pneumoniae, an important human pathogen, mediates horizontal gene transfer for the development of drug resistance, modulation of carriage and virulence traits, and evasion of host immunity. Transformation frequency differs greatly among pneumococcal clinical isolates, but the molecular basis and biological importance of this interstrain variability remain unclear. In this study, we characterized the transformation frequency and other associated phenotypes of 208 S. pneumoniae clinical isolates representing at least 30 serotypes. While the vast majority of these isolates (94.7%) were transformable, the transformation frequency differed by up to 5 orders of magnitude between the least and most transformable isolates. The strain-to-strain differences in transformation frequency were observed among many isolates producing the same capsule types, indicating no general association between transformation frequency and serotype. However, a statistically significant association was observed between the levels of transformation and colonization fitness/virulence in the hypertransformable isolates. Although nontransformable mutants of all the selected hypertransformable isolates were significantly attenuated in colonization fitness and virulence in mouse infection models, such mutants of the strains with relatively low transformability had no or marginal fitness phenotypes under the same experimental settings. This finding strongly suggests that the pneumococci with high transformation capability are "addicted" to a "hypertransformable" state for optimal fitness in the human host. This work has thus provided an intriguing hint for further investigation into how the competence system impacts the fitness, virulence, and other transformation-associated traits of this important human pathogen.
Collapse
|
14
|
Krüger NJ, Knüver MT, Zawilak-Pawlik A, Appel B, Stingl K. Genetic Diversity as Consequence of a Microaerobic and Neutrophilic Lifestyle. PLoS Pathog 2016; 12:e1005626. [PMID: 27166672 PMCID: PMC4864210 DOI: 10.1371/journal.ppat.1005626] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 04/21/2016] [Indexed: 01/10/2023] Open
Abstract
As a neutrophilic bacterium, Helicobacter pylori is growth deficient under extreme acidic conditions. The gastric pathogen is equipped with an acid survival kit, regulating urease activity by a pH-gated urea channel, opening below pH 6.5. After overcoming acid stress, the bacterium’s multiplication site is situated at the gastric mucosa with near neutral pH. The pathogen exhibits exceptional genetic variability, mainly due to its capability of natural transformation, termed competence. Using single cell analysis, we show here that competence is highly regulated in H. pylori. DNA uptake complex activity was reversibly shut down below pH 6.5. pH values above 6.5 opened a competence window, in which competence development was triggered by the combination of pH increase and oxidative stress. In contrast, addition of sublethal concentrations of the DNA-damaging agents ciprofloxacin or mitomycin C did not trigger competence development under our conditions. An oxygen-sensitive mutant lacking superoxide dismutase (sodB) displayed a higher competent fraction of cells than the wild type under comparable conditions. In addition, the sodB mutant was dependent on adenine for growth in broth and turned into non-cultivable coccoid forms in its absence, indicating that adenine had radical quenching capacity. Quantification of periplasmically located DNA in competent wild type cells revealed outstanding median imported DNA amounts of around 350 kb per cell within 10 min of import, with maximally a chromosomal equivalent (1.6 Mb) in individual cells, far exceeding previous amounts detected in other Gram-negative bacteria. We conclude that the pathogen’s high genetic diversity is a consequence of its enormous DNA uptake capacity, triggered by intrinsic and extrinsic oxidative stress once a neutral pH at the site of chronic host colonization allows competence development. Natural transformation, i.e. the capacity to take up DNA from the environment, is one of the crucial means for horizontal gene transfer and genetic diversity in bacteria. The human gastric pathogen Helicobacter pylori is confronted with acid stress before entering its multiplication site, the gastric mucosa. The bacterium causes lifelong chronic gastritis and is perfectly adapted to the human host, crucially by displaying unusual genetic diversity. Using a single cell approach and well-controlled conditions, we show here that the amount of imported DNA in competent H. pylori is outstanding, far exceeding previous measurement with other Gram-negative bacteria. Furthermore, DNA uptake activity was tightly regulated and limited to pH above 6.5, conditions thought to be met in close contact with the gastric mucosa. In addition, we show that within this pH competence window, competence development was triggered by an increase in pH in combination with the level of oxidative stress. Our data provide explanations for the extraordinary high genetic diversity, often referred to as genome plasticity of this unusual microaerobic pathogen.
