1
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Wang Y, Chen X, Chen Q, Liu T, Wu Y, Huang L, Chen Y. Expression of human dCTP pyrophosphatase 1 (DCTPP1) and its association with cisplatin resistance characteristics in ovarian cancer. J Cell Mol Med 2024; 28:e18371. [PMID: 38686496 PMCID: PMC11058668 DOI: 10.1111/jcmm.18371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 04/11/2024] [Accepted: 04/18/2024] [Indexed: 05/02/2024] Open
Abstract
Cisplatin (DDP) resistance is a major challenge in treating ovarian cancer patients. A recently discovered enzyme called dCTP pyrophosphatase 1 (DCTPP1) has been implicated in regulating cancer characteristics, including drug responses. In this study, we aimed to understand the role of DCTPP1 in cancer progression and cisplatin response. Using publicly available databases, we analysed the expression and clinical significance of DCTPP1 in ovarian cancer. Our bioinformatics analysis confirmed that DCTPP1 is significantly overexpressed in ovarian cancer and is closely associated with tumour progression and poor prognosis after cisplatin treatment. We also found that DCTPP1 located in oxidoreductase complex and may be involved in various biological processes related to cisplatin resistance, including pyrimidine nucleotide metabolism, the P53 signalling pathway and cell cycle signalling pathways. We observed higher expression of DCTPP1 in cisplatin-resistant cells (SKOV3/DDP) and samples compared to their sensitive counterparts. Additionally, we found that DCTPP1 expression was only enhanced in SKOV3/S cells when treated with cisplatin, indicating different expression patterns of DCTPP1 in cisplatin-sensitive and cisplatin-resistant cancer cells. Our study further supports the notion that cisplatin induces intracellular reactive oxygen species (ROS) and triggers cancer cell death through excessive oxidative stress. Knocking out DCTPP1 reversed the drug resistance of ovarian cancer cells by enhancing the intracellular antioxidant stress response and accumulating ROS. Based on our research findings, we conclude that DCTPP1 has prognostic value for ovarian cancer patients, and targeting DCTPP1 may be clinically significant in overcoming cisplatin resistance in ovarian cancer.
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Affiliation(s)
- Yu Wang
- Obstetrics and Gynecology center, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
- School of medical laboratory and BiotechnologySouthern Medical UniversityGuangzhouChina
| | - Xiangyun Chen
- School of medical laboratory and BiotechnologySouthern Medical UniversityGuangzhouChina
| | - Qiduan Chen
- Obstetrics and Gynecology center, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Tiancai Liu
- School of medical laboratory and BiotechnologySouthern Medical UniversityGuangzhouChina
| | - Yingsong Wu
- School of medical laboratory and BiotechnologySouthern Medical UniversityGuangzhouChina
| | - Liping Huang
- Obstetrics and Gynecology center, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Yao Chen
- School of medical laboratory and BiotechnologySouthern Medical UniversityGuangzhouChina
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2
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Zhang W, Lyu L, Xu Z, Ni J, Wang D, Lu J, Yao YF. Integrative DNA methylome and transcriptome analysis reveals DNA adenine methylation is involved in Salmonella enterica Typhimurium response to oxidative stress. Microbiol Spectr 2023; 11:e0247923. [PMID: 37882553 PMCID: PMC10715015 DOI: 10.1128/spectrum.02479-23] [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: 09/03/2023] [Accepted: 09/07/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE The intracellular pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) comes across a wide variety of stresses from entry to dissemination, such as reactive oxygen species. To adapt itself to oxidative stress, Salmonella must adopt various and complex strategies. In this study, we revealed that DNA adenine methyltransferase was essential for S. Typhimurium to survive in hydrogen peroxide. We then screened out oxidative stress-responsive genes that were potentially regulated by DNA methylation in S. Typhimurium. Our results show that the DNA methylome is highly stable throughout the genome, and the coupled change of m6A GATC with gene expression is identified in only a few positions, which suggests the complexity of the DNA methylation and gene expression regulation networks. The results may shed light on our understanding of m6A-mediated gene expression regulation in bacteria.
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Affiliation(s)
- Wenting Zhang
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Lyu
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhihiong Xu
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinjing Ni
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Danni Wang
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Lu
- Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
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3
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Nigo F, Nakagawa R, Hirai Y, Imai L, Suzuki Y, Furuta K, Kaito C. Staphylococcus aureus MazG hydrolyzes oxidized guanine nucleotides and contributes to oxidative stress resistance. Biochimie 2023; 209:52-60. [PMID: 36746255 DOI: 10.1016/j.biochi.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/23/2023] [Accepted: 02/02/2023] [Indexed: 02/05/2023]
Abstract
We previously reported that knockout of the mazG (SA1292) gene decreases Staphylococcus aureus killing activity against silkworms. S. aureus MazG (SaMazG) has a nucleotide pyrophosphatase domain conserved among MazG family proteins, but its biochemical characteristics are unknown. In the present study, we purified recombinant N-terminal His-tagged SaMazG protein and examined its biochemical activity. SaMazG hydrolyzed GTP, UTP, dGTP, and TTP into nucleoside monophosphates. Hydrolytic activity of SaMazG against ATP, CTP, dATP, and dCTP was low or not detected. SaMazG exhibited high hydrolytic activity against 8-oxo-GTP and 8-oxo-dGTP, oxidized guanine nucleotides, with a Vmax/Km ratio more than 15-fold that of GTP. Furthermore, the S. aureus mazG knockout mutant was sensitive to hydrogen peroxide compared with the parent strain. These results suggest that SaMazG is a nucleotide pyrophosphatase hydrolyzing oxidized guanine nucleotides that contributes to the oxidative stress resistance of S. aureus.
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Affiliation(s)
- Fuki Nigo
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Kita-ku, Okayama, Japan.
| | - Ryosuke Nakagawa
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Kita-ku, Okayama, Japan.
| | - Yuuki Hirai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
| | - Lina Imai
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Kita-ku, Okayama, Japan.
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
| | - Kazuyuki Furuta
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Kita-ku, Okayama, Japan.
| | - Chikara Kaito
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Kita-ku, Okayama, Japan.
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4
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Wang S, Gao B, Chen A, Zhang Z, Wang S, Lv L, Zhao G, Li J. Structural analysis of the housecleaning nucleoside triphosphate pyrophosphohydrolase MazG from Mycobacterium tuberculosis. Front Microbiol 2023; 14:1137279. [PMID: 36937295 PMCID: PMC10014863 DOI: 10.3389/fmicb.2023.1137279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/10/2023] [Indexed: 03/05/2023] Open
Abstract
The housecleaning enzyme of Mycobacterium tuberculosis (Mtb), MazG, is a nucleoside triphosphate pyrophosphohydrolase (NTP-PPase) and can hydrolyze all canonical or non-canonical NTPs into NMPs and pyrophosphate. The Mycobacterium tuberculosis MazG (Mtb-MazG) contributes to antibiotic resistance in response to oxidative or nitrosative stress under dormancy, making it a promising target for treating TB in latent infection patients. However, the structural basis of Mtb-MazG is not clear. Here we describe the crystal structure of Mtb-MazG (1-185) at 2.7 Å resolution, composed of two similar folded spherical domains in tandem. Unlike other all-α NTP pyrophosphatases, Mtb-MazG has an N-terminal extra region composed of three α-helices and five β-strands. The second domain is global, with five α-helices located in the N-terminal domain. Gel-filtration assay and SAXS analysis show that Mtb-MazG forms an enzyme-active dimer in solution. In addition, the metal ion Mg2+ is bound with four negative-charged residues Glu119, Glu122, Glu138, and Asp141. Different truncations and site-directed mutagenesis revealed that the full-length dimeric form and the metal ion Mg2+ are indispensable for the catalytic activity of Mtb-MazG. Thus, our work provides new insights into understanding the molecular basis of Mtb-MazG.
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Affiliation(s)
- Sen Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Baocai Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Anke Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Zhifei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Sheng Wang
- Shanghai Zelixir Biotech Company Ltd., Shanghai, China
| | - Liangdong Lv
- School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Guoping Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Guoping Zhao,
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
- *Correspondence: Jixi Li,
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Davies CP, Jurkiw T, Haendiges J, Reed E, Anderson N, Grasso-Kelley E, Hoffmann M, Zheng J. Changes in the genomes and methylomes of three Salmonella enterica serovars after long-term storage in ground black pepper. Front Microbiol 2022; 13:970135. [PMID: 36160197 PMCID: PMC9507087 DOI: 10.3389/fmicb.2022.970135] [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: 06/15/2022] [Accepted: 08/16/2022] [Indexed: 11/28/2022] Open
Abstract
Low moisture foods (LMFs) have traditionally been recognized as safe for consumption, as most bacteria require higher water content to grow. However, outbreaks due to LMF foods are increasing, and the microbial pathogen Salmonella enterica is frequently implicated. S. enterica can survive in LMFs for years, but few serovars have been studied, and the mechanisms which underlie this longevity are not well understood. Here, we determine that S. enterica serovars S. Tennessee, S. Anatum, and S. Reading but not S. Oranienburg can survive in the ground black pepper for 6 years. S. Reading was not previously associated with any LMF. Using both Illumina and Pacific Biosciences sequencing technologies, we also document changes in the genomes and methylomes of the surviving serovars over this 6-year period. The three serovars acquired a small number of single nucleotide polymorphisms (SNPs) including seven substitutions (four synonymous, two non-synonymous, and one substitution in a non-coding region), and two insertion-deletions. Nine distinct N6-methyladenine (m6A) methylated motifs across the three serovars were identified including five which were previously known, Gm6ATC, CAGm6AG, BATGCm6AT, CRTm6AYN6CTC, and CCm6AN7TGAG, and four novel serovar-specific motifs, GRTm6AN8TTYG, GAm6ACN7GTA, GAA m6ACY, and CAAm6ANCC. Interestingly, the BATGCAT motif was incompletely methylated (35–64% sites across the genome methylated), suggesting a possible role in gene regulation. Furthermore, the number of methylated BATGCm6AT motifs increased after storage in ground black pepper for 6 years from 475 to 657 (S. Tennessee), 366 to 608 (S. Anatum), and 525 to 570 (S. Reading), thus warranting further study as an adaptive mechanism. This is the first long-term assessment of genomic changes in S. enterica in a low moisture environment, and the first study to examine the methylome of any bacteria over a period of years, to our knowledge. These data contribute to our understanding of S. enterica survival in LMFs, and coupled with further studies, will provide the information necessary to design effective interventions which reduce S. enterica in LMFs and maintain a healthy, safe food supply.