Collapse
Affiliation(s)
- Nora-Johanna Krüger
- Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Marie-Theres Knüver
- Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Anna Zawilak-Pawlik
- Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Department of Microbiology, Wroclaw, Poland
| | - Bernd Appel
- Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Kerstin Stingl
- Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
- * E-mail:
| |
Collapse
|
15
|
Beaulaurier J, Zhang XS, Zhu S, Sebra R, Rosenbluh C, Deikus G, Shen N, Munera D, Waldor MK, Chess A, Blaser MJ, Schadt EE, Fang G. Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes. Nat Commun 2015; 6:7438. [PMID: 26074426 PMCID: PMC4490391 DOI: 10.1038/ncomms8438] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 05/08/2015] [Indexed: 12/22/2022] Open
Abstract
Beyond its role in host defense, bacterial DNA methylation also plays important roles in the regulation of gene expression, virulence and antibiotic resistance. Bacterial cells in a clonal population can generate epigenetic heterogeneity to increase population-level phenotypic plasticity. Single molecule, real-time (SMRT) sequencing enables the detection of N6-methyladenine and N4-methylcytosine, two major types of DNA modifications comprising the bacterial methylome. However, existing SMRT sequencing-based methods for studying bacterial methylomes rely on a population-level consensus that lacks the single-cell resolution required to observe epigenetic heterogeneity. Here, we present SMALR (single-molecule modification analysis of long reads), a novel framework for single molecule-level detection and phasing of DNA methylation. Using seven bacterial strains, we show that SMALR yields significantly improved resolution and reveals distinct types of epigenetic heterogeneity. SMALR is a powerful new tool that enables de novo detection of epigenetic heterogeneity and empowers investigation of its functions in bacterial populations. Bacterial DNA methylation is involved in many processes, from host defense to antibiotic resistance, however current methods for examining methylated genomes lack single-cell resolution. Here Beaulaurier et al. present Single Molecule Modification Analysis of Long Reads, a new tool for de novo detection of epigenetic heterogeneity.
Collapse
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 10029, USA
| | - Xue-Song Zhang
- Department of Medicine, New York University School of Medicine, New York 10016, USA
| | - Shijia Zhu
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Chaggai Rosenbluh
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Nan Shen
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Diana Munera
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, and the Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, and the Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
| | - Andrew Chess
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Martin J Blaser
- Department of Medicine, New York University School of Medicine, New York 10016, 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 10029, 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 10029, USA
| |
Collapse
|
16
|
A specific A/T polymorphism in Western tyrosine phosphorylation B-motifs regulates Helicobacter pylori CagA epithelial cell interactions. PLoS Pathog 2015; 11:e1004621. [PMID: 25646814 PMCID: PMC4412286 DOI: 10.1371/journal.ppat.1004621] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Accepted: 12/16/2014] [Indexed: 12/15/2022] Open
Abstract
Helicobacter pylori persistently colonizes the human stomach, with mixed roles in human health. The CagA protein, a key host-interaction factor, is translocated by a type IV secretion system into host epithelial cells, where its EPIYA tyrosine phosphorylation motifs (TPMs) are recognized by host cell kinases, leading to multiple host cell signaling cascades. The CagA TPMs have been described as type A, B, C or D, each with a specific conserved amino acid sequence surrounding EPIYA. Database searching revealed strong non-random distribution of the B-motifs (including EPIYA and EPIYT) in Western H. pylori isolates. In silico analysis of Western H. pylori CagA sequences provided evidence that the EPIYT B-TPMs are significantly less associated with gastric cancer than the EPIYA B-TPMs. By generating and using a phosphorylated CagA B-TPM-specific antibody, we demonstrated the phosphorylated state of the CagA B-TPM EPIYT during H. pylori co-culture with host cells. We also showed that within host cells, CagA interaction with phosphoinositol 3-kinase (PI3-kinase) was B-TPM tyrosine-phosphorylation-dependent, and the recombinant CagA with EPIYT B-TPM had higher affinity to PI3-kinase and enhanced induction of AKT than the isogenic CagA with EPIYA B-TPM. Structural modeling of the CagA B-TPM motif bound to PI3-kinase indicated that the threonine residue at the pY+1 position forms a side-chain hydrogen bond to N-417 of PI3-kinase, which cannot be formed by alanine. During co-culture with AGS cells, an H. pylori strain with a CagA EPIYT B-TPM had significantly attenuated induction of interleukin-8 and hummingbird phenotype, compared to the isogenic strain with B-TPM EPIYA. These results suggest that the A/T polymorphisms could regulate CagA activity through interfering with host signaling pathways related to carcinogenesis, thus influencing cancer risk.