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Affiliation(s)
- Cary P. Davies
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, NEA, U.S. Department of Agriculture, Beltsville, MD, United States
- *Correspondence: Cary P. Davies,
| | - Thomas Jurkiw
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Julie Haendiges
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Elizabeth Reed
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Nathan Anderson
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Bedford Park, IL, United States
| | - Elizabeth Grasso-Kelley
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Bedford Park, IL, United States
| | - Maria Hoffmann
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Jie Zheng
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
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6
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Wu M, Shan W, Zhao GP, Lyu LD. The H2O2 Concentration-Dependent Kinetics of Gene Expression: Linking the Intensity of Oxidative Stress and Mycobacterial Physiological Adaptation. Emerg Microbes Infect 2022; 11:573-584. [PMID: 35076334 PMCID: PMC8856045 DOI: 10.1080/22221751.2022.2034484] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Defence against oxidative stress is crucial for Mycobacterium tuberculosis to survive and replicate within macrophages. Mycobacteria have evolved multilayer antioxidant systems, including scavenging enzymes, iron homeostasis, repair pathways, and metabolic adaptation, for coping with oxidative stress. How these systems are coordinated to enable the physiological adaptation to different intensities of oxidative stress, however, remains unclear. To address this, we investigated the expression kinetics of the well-characterized antioxidant genes at bacteriostatic H2O2 concentrations ranging from 1 mM to 10 mM employing Mycolicibacterium smegmatis as a model. Our results showed that most of the selected genes were expressed in a H2O2 concentration-dependent manner, whereas a subset exhibited sustained induction or repression without dose–effect, reflecting H2O2 concentration-dependent physiological adaptations. Through analyzing the dynamics of the coordinated gene expression, we demonstrated that the expressions of the H2O2 scavenging enzymes, DNA damage response, and Fe–S cluster repair function were strikingly correlated to the intensity of oxidative stress. The sustained induction of mbtB, irtA, and dnaE2 indicated that mycobacteria might deploy increased iron acquisition and error-prone lesion bypass function as fundamental strategies to counteract oxidative damages, which are distinct from the defence tactics of Escherichia coli characterized by shrinking the iron pool and delaying the DNA repair. Moreover, the distinct gene expression kinetics among the tricarboxylic acid cycle, glyoxylate shunt, and methylcitrate cycle suggested that mycobacteria could dynamically redirect its metabolic fluxes according to the intensity of oxidative stress. This work defines the H2O2 concentration-dependent gene expression kinetics and provides unique insights into mycobacterial antioxidant defence strategies.
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Affiliation(s)
- Mengying Wu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, 200032 Shanghai, China
| | - Wenyan Shan
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, 200032 Shanghai, China
| | - Guo-Ping Zhao
- Department of Microbiology, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Liang-Dong Lyu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, 200032 Shanghai, China
- Shanghai Clinical Research Center for Infectious Disease (Tuberculosis), Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, 200433 Shanghai, China
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7
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Zaide G, Elia U, Cohen-Gihon I, Israeli M, Rotem S, Israeli O, Ehrlich S, Cohen H, Lazar S, Beth-Din A, Shafferman A, Zvi A, Cohen O, Chitlaru T. Comparative Analysis of the Global Transcriptomic Response to Oxidative Stress of Bacillus anthracis htrA-Disrupted and Parental Wild Type Strains. Microorganisms 2020; 8:microorganisms8121896. [PMID: 33265965 PMCID: PMC7760947 DOI: 10.3390/microorganisms8121896] [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: 11/03/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/30/2022] Open
Abstract
We previously demonstrated that the HtrA (High Temperature Requirement A) protease/chaperone active in the quality control of protein synthesis, represents an important virulence determinant of Bacillus anthracis. Virulence attenuation of htrA-disrupted Bacillus anthracis strains was attributed to susceptibility of ΔhtrA strains to stress insults, as evidenced by affected growth under various stress conditions. Here, we report a comparative RNA-seq transcriptomic study generating a database of differentially expressed genes in the B. anthracishtrA-disrupted and wild type parental strains under oxidative stress. The study demonstrates that, apart from protease and chaperone activities, HtrA exerts a regulatory role influencing expression of more than 1000 genes under stress. Functional analysis of groups or individual genes exhibiting strain-specific modulation, evidenced (i) massive downregulation in the ΔhtrA and upregulation in the WT strains of various transcriptional regulators, (ii) downregulation of translation processes in the WT strain, and (iii) downregulation of metal ion binding functions and upregulation of sporulation-associated functions in the ΔhtrA strain. These modulated functions are extensively discussed. Fifteen genes uniquely upregulated in the wild type strain were further interrogated for their modulation in response to other stress regimens. Overexpression of one of these genes, encoding for MazG (a nucleoside triphosphate pyrophosphohydrolase involved in various stress responses in other bacteria), in the ΔhtrA strain resulted in partial alleviation of the H2O2-sensitive phenotype.
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8
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Shahbaaz M, Potemkin V, Bisetty K, Hassan MI, Hussien MA. Classification and functional analyses of putative virulence factors of Mycobacterium tuberculosis: A combined sequence and structure based study. Comput Biol Chem 2020; 87:107270. [PMID: 32438116 DOI: 10.1016/j.compbiolchem.2020.107270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 04/16/2020] [Accepted: 04/26/2020] [Indexed: 11/17/2022]
Abstract
The emergence of the drug-resistant mechanisms in Mycobacterium tuberculosis poses the biggest challenges to the current therapeutic measures, which necessitates the identification of new drug targets. The Hypothetical Proteins (HPs), a class of functionally uncharacterized proteins, may provide a new class of undiscovered therapeutic targets. The genome of M. tuberculosis contains 1000 HPs with their sequences were analyzed using a variety of bioinformatics tools and the functional annotations were performed. The functions of 662 HPs were successfully predicted and further classified 483 HPs as enzymes, 141 HPs were predicted to be involved in the diverse cellular mechanisms and 38 HPs may function as transporters and carriers proteins. Furthermore, 28 HPs were predicted to be virulent in nature. Amongst them, the HP P95201, HP P9WM79, HP I6WZ30, HP I6 × 9T8, HP P9WKP3, and HP P9WK89 showed the highest virulence scores. Therefore, these proteins were subjected to extensive structure analyses and dynamics of their conformations were investigated using the principles of molecular dynamics simulations, each for a 150 ns time scale. This study provides a deeper understanding of the undiscovered drug targets and the generated outputs will facilitate the process of drug design and discovery against the infection of M. tuberculosis.
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Affiliation(s)
- Mohd Shahbaaz
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute (SANBI), University of the Western Cape, Private Bag X17, Bellville 7535, Cape Town, South Africa; Laboratory of Computational Modeling of Drugs, South Ural State University, 76 Lenin prospekt, 454080 Chelyabinsk, Russia
| | - Vladimir Potemkin
- Laboratory of Computational Modeling of Drugs, South Ural State University, 76 Lenin prospekt, 454080 Chelyabinsk, Russia
| | - Krishna Bisetty
- Department of Chemistry, Durban University of Technology, Durban, 4000, South Africa
| | - Md Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mostafa A Hussien
- Department of Chemistry, Faculty of Science, King Abdulaziz University, P.O. Box 80203 Jeddah 21589, Saudi Arabia; Department of Chemistry, Faculty of Science, Port Said University, Port Said, 42521, Egypt
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9
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Wang D, Jiang Y, Xiao S, Wang M, Liu Q, Huang L, Xue C, Wang Q, Lin T, Shao H, McMinn A. Characterization and Genome Analysis of a Novel Alteromonas Phage JH01 Isolated from the Qingdao Coast of China. Curr Microbiol 2019; 76:1256-1263. [PMID: 31372731 DOI: 10.1007/s00284-019-01751-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/31/2019] [Accepted: 07/26/2019] [Indexed: 12/27/2022]
Abstract
A novel Alteromonas phage JH01, with the host strain identified to be Alteromonas marina SW-47(T), was isolated from the Qingdao coast during the summer of 2017. Transmission electron microscopy analysis showed that phage JH01 can be categorized into the Siphoviridae family, with an icosahedral head of 62 ± 5 nm and a long contractile tail of 254 ± 10 nm. The bioinformatic analysis shows that this phage consists of a linear, double-stranded 46,500 bp DNA molecule with a GC content of 44.39%, and 58 ORFs with no tRNA genes. The ORFs are classified into four groups, including phage packaging, phage structure, DNA replication and regulation, and hypothetical protein. The phylogenetic tree, constructed using neighbor-joining analysis, shows that phage JH01 has altitudinal homology with some Vibrio and Pseudoalteromonas phage B8b. Comparative analysis reveals the high similarity between phage JH01 and phage B8b. Additionally, our study of phage JH01 provides useful information for further research on the interaction between Alteromonas phages and their hosts.
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Affiliation(s)
- Dongxu Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yong Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China. .,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China. .,Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, 266003, China.
| | - Shicong Xiao
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Min Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China. .,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China. .,Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, 266003, China.
| | - Qian Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Liyang Huang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Chenglong Xue
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Qi Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Tongtong Lin
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Hongbing Shao
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Andrew McMinn
- Institute for Marine and Antarctic Studies, University of Tasmania, TAS, Private Bag 129, Hobart, 7001, Australia
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10
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Rihtman B, Bowman‐Grahl S, Millard A, Corrigan RM, Clokie MRJ, Scanlan DJ. Cyanophage MazG is a pyrophosphohydrolase but unable to hydrolyse magic spot nucleotides. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:448-455. [PMID: 30809954 PMCID: PMC6850273 DOI: 10.1111/1758-2229.12741] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/26/2019] [Accepted: 02/26/2019] [Indexed: 05/28/2023]
Abstract
Bacteriophage possess a variety of auxiliary metabolic genes of bacterial origin. These proteins enable them to maximize infection efficiency, subverting bacterial metabolic processes for the purpose of viral genome replication and synthesis of the next generation of virion progeny. Here, we examined the enzymatic activity of a cyanophage MazG protein - a putative pyrophosphohydrolase previously implicated in regulation of the stringent response via reducing levels of the central alarmone molecule (p)ppGpp. We demonstrate, however, that the purified viral MazG shows no binding or hydrolysis activity against (p)ppGpp. Instead, dGTP and dCTP appear to be the preferred substrates of this protein, consistent with a role preferentially hydrolysing deoxyribonucleotides from the high GC content host Synechococcus genome. This showcases a new example of the fine-tuned nature of viral metabolic processes.
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Affiliation(s)
| | | | - Andrew Millard
- Department of Infection, Immunity and InflammationUniversity of LeicesterLeicesterUK
| | - Rebecca M. Corrigan
- Department of Molecular Biology & BiotechnologyUniversity of SheffieldSheffieldUK
| | - Martha R. J. Clokie
- Department of Infection, Immunity and InflammationUniversity of LeicesterLeicesterUK
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11
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Costa AR, Monteiro R, Azeredo J. Genomic analysis of Acinetobacter baumannii prophages reveals remarkable diversity and suggests profound impact on bacterial virulence and fitness. Sci Rep 2018; 8:15346. [PMID: 30337588 PMCID: PMC6193963 DOI: 10.1038/s41598-018-33800-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 09/18/2018] [Indexed: 12/12/2022] Open
Abstract
The recent nomination by the World Health Organization of Acinetobacter baumannii as the number one priority pathogen for the development of new antibiotics is a direct consequence of its fast evolution of pathogenicity, and in particular of multidrug resistance. While the development of new antibiotics is critical, understanding the mechanisms behind the crescent bacterial antibiotic resistance is equally relevant. Often, resistance and other bacterial virulence elements are contained on highly mobile pieces of DNA that can easily spread to other bacteria. Prophages are one of the mediators of this form of gene transfer, and have been frequently found in bacterial genomes, often offering advantageous features to the host. Here we assess the contribution of prophages for the evolution of A. baumannii pathogenicity. We found prophages to be notably diverse and widely disseminated in A. baumannii genomes. Also remarkably, A. baumannii prophages encode for multiple putative virulence factors that may be implicated in the bacterium’s capacity to colonize host niches, evade the host immune system, subsist in unfavorable environments, and tolerate antibiotics. Overall our results point towards a significant contribution of prophages for the dissemination and evolution of pathogenicity in A. baumannii, and highlight their clinical relevance.
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Affiliation(s)
- Ana Rita Costa
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Rodrigo Monteiro
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Joana Azeredo
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal.
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12
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Gruber CC, Walker GC. Incomplete base excision repair contributes to cell death from antibiotics and other stresses. DNA Repair (Amst) 2018; 71:108-117. [PMID: 30181041 DOI: 10.1016/j.dnarep.2018.08.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Numerous lethal stresses in bacteria including antibiotics, thymineless death, and MalE-LacZ expression trigger an increase in the production of reactive oxygen species. This results in the oxidation of the nucleotide pool by radicals produced by Fenton chemistry. Following the incorporation of these oxidized nucleotides into the genome, the cell's unsuccessful attempt to repair these lesions through base excision repair (BER) contributes causally to the lethality of these stresses. We review the evidence for this phenomenon of incomplete BER-mediated cell death and discuss how better understanding this pathway could contribute to the development of new antibiotics.
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Affiliation(s)
- Charley C Gruber
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States
| | - Graham C Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States.
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13
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Lu J, Dong W, He H, Han Z, Zhuo Y, Mo R, Liang Y, Zhu J, Li R, Qu H, Zhang L, Wang S, Ma R, Jia Z, Zhong W. Autophagy induced by overexpression of DCTPP1 promotes tumor progression and predicts poor clinical outcome in prostate cancer. Int J Biol Macromol 2018; 118:599-609. [PMID: 29874556 DOI: 10.1016/j.ijbiomac.2018.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/21/2018] [Accepted: 06/02/2018] [Indexed: 01/15/2023]
Abstract
Although dCTP pyrophosphatase 1 (DCTPP1) has been reported to be associated with poor clinical outcomes in various cancers, whether it plays an important role in prostate cancer (PCa) remains unclear. In this study, an immunohistochemical assay showed the protein expression level of DCTPP1 was significantly higher in PCa tissues than in non-cancerous tissues. Moreover, DCTPP1 was upregulated at both protein and mRNA levels in the PCa tissues from high Gleason score patients versus low Gleason score patients. The analysis of The Cancer Genome Atlas RNA-seq data suggested that upregulation of DCTPP1 was inversely correlated with biochemical recurrence free survival and overall survival. The roles of DCTPP1 in tumor progression and autophagy were further validated through cells invasion, migration, apoptosis and proliferation assays in vitro, as well as EMT and autophagy assays in vivo. Advanced bioinformatics analysis identified the evidence supporting the promotional role of DCTPP1 in tumor progression associated with autophagy. We conclude that DCTPP1 may play an important role in PCa progression associated with high autophagy. Overexpression of DCTPP1 may server as a biomarker for predicting poor BCR-free survival and overall survival for PCa patients.
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Affiliation(s)
- Jianming Lu
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou 510180, China; Department of Botany and Plant Sciences, University of California, Riverside 92507, USA
| | - Weimin Dong
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou 510180, China; Urology Key Laboratory of Guangdong Province, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510230, China
| | - Huichan He
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou 510180, China; Urology Key Laboratory of Guangdong Province, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510230, China
| | - Zhaodong Han
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou 510180, China
| | - YangJia Zhuo
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou 510180, China
| | - RuJun Mo
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou 510180, China
| | - Yingke Liang
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou 510180, China
| | - JianGuo Zhu
- Department of Urology, Guizhou Provincial People's Hospital, The Affiliated Hospital of Guizhou Medicine University, Guiyang, Guizhou Province 550002, China
| | - Ruidong Li
- Department of Botany and Plant Sciences, University of California, Riverside 92507, USA
| | - Han Qu
- Department of Botany and Plant Sciences, University of California, Riverside 92507, USA
| | - Le Zhang
- Department of Botany and Plant Sciences, University of California, Riverside 92507, USA
| | - Shibo Wang
- Department of Botany and Plant Sciences, University of California, Riverside 92507, USA
| | - Renyuan Ma
- Department of Botany and Plant Sciences, University of California, Riverside 92507, USA; Department of Mathematics, Bowdoin College, Brunswick, ME 04011, USA
| | - Zhenyu Jia
- Department of Botany and Plant Sciences, University of California, Riverside 92507, USA.
| | - Weide Zhong
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou 510180, China; Urology Key Laboratory of Guangdong Province, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510230, China.
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14
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Data Mining Mycobacterium tuberculosis Pathogenic Gene Transcription Factors and Their Regulatory Network Nodes. Int J Genomics 2018; 2018:3079730. [PMID: 29725597 PMCID: PMC5872665 DOI: 10.1155/2018/3079730] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 11/06/2017] [Accepted: 12/05/2017] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis (TB) is one of the deadliest infectious diseases worldwide. In Mycobacterium tuberculosis, changes in gene expression are highly variable and involve many genes, so traditional single-gene screening of M. tuberculosis targets has been unable to meet the needs of clinical diagnosis. In this study, using the National Center for Biotechnology Information (NCBI) GEO Datasets, whole blood gene expression profile data were obtained in patients with active pulmonary tuberculosis. Linear model-experience Bayesian statistics using the Limma package in R combined with t-tests were applied for nonspecific filtration of the expression profile data, and the differentially expressed human genes were determined. Using DAVID and KEGG, the functional analysis of differentially expressed genes (GO analysis) and the analysis of signaling pathways were performed. Based on the differentially expressed gene, the transcriptional regulatory element databases (TRED) were integrated to construct the M. tuberculosis pathogenic gene regulatory network, and the correlation of the network genes with disease was analyzed with the DAVID online annotation tool. It was predicted that IL-6, JUN, and TP53, along with transcription factors SRC, TNF, and MAPK14, could regulate the immune response, with their function being extracellular region activity and protein binding during infection with M. tuberculosis.