Collapse
|
17
|
Maldonado-Contreras A, Mane SP, Zhang XS, Pericchi L, Alarcón T, Contreras M, Linz B, Blaser MJ, Domínguez-Bello MG. Phylogeographic evidence of cognate recognition site patterns and transformation efficiency differences in H. pylori: theory of strain dominance. BMC Microbiol 2013; 13:211. [PMID: 24050390 PMCID: PMC3849833 DOI: 10.1186/1471-2180-13-211] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 08/28/2013] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Helicobacter pylori has diverged in parallel to its human host, leading to distinct phylogeographic populations. Recent evidence suggests that in the current human mixing in Latin America, European H. pylori (hpEurope) are increasingly dominant at the expense of Amerindian haplotypes (hspAmerind). This phenomenon might occur via DNA recombination, modulated by restriction-modification systems (RMS), in which differences in cognate recognition sites (CRS) and in active methylases will determine direction and frequency of gene flow. We hypothesized that genomes from hspAmerind strains that evolved from a small founder population have lost CRS for RMS and active methylases, promoting hpEurope's DNA invasion. We determined the observed and expected frequencies of CRS for RMS in DNA from 7 H. pylori whole genomes and 110 multilocus sequences. We also measured the number of active methylases by resistance to in vitro digestion by 16 restriction enzymes of genomic DNA from 9 hpEurope and 9 hspAmerind strains, and determined the direction of DNA uptake in co-culture experiments of hspAmerind and hpEurope strains. RESULTS Most of the CRS were underrepresented with consistency between whole genomes and multilocus sequences. Although neither the frequency of CRS nor the number of active methylases differ among the bacterial populations (average 8.6 ± 2.6), hspAmerind strains had a restriction profile distinct from that in hpEurope strains, with 15 recognition sites accounting for the differences. Amerindians strains also exhibited higher transformation rates than European strains, and were more susceptible to be subverted by larger DNA hpEurope-fragments than vice versa. CONCLUSIONS The geographical variation in the pattern of CRS provides evidence for ancestral differences in RMS representation and function, and the transformation findings support the hypothesis of Europeanization of the Amerindian strains in Latin America via DNA recombination.
Collapse
|
18
|
Huddleston JR, Brokaw JM, Zak JC, Jeter RM. Natural transformation as a mechanism of horizontal gene transfer among environmental Aeromonas species. Syst Appl Microbiol 2013; 36:224-34. [PMID: 23541366 DOI: 10.1016/j.syapm.2013.01.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 01/15/2013] [Accepted: 01/20/2013] [Indexed: 10/27/2022]
Abstract
Aeromonas species are common inhabitants of aquatic environments and relevant as human pathogens. Their potential as pathogens may be related in part to lateral transfer of genes associated with toxin production, biofilm formation, antibiotic resistance, and other virulence determinants. Natural transformation has not been characterized in aeromonads. DNA from wild-type, prototrophic strains that had been isolated from environmental sources was used as donor DNA in transformation assays with auxotrophs as the recipients. Competence was induced in 20% nutrient broth during the stationary phase of growth. Optimal transformation assay conditions for one chosen isolate were in Tris buffer with magnesium or calcium, pH 5-8, and a saturating concentration of 0.5 μg of DNA per assay (3.3 ng of DNA μl⁻¹) at 30°C. Sodium was also required and could not be replaced with ammonium, potassium, or lithium. The maximal transformation frequency observed was 1.95 × 10⁻³ transformants (recipient cell)⁻¹. A survey of environmental Aeromonas auxotrophic recipients (n=37), assayed with donor DNA from other wild-type environmental aeromonads under optimal assay conditions, demonstrated that 73% were able to act as recipients, and 100% were able to act as donors to at least some other aeromonads. Three different transformation groups were identified based on each isolates' ability to transform other strains with its DNA. The transformation groups roughly corresponded to phylogenetic groups. These results demonstrate that natural transformation is a general property of Aeromonas environmental isolates with implications for the genetic structures of coincident Aeromonas populations.
Collapse
Affiliation(s)
- Jennifer R Huddleston
- Biology Department, ACU Box 27868, Abilene Christian University, Abilene, Texas 79699, USA.
| | | | | | | |
Collapse
|
19
|
Dwivedi GR, Sharma E, Rao DN. Helicobacter pylori DprA alleviates restriction barrier for incoming DNA. Nucleic Acids Res 2013; 41:3274-88. [PMID: 23355610 PMCID: PMC3597690 DOI: 10.1093/nar/gkt024] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Helicobacter pylori is a Gram-negative bacterium that colonizes human stomach and causes gastric inflammation. The species is naturally competent and displays remarkable diversity. The presence of a large number of restriction-modification (R-M) systems in this bacterium creates a barrier against natural transformation by foreign DNA. Yet, mechanisms that protect incoming double-stranded DNA (dsDNA) from restriction enzymes are not well understood. A DNA-binding protein, DNA Processing Protein A (DprA) has been shown to facilitate natural transformation of several Gram-positive and Gram-negative bacteria by protecting incoming single-stranded DNA (ssDNA) and promoting RecA loading on it. However, in this study, we report that H. pylori DprA (HpDprA) binds not only ssDNA but also dsDNA thereby conferring protection to both from various exonucleases and Type II restriction enzymes. Here, we observed a stimulatory role of HpDprA in DNA methylation through physical interaction with methyltransferases. Thus, HpDprA displayed dual functional interaction with H. pylori R-M systems by not only inhibiting the restriction enzymes but also stimulating methyltransferases. These results indicate that HpDprA could be one of the factors that modulate the R-M barrier during inter-strain natural transformation in H. pylori.
Collapse
|