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15
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Antibiotic killing through oxidized nucleotides. Proc Natl Acad Sci U S A 2018; 115:1967-1969. [PMID: 29444858 DOI: 10.1073/pnas.1800255115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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16
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Oxidation of dCTP contributes to antibiotic lethality in stationary-phase mycobacteria. Proc Natl Acad Sci U S A 2018; 115:2210-2215. [PMID: 29382762 DOI: 10.1073/pnas.1719627115] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Growing evidence shows that generation of reactive oxygen species (ROS) derived from antibiotic-induced metabolic perturbation contribute to antibiotic lethality. However, our knowledge of the mechanisms by which antibiotic-induced oxidative stress actually kills cells remains elusive. Here, we show that oxidation of dCTP underlies ROS-mediated antibiotic lethality via induction of DNA double-strand breaks (DSBs). Deletion of mazG-encoded 5-OH-dCTP-specific pyrophosphohydrolase potentiates antibiotic killing of stationary-phase mycobacteria, but did not affect antibiotic efficacy in exponentially growing cultures. Critically, the effect of mazG deletion on potentiating antibiotic killing is associated with antibiotic-induced ROS and accumulation of 5-OH-dCTP. Independent lines of evidence presented here indicate that the increased level of DSBs observed in the ΔmazG mutant is a dead-end event accounting for enhanced antibiotic killing. Moreover, we provided genetic evidence that 5-OH-dCTP is incorporated into genomic DNA via error-prone DNA polymerase DnaE2 and repair of 5-OH-dC lesions via the endonuclease Nth leads to the generation of lethal DSBs. This work provides a mechanistic view of ROS-mediated antibiotic lethality in stationary phase and may have broad implications not only with respect to antibiotic lethality but also to the mechanism of stress-induced mutagenesis in bacteria.
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Singh A. Guardians of the mycobacterial genome: A review on DNA repair systems in Mycobacterium tuberculosis. MICROBIOLOGY-SGM 2017; 163:1740-1758. [PMID: 29171825 DOI: 10.1099/mic.0.000578] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The genomic integrity of Mycobacterium tuberculosis is continuously threatened by the harsh survival conditions inside host macrophages, due to immune and antibiotic stresses. Faithful genome maintenance and repair must be accomplished under stress for the bacillus to survive in the host, necessitating a robust DNA repair system. The importance of DNA repair systems in pathogenesis is well established. Previous examination of the M. tuberculosis genome revealed homologues of almost all the major DNA repair systems, i.e. nucleotide excision repair (NER), base excision repair (BER), homologous recombination (HR) and non-homologous end joining (NHEJ). However, recent developments in the field have pointed to the presence of novel proteins and pathways in mycobacteria. Homologues of archeal mismatch repair proteins were recently reported in mycobacteria, a pathway previously thought to be absent. RecBCD, the major nuclease-helicase enzymes involved in HR in E. coli, were implicated in the single-strand annealing (SSA) pathway. Novel roles of archeo-eukaryotic primase (AEP) polymerases, previously thought to be exclusive to NHEJ, have been reported in BER. Many new proteins with a probable role in DNA repair have also been discovered. It is now realized that the DNA repair systems in M. tuberculosis are highly evolved and have redundant backup mechanisms to mend the damage. This review is an attempt to summarize our current understanding of the DNA repair systems in M. tuberculosis.
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Affiliation(s)
- Amandeep Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
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18
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Elghraoui A, Modlin SJ, Valafar F. SMRT genome assembly corrects reference errors, resolving the genetic basis of virulence in Mycobacterium tuberculosis. BMC Genomics 2017; 18:302. [PMID: 28415976 PMCID: PMC5393005 DOI: 10.1186/s12864-017-3687-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 04/06/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The genetic basis of virulence in Mycobacterium tuberculosis has been investigated through genome comparisons of virulent (H37Rv) and attenuated (H37Ra) sister strains. Such analysis, however, relies heavily on the accuracy of the sequences. While the H37Rv reference genome has had several corrections to date, that of H37Ra is unmodified since its original publication. RESULTS Here, we report the assembly and finishing of the H37Ra genome from single-molecule, real-time (SMRT) sequencing. Our assembly reveals that the number of H37Ra-specific variants is less than half of what the Sanger-based H37Ra reference sequence indicates, undermining and, in some cases, invalidating the conclusions of several studies. PE_PPE family genes, which are intractable to commonly-used sequencing platforms because of their repetitive and GC-rich nature, are overrepresented in the set of genes in which all reported H37Ra-specific variants are contradicted. Further, one of the sequencing errors in H37Ra masks a true variant in common with the clinical strain CDC1551 which, when considered in the context of previous work, corresponds to a sequencing error in the H37Rv reference genome. CONCLUSIONS Our results constrain the set of genomic differences possibly affecting virulence by more than half, which focuses laboratory investigation on pertinent targets and demonstrates the power of SMRT sequencing for producing high-quality reference genomes.
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Affiliation(s)
- Afif Elghraoui
- Biological and Medical Informatics Research Center, San Diego State University, Campanile Drive, San Diego, 92182, USA
| | - Samuel J Modlin
- Biological and Medical Informatics Research Center, San Diego State University, Campanile Drive, San Diego, 92182, USA
| | - Faramarz Valafar
- Biological and Medical Informatics Research Center, San Diego State University, Campanile Drive, San Diego, 92182, USA.
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19
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Jia X, Yang L, Dong M, Chen S, Lv L, Cao D, Fu J, Yang T, Zhang J, Zhang X, Shang Y, Wang G, Sheng Y, Huang H, Chen F. The Bioinformatics Analysis of Comparative Genomics of Mycobacterium tuberculosis Complex (MTBC) Provides Insight into Dissimilarities between Intraspecific Groups Differing in Host Association, Virulence, and Epitope Diversity. Front Cell Infect Microbiol 2017; 7:88. [PMID: 28377903 PMCID: PMC5360109 DOI: 10.3389/fcimb.2017.00088] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 03/06/2017] [Indexed: 12/31/2022] Open
Abstract
Tuberculosis now exceeds HIV as the top infectious disease cause of mortality, and is caused by the Mycobacterium tuberculosis complex (MTBC). MTBC strains have highly conserved genome sequences (similarity >99%) but dramatically different phenotypes. To analyze the relationship between genotype and phenotype, we conducted the comparative genomic analysis on 12 MTBC strains representing different lineages (i.e., Mycobacterium bovis; M. bovis BCG; M. microti; M. africanum; M. tuberculosis H37Rv; M. tuberculosis H37Ra, and six M. tuberculosis clinical isolates). The analysis focused on the three aspects of pathogenicity: host association, virulence, and epitope variations. Host association analysis indicated that eight mce3 genes, two enoyl-CoA hydratases, and five PE/PPE family genes were present only in human isolates; these may have roles in host-pathogen interactions. There were 15 SNPs found on virulence factors (including five SNPs in three ESX secretion proteins) only in the Beijing strains, which might be related to their more virulent phenotype. A comparison between the virulent H37Rv and non-virulent H37Ra strains revealed three SNPs that were likely associated with the virulence attenuation of H37Ra: S219L (PhoP), A219E (MazG) and a newly identified I228M (EspK). Additionally, a comparison of animal-associated MTBC strains showed that the deletion of the first four genes (i.e., pe35, ppe68, esxB, esxA), rather than all eight genes of RD1, might play a central role in the virulence attenuation of animal isolates. Finally, by comparing epitopes among MTBC strains, we found that four epitopes were lost only in the Beijing strains; this may render them better capable of evading the human immune system, leading to enhanced virulence. Overall, our comparative genomic analysis of MTBC strains reveals the relationship between the highly conserved genotypes and the diverse phenotypes of MTBC, provides insight into pathogenic mechanisms, and facilitates the development of potential molecular targets for the prevention and treatment of tuberculosis.
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Affiliation(s)
- Xinmiao Jia
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China; College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Li Yang
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China; College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Mengxing Dong
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China; College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Suting Chen
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute Beijing, China
| | - Lingna Lv
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute Beijing, China
| | - Dandan Cao
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China
| | - Jing Fu
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China; College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Tingting Yang
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China; College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Ju Zhang
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China
| | - Xiangli Zhang
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China; College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Yuanyuan Shang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute Beijing, China
| | - Guirong Wang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute Beijing, China
| | - Yongjie Sheng
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University Changchun, China
| | - Hairong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute Beijing, China
| | - Fei Chen
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China; College of Life Sciences, University of Chinese Academy of SciencesBeijing, China; Sino-Danish College, University of Chinese Academy of SciencesBeijing, China; Collaborative Innovation Center for Genetics and DevelopmentShanghai, China
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20
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Fluorescent Reporter DS6A Mycobacteriophages Reveal Unique Variations in Infectibility and Phage Production in Mycobacteria. J Bacteriol 2016; 198:3220-3232. [PMID: 27672191 DOI: 10.1128/jb.00592-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 09/13/2016] [Indexed: 12/22/2022] Open
Abstract
Mycobacteriophage DS6A is unique among the more than 8,000 isolated mycobacteriophages due to its ability to form plaques exclusively on mycobacteria belonging to the Mycobacterium tuberculosis complex (MTBC). Speculation surrounding this specificity has led to unsupported assertions in published studies and patents that nontuberculous mycobacteria (NTM) are wholly resistant to DS6A infection. In this study, we identified two independent nonessential regions in the DS6A genome and replaced them with an mVenus-expressing plasmid to generate fluorescent reporter phages Φ2GFP12 and Φ2GFP13. We show that even though DS6A is able to form plaques only on MTBC bacteria, infection of various NTM results in mVenus expression in transduced cells. The efficiency of DS6A in delivering DNA varied between NTM species. Additionally, we saw a striking difference in the efficiency of DNA delivery between the closely related members of the Mycobacterium abscessus complex, M. abscessus and Mycobacterium massiliense We also demonstrated that TM4 and DS6A, two phages that do not form plaques on M. massiliense, differ in their ability to deliver DNA, suggesting that there is a phage-specific restriction between mycobacterial species. Phylogenetic analysis reveals that the DS6A genome has a characteristically mosaic structure but provided few insights into the basis for the specificity for MTBC hosts. This study demonstrates that the inability of the MTBC-specific phage DS6A to form plaques on NTM is more complex than previously thought. Moreover, the DS6A-derived fluorophages provide important new tools for the study of mycobacterial biology. IMPORTANCE The coevolution of bacteria and their infecting phages involves a constant arms race for bacteria to prevent phage infection and phage to overcome these preventions. Although a diverse array of phage defense systems is well characterized in bacteria, very few phage restriction systems are known in mycobacteria. The DS6A mycobacteriophage is unique in the mycobacterial world in that it forms plaques only on members of the Mycobacterium tuberculosis complex. However, the novel DS6A reporter phages developed in this work demonstrate that DS6A can infect nontuberculous mycobacteria at various efficiencies. By comparing the abilities of DS6A and another phage, TM4, to infect and form plaques on various mycobacterial species, we can begin to discern new phage restriction systems employed within the genus.
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Dömötör D, Frank T, Rákhely G, Doffkay Z, Schneider G, Kovács T. Comparative analysis of two bacteriophages of Xanthomonas arboricola pv. juglandis. INFECTION GENETICS AND EVOLUTION 2016; 43:371-7. [PMID: 27275846 DOI: 10.1016/j.meegid.2016.06.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 05/24/2016] [Accepted: 06/04/2016] [Indexed: 12/21/2022]
Abstract
Walnut blight caused by Xanthomonas arboricola pv. juglandis (Xaj) is one of the most frequent infective diseases of walnut, resulting in serious economic losses. One potential solution to control this disease could be the application of bacteriophages. In this study, 24 phages were isolated from soil and walnut aerial tissues infected with Xaj. Two polyvalent bacteriophages, Xaj2 and Xaj24 were chosen for further characterization including their morphological, physiological and genomic analyses. Xaj2 was classified as Siphoviridae whereas Xaj24 belonged to the Podoviridae family. Both phages demonstrated lytic effect on Xaj in laboratory trials. Complete genomes of Xaj2 and Xaj24 were determined. Genomes of Xaj2 and Xaj24 consisted of 49.241 and 44.861 nucleotides encoding 80 and 53 genes, respectively. Comparative genome analyses have revealed that Xaj2 had a unique genome sequence, while Xaj24 was a phiKMV-like phage and it was most similar to the Prado phage which is virulent for Xylella fastidiosa and Xanthomonas spp. In this study, we present the first two complete Xaj phage sequences enabling an insight into the genomics of Xaj phages.
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Affiliation(s)
- Dóra Dömötör
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Pécs, Hungary
| | - Tamara Frank
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Pécs, Hungary; Faculty of Engineering, University of Pannonia, Veszprém, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary; Institute of Biophysics, Biological Research Center, Szeged, Hungary
| | - Zsolt Doffkay
- Institute of Biophysics, Biological Research Center, Szeged, Hungary
| | - György Schneider
- Institute of Medical Microbiology and Immunology, University of Pécs, Pécs, Hungary
| | - Tamás Kovács
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Pécs, Hungary.
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22
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Ramisetty BCM, Raj S, Ghosh D. Escherichia coli MazEF toxin-antitoxin system does not mediate programmed cell death. J Basic Microbiol 2016; 56:1398-1402. [PMID: 27259116 DOI: 10.1002/jobm.201600247] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 05/20/2016] [Indexed: 11/06/2022]
Abstract
Toxin-antitoxins systems (TAS) are prokaryotic operons containing two small overlapping genes which encode two components referred to as toxin and antitoxin. Involvement of TAS in bacterial programmed cell death (PCD) is highly controversial. MazEF, a typical type II TAS, is particularly implicated in mediating PCD in Escherichia coli. Hence, we compared the metabolic fitness and stress tolerance of E. coli strains (MC4100 and its mazEF-derivative) which were extensively used by proponents of mazEF-mediated PCD. We found that both the strains are deficient in relA gene and that the ΔmazEF strain has lower fitness and stress tolerance compared to wild type MC4100. We could not reproduce mazEF mediated PCD which emphasizes the need for skeptic approach to the PCD hypothesis.
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Affiliation(s)
| | - Swati Raj
- School of Chemical and Biotechnology, SASTRA University, Thirumalaisamudram, Thanjavur, India
| | - Dimpy Ghosh
- School of Chemical and Biotechnology, SASTRA University, Thirumalaisamudram, Thanjavur, India
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23
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Crystal structure of the Bacillus-conserved MazG protein, a nucleotide pyrophosphohydrolase. Biochem Biophys Res Commun 2016; 472:237-42. [DOI: 10.1016/j.bbrc.2016.02.097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 02/22/2016] [Indexed: 11/22/2022]
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24
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Tan Y, Xu Z, Tao J, Ni J, Zhao W, Lu J, Yao YF. A SIRT4-like auto ADP-ribosyltransferase is essential for the environmental growth of Mycobacterium smegmatis. Acta Biochim Biophys Sin (Shanghai) 2016; 48:145-52. [PMID: 26685303 DOI: 10.1093/abbs/gmv121] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 09/26/2015] [Indexed: 01/12/2023] Open
Abstract
SIRT family proteins are highly conserved both in the structure and function among all the organisms, and are involved in gene silencing, DNA damage repair, cell growth and metabolism. Here, a SIRT4 homologue MSMEG_4620 was identified and characterized in Mycobacterium smegmatis. MSMEG_4620 exhibits deacetylase activity that can be activated by fatty acids. Interestingly, MSMEG_4620 also possesses auto ADP-ribosylation activity. MSMEG_4620 is modified on arginine residues as revealed by a chemical stability assay. Moreover, the auto ADP-ribosylation activity of MSMEG_4620 was found to be enhanced by ferric ion. Notably, the SIRT4 homologues are widely distributed in the genomes of environmental mycobacterial species instead of pathogenic mycobacterial species. When MSMEG_4620 was deleted in M. smegmatis, the mutant strain showed a growth defect in 7H9 minimal medium compared with the parental strain. Taken together, these results provided the characteristics of a SIRT4 homologue in prokaryotes and implicated its critical roles in the growth of environmental mycobacterial species.
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Affiliation(s)
- Yongcong Tan
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zhihong Xu
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jing Tao
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jinjing Ni
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Wei Zhao
- Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jie Lu
- Department of Infectious Diseases, Shanghai Ruijin Hospital, Shanghai 200025, China
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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Squires AH, Atas E, Meller A. Genomic Pathogen Typing Using Solid-State Nanopores. PLoS One 2015; 10:e0142944. [PMID: 26562833 PMCID: PMC4643041 DOI: 10.1371/journal.pone.0142944] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/28/2015] [Indexed: 11/17/2022] Open
Abstract
In clinical settings, rapid and accurate characterization of pathogens is essential for effective treatment of patients; however, subtle genetic changes in pathogens which elude traditional phenotypic typing may confer dangerous pathogenic properties such as toxicity, antibiotic resistance, or virulence. Existing options for molecular typing techniques characterize the critical genomic changes that distinguish harmful and benign strains, yet the well-established approaches, in particular those that rely on electrophoretic separation of nucleic acid fragments on a gel, have room for only incremental future improvements in speed, cost, and complexity. Solid-state nanopores are an emerging class of single-molecule sensors that can electrophoretically characterize charged biopolymers, and which offer significant advantages in terms of sample and reagent requirements, readout speed, parallelization, and automation. We present here the first application of nanopores for single-molecule molecular typing using length based "fingerprints" of critical sites in bacterial genomes. This technique is highly adaptable for detection of different types of genetic variation; as we illustrate using prototypical examples including Mycobacterium tuberculosis and methicillin-resistant Streptococcus aureus, the solid-state nanopore diagnostic platform may be used to detect large insertions or deletions, small insertions or deletions, and even single-nucleotide variations in bacterial DNA. We further show that Bayesian classification of test samples can provide highly confident pathogen typing results based on only a few tens of independent single-molecule events, making this method extremely sensitive and statistically robust.
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Affiliation(s)
- Allison H Squires
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215, United States of America
| | - Evrim Atas
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215, United States of America
| | - Amit Meller
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215, United States of America.,Department of Biomedical Engineering, The Technion-Israel Institute of Technology, Haifa, 32000, Israel
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Human dCTP pyrophosphatase 1 promotes breast cancer cell growth and stemness through the modulation on 5-methyl-dCTP metabolism and global hypomethylation. Oncogenesis 2015; 4:e159. [PMID: 26075750 PMCID: PMC4491611 DOI: 10.1038/oncsis.2015.10] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 03/24/2015] [Accepted: 04/02/2015] [Indexed: 12/11/2022] Open
Abstract
Human DCTPP1 (dCTP pyrophosphatase 1), also known as XTP3-transactivated protein A, belongs to MazG-like nucleoside triphosphate pyrophosphatase (NTP-PPase) superfamily. Being a newly identified pyrophosphatase, its relevance to tumorigenesis and the mechanisms are not well investigated. In the present study, we have confirmed our previous study that DCTPP1 was significantly hyperexpressed in breast cancer and further demonstrated its strong association with tumor progression and poor prognosis in breast cancer. Knockdown of DCTPP1 in breast cancer cell line MCF-7 cells remarkably retarded proliferation and colony formation in vitro. The capacity of mammosphere formation of MCF-7 was suppressed with the silence of DCTPP1, which was consistent with the enhanced mammosphere-forming ability in DCTPP1-overexpressed MDA-MB-231 cells. To further dissect the mechanisms of DCTPP1 in promoting tumor cell growth and stemness maintenance, its biochemical properties and biological functions were investigated. DCTPP1 displayed bioactive form with tetrameric structure similar to other MazG domain-containing pyrophosphatases based on structure simulation. A substrate preference for dCTP and its methylated or halogen-modified derivatives over the other canonical (deoxy-) NTPs was demonstrated from enzymatic assay. This substrate preference was also proved in breast cancer cells that the intracellular 5-methyl-dCTP level increased in DCTPP1-deficient MCF-7 cells but decreased in DCTPP1-overexpressed MDA-MB-231 cells. Moreover, global methylation level was elevated in DCTPP1-knockdown MCF-7 cells or mammosphere-forming MCF-7 cells but decreased significantly in DCTPP1-overexpressed MDA-MB-231 cells and its mammospheres. Our results thus indicated that human DCTPP1 was capable of modulating the concentration of intracellular 5-methyl-dCTP. This in turn affected global methylation, contributing to a known phenomenon of hypomethylation related to the cancer cell growth and stemness maintenance. Our current investigations point to the pathological functions of DCTPP1 overexpression in breast cancer cells with aberrant dCTP metabolism and epigenetic modification.
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Halmillawewa AP, Restrepo-Córdoba M, Yost CK, Hynes MF. Genomic and phenotypic characterization of Rhizobium gallicum phage vB_RglS_P106B. MICROBIOLOGY-SGM 2015; 161:611-20. [PMID: 25627439 DOI: 10.1099/mic.0.000022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The phage P106B (vB_RglS_P106B) is a Siphoviridae phage with a narrow spectrum of infectivity, which has been isolated from soils with a history of pea cultivation. The trapping host of P106B is an indigenous strain of Rhizobium gallicum (SO14B-4) isolated from soils associated with Vicia cracca. Phenotypic characterization of the phage revealed that P106B has an approximate burst size of 21 p.f.u. per infected cell with 60 min and 100 min eclipse and latent periods, respectively. Phage P106B was unable to transduce under the conditions tested. The genome of P106B is 56 024 bp in length with a mean DNA G+C content of 47.9 %. The complete genome sequence contains 95 putative ORFs and a single tRNA gene coding for leucine with the anticodon TTA. Putative functions could only be assigned to 22 of the predicted ORFs while a significant number of ORFs (47) shared no sequence similarities to previously characterized proteins. The remaining 26 putative protein-coding genes exhibited a sequence resemblance to other hypothetical proteins. No lysogeny-related genes were found in the P106B genome.
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Affiliation(s)
| | | | | | - Michael F Hynes
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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McHugh CA, Fontana J, Nemecek D, Cheng N, Aksyuk AA, Heymann JB, Winkler DC, Lam AS, Wall JS, Steven AC, Hoiczyk E. A virus capsid-like nanocompartment that stores iron and protects bacteria from oxidative stress. EMBO J 2014; 33:1896-911. [PMID: 25024436 DOI: 10.15252/embj.201488566] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Living cells compartmentalize materials and enzymatic reactions to increase metabolic efficiency. While eukaryotes use membrane-bound organelles, bacteria and archaea rely primarily on protein-bound nanocompartments. Encapsulins constitute a class of nanocompartments widespread in bacteria and archaea whose functions have hitherto been unclear. Here, we characterize the encapsulin nanocompartment from Myxococcus xanthus, which consists of a shell protein (EncA, 32.5 kDa) and three internal proteins (EncB, 17 kDa; EncC, 13 kDa; EncD, 11 kDa). Using cryo-electron microscopy, we determined that EncA self-assembles into an icosahedral shell 32 nm in diameter (26 nm internal diameter), built from 180 subunits with the fold first observed in bacteriophage HK97 capsid. The internal proteins, of which EncB and EncC have ferritin-like domains, attach to its inner surface. Native nanocompartments have dense iron-rich cores. Functionally, they resemble ferritins, cage-like iron storage proteins, but with a massively greater capacity (~30,000 iron atoms versus ~3,000 in ferritin). Physiological data reveal that few nanocompartments are assembled during vegetative growth, but they increase fivefold upon starvation, protecting cells from oxidative stress through iron sequestration.
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Affiliation(s)
- Colleen A McHugh
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Juan Fontana
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Daniel Nemecek
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Naiqian Cheng
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Anastasia A Aksyuk
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - J Bernard Heymann
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Dennis C Winkler
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Alan S Lam
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Joseph S Wall
- Department of Biology, Brookhaven National Laboratory, Upton, NY, USA
| | - Alasdair C Steven
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Egbert Hoiczyk
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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Vercruysse M, Köhrer C, Davies BW, Arnold MFF, Mekalanos JJ, RajBhandary UL, Walker GC. The highly conserved bacterial RNase YbeY is essential in Vibrio cholerae, playing a critical role in virulence, stress regulation, and RNA processing. PLoS Pathog 2014; 10:e1004175. [PMID: 24901994 PMCID: PMC4047096 DOI: 10.1371/journal.ppat.1004175] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 04/24/2014] [Indexed: 11/18/2022] Open
Abstract
YbeY, a highly conserved protein, is an RNase in E. coli and plays key roles in both processing of the critical 3′ end of 16 S rRNA and in 70 S ribosome quality control under stress. These central roles account for YbeY's inclusion in the postulated minimal bacterial genome. However, YbeY is not essential in E. coli although loss of ybeY severely sensitizes it to multiple physiological stresses. Here, we show that YbeY is an essential endoribonuclease in Vibrio cholerae and is crucial for virulence, stress regulation, RNA processing and ribosome quality control, and is part of a core set of RNases essential in most representative pathogens. To understand its function, we analyzed the rRNA and ribosome profiles of a V. cholerae strain partially depleted for YbeY and other RNase mutants associated with 16 S rRNA processing; our results demonstrate that YbeY is also crucial for 16 S rRNA 3′ end maturation in V. cholerae and that its depletion impedes subunit assembly into 70 S ribosomes. YbeY's importance to V. cholerae pathogenesis was demonstrated by the complete loss of mice colonization and biofilm formation, reduced cholera toxin production, and altered expression levels of virulence-associated small RNAs of a V. cholerae strain partially depleted for YbeY. Notably, the ybeY genes of several distantly related pathogens can fully complement an E. coli ΔybeY strain under various stress conditions, demonstrating the high conservation of YbeY's activity in stress regulation. Taken together, this work provides the first comprehensive exploration of YbeY's physiological role in a human pathogen, showing its conserved function across species in essential cellular processes. Bacteria adapt and survive unfavorable environments by quickly changing their gene expression and physiology, for example as pathogens do during infection of host cells. Gene expression is often determined by RNA turnover, a balance between transcription and RNA decay carried out by multiple RNases. The recently identified RNase YbeY was shown in E. coli to participate in rRNA maturation and 70 S ribosome quality control, however YbeY's roles in other organisms and the extent of functional conservation is unknown. Here, we show that YbeY is an essential RNase in the pathogen Vibrio cholerae, critical for cell fitness and general stress tolerance. We demonstrate that YbeY is crucial for 16 S rRNA 3′ end maturation, assembly of functional 70 S ribosomes and ribosome quality control. Moreover, YbeY regulates virulence-associated small RNAs and its depletion leads to an overall reduction in pathogenesis, exemplified by significantly decreased biofilm formation, mouse colonization and cholera toxin production. We also show that YbeY belongs to a minimal core set of RNases essential in most representative pathogens. The multifaceted roles of YbeY in several essential cellular processes and its highly conserved function across bacterial species, suggest that YbeY could be an attractive new antimicrobial target.
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Affiliation(s)
- Maarten Vercruysse
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Caroline Köhrer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Bryan W. Davies
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Markus F. F. Arnold
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - John J. Mekalanos
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachussets, United States of America
| | - Uttam L. RajBhandary
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Graham C. Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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Lyu LD, Tang BK, Fan XY, Ma H, Zhao GP. Mycobacterial MazG safeguards genetic stability via housecleaning of 5-OH-dCTP. PLoS Pathog 2013; 9:e1003814. [PMID: 24339782 PMCID: PMC3855555 DOI: 10.1371/journal.ppat.1003814] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 10/23/2013] [Indexed: 01/05/2023] Open
Abstract
Generation of reactive oxygen species and reactive nitrogen species in phagocytes is an important innate immune response mechanism to eliminate microbial pathogens. It is known that deoxynucleotides (dNTPs), the precursor nucleotides to DNA synthesis, are one group of the significant targets for these oxidants and incorporation of oxidized dNTPs into genomic DNA may cause mutations and even cell death. Here we show that the mycobacterial dNTP pyrophosphohydrolase MazG safeguards the bacilli genome by degrading 5-OH-dCTP, thereby, preventing it from incorporation into DNA. Deletion of the (d)NTP pyrophosphohydrolase-encoding mazG in mycobacteria leads to a mutator phenotype both under oxidative stress and in the stationary phase of growth, resulting in increased CG to TA mutations. Biochemical analyses demonstrate that mycobacterial MazG can efficiently hydrolyze 5-OH-dCTP, an oxidized nucleotide that induces CG to TA mutation upon incorporation by polymerase. Moreover, chemical genetic analyses show that direct incorporation of 5-OH-dCTP into mazG-null mutant strain of Mycobacterium smegmatis (Msm) leads to a dose-dependent mutagenesis phenotype, indicating that 5-OH-dCTP is a natural substrate of mycobacterial MazG. Furthermore, deletion of mazG in Mycobacterium tuberculosis (Mtb) leads to reduced survival in activated macrophages and in the spleen of infected mice. This study not only characterizes the mycobacterial MazG as a novel pyrimidine-specific housecleaning enzyme that prevents CG to TA mutation by degrading 5-OH-dCTP but also reveals a genome-safeguarding mechanism for survival of Mtb in vivo. The cellular nucleotide pool is a significant target for oxidation by reactive oxygen species and reactive nitrogen species. Misincorporation of these oxidized non-canonical nucleotides into DNA is known to cause mutations, and may be related to carcinogenesis, aging and neurodegeneration. Cells have evolved a group of bio-degradation housecleaning enzymes that may specifically eliminate certain non-canonical nucleotide from the nucleotide pool and thus prevent their incorporation into DNA. The most well-characterized housecleaning enzymes are the MutT-like proteins which specifically hydrolyze the oxidized purine nucleotides, such as 8-oxo-dGTP and 2-OH-dATP. Lack of MutT activity in cells leads to significant increase of AT-CG mutation and genetic instability. However, housecleaning enzymes specific for oxidized pyrimidine nucleotides are yet to be identified. Here we show that the dNTP pyrophosphohydrolase MazG from mycobacteria is a 5-OH-dCTP-specific housecleaning enzyme. Deletion of mazG in mycobacteria results in increased CG to TA mutation under oxidative stress and in the stationary phase of growth. Both biochemical and chemical genetic analyses demonstrate that 5-OH-dCTP is a natural substrate of mycobacterial MazG. Furthermore, deletion of mazG in Mtb leads to reduced survival in activated macrophages and in the spleen of infected mice. These results reveal a novel housecleaning pathway for mycobacteria to maintain genetic stability and survival in vivo.
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Affiliation(s)
- Liang-Dong Lyu
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- * E-mail: (LDL); (GPZ)
| | - Bi-Kui Tang
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Anhui Key Laboratory of Infection and Immunity, Department of Life Science, Bengbu Medical College, Bengbu, China
| | - Xiao-Yong Fan
- Shanghai Public Health Clinical Center Affiliated with Fudan University, Shanghai, China
| | - Hui Ma
- Shanghai Public Health Clinical Center Affiliated with Fudan University, Shanghai, China
| | - Guo-Ping Zhao
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Key Laboratory of Medical Molecular Virology affiliated with the Ministry of Education and Health, Shanghai Medical College, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai-MOST Key Laboratory for Health and Disease Genomics, Chinese National Human Genome Center, Shanghai, China
- * E-mail: (LDL); (GPZ)
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Comparative proteomic analysis of Mycobacterium tuberculosis strain H37Rv versus H37Ra. Int J Mycobacteriol 2013; 2:220-6. [PMID: 26786126 DOI: 10.1016/j.ijmyco.2013.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Revised: 10/11/2013] [Accepted: 10/14/2013] [Indexed: 10/26/2022] Open
Abstract
BACKGROUND Mycobacterium tuberculosis (MTB) H37Ra is an attenuated tubercle bacillus closely related to the virulent type strain MTB H37Rv. In spite of extensive study, variation in virulence between the MTB H37Rv and MTB H37Ra strains is still to be understood. The difference in protein expression or structure due to mutation may probably be an important factor for the virulence property of MTB H37Rv strain. METHODS In this study, a whole proteome comparison between these two strains was carried out using bioinformatics approaches to elucidate differences in their protein sequences. RESULTS On comparison of whole proteome using NCBI standalone BLAST program between these two strains, 3759 identical proteins in both the strains out of 4003 proteins were revealed in MTB H37Rv and 4034 proteins were revealed in MTB H37Ra; 244 proteins of MTB H37Rv and 260 proteins of MTB H37Ra were found to be non-identical. A total of 172 proteins were identified with mutations (Insertions/deletions/substitutions) in MTB H37Ra while 53 proteins of MTB H37Rv and 85 proteins of MTB H37Ra were found to be distinct. Among 244 non-identical proteins, 19 proteins were reported to have an important biological function; In this study, mutation was shown in these proteins of MTB H37Ra. CONCLUSION This study reports the protein differences with mutations between MTB H37Rv and H37Ra, which may help in better understanding the pathogenesis and virulence properties of MTB H37Rv.
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Zhang Y, Ye WY, Wang JQ, Wang SJ, Ji P, Zhou GY, Zhao GP, Ge HL, Wang Y. dCTP pyrophosphohydrase exhibits nucleic accumulation in multiple carcinomas. Eur J Histochem 2013; 57:e29. [PMID: 24085278 PMCID: PMC3794360 DOI: 10.4081/ejh.2013.e29] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 08/28/2013] [Accepted: 09/02/2013] [Indexed: 11/25/2022] Open
Abstract
Nucleoside triphosphate pyrophosphohydrolase (NTP-PPase) functions as one of the mechanisms to guarantee the fidelity of DNA replication through the cleavage of non-canonical nucleotides into di- or monophosphates. Human NTP-PPase is poorly understood and investigated. In the present study, by using tissue microarrays with the paired cancer and adjacent regions, we found that with the prevalent expression of dCTP pyrophosphohydrase (DCTPP1) in the cytosol and nucleus in tumors investigated, DCTPP1 was inclined to accumulate in the nucleus of cancer cells compared to the paired adjacent tissue cells in multiple carcinomas including lung, breast, liver, cervical, gastric and esophagus cancer. More significantly, the higher DCTPP1 expression in the nucleus of lung, gastric and esophagus cancer cells was associated with histological subtypes. The nucleic accumulation of DCTPP1 was apparently observed as well when tumor cell line MCF-7 was treated with H2O2in vitro. Considering the roles of DCTPP1 on restricting the concentration of non-canonical nucleotides in the nucleotide pool, accumulation of DCTPP1 in the nucleus of tumor cells might suffice for maintaining the proper DNA replication in order to fulfill the requirement for the survival and proliferation of tumor cells.
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Affiliation(s)
- Y Zhang
- Shanghai Jiaotong University School of Medicine.
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Genome of a SAR116 bacteriophage shows the prevalence of this phage type in the oceans. Proc Natl Acad Sci U S A 2013; 110:12343-8. [PMID: 23798439 DOI: 10.1073/pnas.1219930110] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The abundance, genetic diversity, and crucial ecological and evolutionary roles of marine phages have prompted a large number of metagenomic studies. However, obtaining a thorough understanding of marine phages has been hampered by the low number of phage isolates infecting major bacterial groups other than cyanophages and pelagiphages. Therefore, there is an urgent requirement for the isolation of phages that infect abundant marine bacterial groups. In this study, we isolated and characterized HMO-2011, a phage infecting a bacterium of the SAR116 clade, one of the most abundant marine bacterial lineages. HMO-2011, which infects "Candidatus Puniceispirillum marinum" strain IMCC1322, has an ~55-kb dsDNA genome that harbors many genes with novel features rarely found in cultured organisms, including genes encoding a DNA polymerase with a partial DnaJ central domain and an atypical methanesulfonate monooxygenase. Furthermore, homologs of nearly all HMO-2011 genes were predominantly found in marine metagenomes rather than cultured organisms, suggesting the novelty of HMO-2011 and the prevalence of this phage type in the oceans. A significant number of the viral metagenome sequences obtained from the ocean surface were best assigned to the HMO-2011 genome. The number of reads assigned to HMO-2011 accounted for 10.3%-25.3% of the total reads assigned to viruses in seven viromes from the Pacific and Indian Oceans, making the HMO-2011 genome the most or second-most frequently assigned viral genome. Given its ability to infect the abundant SAR116 clade and its widespread distribution, Puniceispirillum phage HMO-2011 could be an important resource for marine virus research.
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Yoshida-Takashima Y, Takaki Y, Shimamura S, Nunoura T, Takai K. Genome sequence of a novel deep-sea vent epsilonproteobacterial phage provides new insight into the co-evolution of Epsilonproteobacteria and their phages. Extremophiles 2013; 17:405-19. [PMID: 23512119 DOI: 10.1007/s00792-013-0529-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 01/31/2013] [Indexed: 11/26/2022]
Abstract
Epsilonproteobacteria are among the predominant primary producers in deep-sea hydrothermal vent ecosystems. However, phages infecting deep-sea vent Epsilonproteobacteria have never been isolated and characterized. Here, we successfully isolated a novel temperate phage, NrS-1, that infected a deep-sea vent chemolithoautotrophic isolate of Epsilonproteobacteria, Nitratiruptor sp. SB155-2, and its entire genome sequence was obtained and analyzed. The NrS-1 genome is linear, circularly permuted, and terminally redundant. The NrS-1 genome is 37,159 bp in length and contains 51 coding sequences. Five major structural proteins including major capsid protein and tape measure protein were identified by SDS-PAGE and mass spectrometry analysis. NrS-1 belongs to the family Siphoviridae, but its sequence and genomic organization are distinct from those of any other previously known Siphoviridae phages. Homologues of genes encoded in the NrS-1 genome were widely distributed among the genomes of diverse Epsilonproteobacteria. The distribution patterns had little relation to the evolutionary traits and ecological and physiological differentiation of the host epsilonproteobacterial species. The widespread occurrence of phage genes in diverse Epsilonproteobacteria supports early co-evolution between temperate phages and Epsilonproteobacteria prior to the divergence of their habitats and physiological adaptation.
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Affiliation(s)
- Yukari Yoshida-Takashima
- Subsurface Geobiology Advanced Research (SUGAR) Team, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan.
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WAN BS, ZHANG QF, ZHOU AP, ZHAO GP, YAO YF. Genomics and Genome Evolution of Mycobacterium tuberculosis*. PROG BIOCHEM BIOPHYS 2012. [DOI: 10.3724/sp.j.1206.2011.00469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Abstract
With the rapid advances in sequencing technologies in recent years, the human genome is now considered incomplete without the complementing microbiome, which outnumbers human genes by a factor of one hundred. The human microbiome, and more specifically the gut microbiome, has received considerable attention and research efforts over the past decade. Many studies have identified and quantified "who is there?," while others have determined some of their functional capacity, or "what are they doing?" In a recent study, we identified novel salt-tolerance loci from the human gut microbiome using combined functional metagenomic and bioinformatics based approaches. Herein, we discuss the identified loci, their role in salt-tolerance and their importance in the context of the gut environment. We also consider the utility and power of functional metagenomics for mining such environments for novel genes and proteins, as well as the implications and possible applications for future research.
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Affiliation(s)
- Eamonn P. Culligan
- Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland,Department of Microbiology; University College Cork; Cork, Ireland
| | - Julian R. Marchesi
- Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland,Cardiff School of Biosciences; Cardiff University; Cardiff, UK,Correspondence to: Julian R. Marchesi, and Colin Hill, and Roy D. Sleator,
| | - Colin Hill
- Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland,Department of Microbiology; University College Cork; Cork, Ireland,Correspondence to: Julian R. Marchesi, and Colin Hill, and Roy D. Sleator,
| | - Roy D. Sleator
- Department of Biological Sciences; Cork Institute of Technology; Bishopstown, Cork, Ireland,Correspondence to: Julian R. Marchesi, and Colin Hill, and Roy D. Sleator,
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Culligan EP, Sleator RD, Marchesi JR, Hill C. Functional metagenomics reveals novel salt tolerance loci from the human gut microbiome. ISME JOURNAL 2012; 6:1916-25. [PMID: 22534607 DOI: 10.1038/ismej.2012.38] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Metagenomics is a powerful tool that allows for the culture-independent analysis of complex microbial communities. One of the most complex and dense microbial ecosystems known is that of the human distal colon, with cell densities reaching up to 10(12) per gram of faeces. With the majority of species as yet uncultured, there are an enormous number of novel genes awaiting discovery. In the current study, we conducted a functional screen of a metagenomic library of the human gut microbiota for potential salt-tolerant clones. Using transposon mutagenesis, three genes were identified from a single clone exhibiting high levels of identity to a species from the genus Collinsella (closest relative being Collinsella aerofaciens) (COLAER_01955, COLAER_01957 and COLAER_01981), a high G+C, Gram-positive member of the Actinobacteria commonly found in the human gut. The encoded proteins exhibit a strong similarity to GalE, MurB and MazG. Furthermore, pyrosequencing and bioinformatic analysis of two additional fosmid clones revealed the presence of an additional galE and mazG gene, with the highest level of genetic identity to Akkermansia muciniphila and Eggerthella sp. YY7918, respectively. Cloning and heterologous expression of the genes in the osmosensitive strain, Escherichia coli MKH13, resulted in increased salt tolerance of the transformed cells. It is hoped that the identification of atypical salt tolerance genes will help to further elucidate novel salt tolerance mechanisms, and will assist our increased understanding how resident bacteria cope with the osmolarity of the gastrointestinal tract.
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Affiliation(s)
- Eamonn P Culligan
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
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Base excision and nucleotide excision repair pathways in mycobacteria. Tuberculosis (Edinb) 2011; 91:533-43. [DOI: 10.1016/j.tube.2011.06.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 06/01/2011] [Accepted: 06/12/2011] [Indexed: 01/13/2023]
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Dreher TW, Brown N, Bozarth CS, Schwartz AD, Riscoe E, Thrash C, Bennett SE, Tzeng SC, Maier CS. A freshwater cyanophage whose genome indicates close relationships to photosynthetic marine cyanomyophages. Environ Microbiol 2011; 13:1858-74. [PMID: 21605306 PMCID: PMC4185292 DOI: 10.1111/j.1462-2920.2011.02502.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Bacteriophage S-CRM01 has been isolated from a freshwater strain of Synechococcus and shown to be present in the upper Klamath River valley in northern California and Oregon. The genome of this lytic T4-like phage has a 178,563 bp circular genetic map with 297 predicted protein-coding genes and 33 tRNA genes that represent all 20-amino-acid specificities. Analyses based on gene sequence and gene content indicate a close phylogenetic relationship to the 'photosynthetic' marine cyanomyophages infecting Synechococcus and Prochlorococcus. Such relatedness suggests that freshwater and marine phages can draw on a common gene pool. The genome can be considered as being comprised of three regions. Region 1 is populated predominantly with structural genes, recognized as such by homology to other T4-like phages and by identification in a proteomic analysis of purified virions. Region 2 contains most of the genes with roles in replication, recombination, nucleotide metabolism and regulation of gene expression, as well as 5 of the 6 signature genes of the photosynthetic cyanomyophages (hli03, hsp20, mazG, phoH and psbA; cobS is present in Region 3). Much of Regions 1 and 2 are syntenic with marine cyanomyophage genomes, except that a segment encompassing Region 2 is inverted. Region 3 contains a high proportion (85%) of genes that are unique to S-CRM01, as well as most of the tRNA genes. Regions 1 and 2 contain many predicted late promoters, with a combination of CTAAATA and ATAAATA core sequences. Two predicted genes that are unusual in phage genomes are homologues of cellular spoT and nusG.
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Affiliation(s)
- Theo W Dreher
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331, USA.
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Xiao M, Xu P, Zhao J, Wang Z, Zuo F, Zhang J, Ren F, Li P, Chen S, Ma H. Oxidative stress-related responses of Bifidobacterium longum subsp. longum BBMN68 at the proteomic level after exposure to oxygen. Microbiology (Reading) 2011; 157:1573-1588. [DOI: 10.1099/mic.0.044297-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Bifidobacterium longum subsp. longum BBMN68, an anaerobic probiotic isolated from healthy centenarian faeces, shows low oxygen (3 %, v/v) tolerance. To understand the effects of oxidative stress and the mechanisms protecting against it in this strain, a proteomic approach was taken to analyse changes in the cellular protein profiles of BBMN68 under the following oxygen-stress conditions. Mid-exponential phase BBMN68 cells grown in MRS broth at 37 °C were exposed to 3 % O2 for 1 h (I) or 9 h (II), and stationary phase cells were subjected to 3 % O2 for 1 h (III). Respective controls were grown under identical conditions but were not exposed to O2. A total of 51 spots with significant changes after exposure to oxygen were identified, including the oxidative stress-protective proteins alkyl hydroperoxide reductase C22 (AhpC) and pyridine nucleotide-disulfide reductase (PNDR), and the DNA oxidative damage-protective proteins DNA-binding ferritin-like protein (Dps), ribonucleotide reductase (NrdA) and nucleotide triphosphate (NTP) pyrophosphohydrolases (MutT1). Changes in polynucleotide phosphorylase (PNPase) plus enolase, which may play important roles in scavenging oxidatively damaged RNA, were also found. Following validation at the transcriptional level of differentially expressed proteins, the physiological and biochemical functions of BBMN68 Dps were further proven by in vitro and in vivo tests under oxidative stress. Our results reveal the key oxidative stress-protective proteins and DNA oxidative damage-protective proteins involved in the defence strategy of BBMN68 against oxygen, and provide the first proteomic information toward understanding the responses of Bifidobacterium and other anaerobes to oxygen stress.
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Affiliation(s)
- Man Xiao
- Key Laboratory of Functional Dairy Science of Chinese Ministry of Education and Municipal Government of Beijing, and Beijing Higher Institution Engineering Research Center of Animal Product, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, PR China
| | - Pan Xu
- Key Laboratory of Functional Dairy Science of Chinese Ministry of Education and Municipal Government of Beijing, and Beijing Higher Institution Engineering Research Center of Animal Product, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, PR China
| | - Jianyun Zhao
- Key Laboratory of Functional Dairy Science of Chinese Ministry of Education and Municipal Government of Beijing, and Beijing Higher Institution Engineering Research Center of Animal Product, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, PR China
| | - Zeng Wang
- College of Agriculture and Biotechnology, China Agricultural University, Beijing 100193, PR China
| | - Fanglei Zuo
- Key Laboratory of Functional Dairy Science of Chinese Ministry of Education and Municipal Government of Beijing, and Beijing Higher Institution Engineering Research Center of Animal Product, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, PR China
| | - Jiangwei Zhang
- Key Laboratory of Functional Dairy Science of Chinese Ministry of Education and Municipal Government of Beijing, and Beijing Higher Institution Engineering Research Center of Animal Product, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, PR China
| | - Fazheng Ren
- Key Laboratory of Functional Dairy Science of Chinese Ministry of Education and Municipal Government of Beijing, and Beijing Higher Institution Engineering Research Center of Animal Product, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, PR China
| | - Pinglan Li
- Key Laboratory of Functional Dairy Science of Chinese Ministry of Education and Municipal Government of Beijing, and Beijing Higher Institution Engineering Research Center of Animal Product, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, PR China
| | - Shangwu Chen
- Key Laboratory of Functional Dairy Science of Chinese Ministry of Education and Municipal Government of Beijing, and Beijing Higher Institution Engineering Research Center of Animal Product, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, PR China
| | - Huiqin Ma
- College of Agriculture and Biotechnology, China Agricultural University, Beijing 100193, PR China
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