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Si D, Sun J, Guo L, Yang F, Li J, He S. Mycoplasma synoviae lipid-associated membrane proteins identification and expression changes when exposed to chicken cells. Front Vet Sci 2023; 10:1249499. [PMID: 38026678 PMCID: PMC10652285 DOI: 10.3389/fvets.2023.1249499] [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: 06/28/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
Mycoplasma synoviae is a significant cause of respiratory disease and synovitis among chickens, and has an adverse economic impact on broiler breeding efforts. The present study was designed to develop a systematic understanding of the role that M. synoviae lipid-associated membrane proteins (LAMPs) may play in the virulence of this pathogen. Bioinformatics tools were used to identify 146 predicted membrane proteins and lipoproteins in the M. synoviae proteome. Then, Triton X-114 was used to extract LAMPs that were subsequently identified via LC-MS/MS. This approach enabled the detection of potential LAMPs, and the top 200 most abundant proteins detected using this strategy were subject to further analysis. M. synoviae cells (100 MOI) were exposed to chicken fibroblasts (DF-1) and macrophages (HD-11) in a 1:1 mixed culture. Analysis of LAMP transcripts identified 72 up-regulated LAMP genes which were analyzed in depth by bioinformatics. GO analysis revealed these genes to be enriched in the nucleotide binding, sulfur amino acid transmembrane transporter activity, tRNA binding, rRNA modification, and transition metal ion transport pathways. Moreover, KEGG enrichment analysis suggested that these genes were enriched in the biosynthesis of secondary metabolites, carbon metabolism, glycolysis/gluconeogenesis, and nitrogen metabolism pathways.
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Affiliation(s)
- Duoduo Si
- College of Animal Science and Technology, Clinical Veterinary Laboratory, Ningxia University, Yinchuan, China
| | - Jialin Sun
- College of Animal Science and Technology, Clinical Veterinary Laboratory, Ningxia University, Yinchuan, China
| | - Lei Guo
- Ningxia Xiaoming Agriculture and Animal Husbandry Co., Ltd., Yinchuan, China
| | - Fei Yang
- College of Animal Science and Technology, Clinical Veterinary Laboratory, Ningxia University, Yinchuan, China
| | - Jidong Li
- College of Animal Science and Technology, Clinical Veterinary Laboratory, Ningxia University, Yinchuan, China
| | - Shenghu He
- College of Animal Science and Technology, Clinical Veterinary Laboratory, Ningxia University, Yinchuan, China
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2
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Yueyue W, Feichen X, Yixuan X, Lu L, Yiwen C, Xiaoxing Y. Pathogenicity and virulence of Mycoplasma genitalium: Unraveling Ariadne's Thread. Virulence 2022; 13:1161-1183. [PMID: 35791283 PMCID: PMC9262362 DOI: 10.1080/21505594.2022.2095741] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Mycoplasma genitalium, a pathogen from class Mollicutes, has been linked to sexually transmitted diseases and sparked widespread concern. To adapt to its environment, M. genitalium has evolved specific adhesins and motility mechanisms that allow it to adhere to and invade various eukaryotic cells, thereby causing severe damage to the cells. Even though traditional exotoxins have not been identified, secreted nucleases or membrane lipoproteins have been shown to cause cell death and inflammatory injury in M. genitalium infection. However, as both innate and adaptive immune responses are important for controlling infection, the immune responses that develop upon infection do not necessarily eliminate the organism completely. Antigenic variation, detoxifying enzymes, immunoglobulins, neutrophil extracellular trap-degrading enzymes, cell invasion, and biofilm formation are important factors that help the pathogen overcome the host defence and cause chronic infections in susceptible individuals. Furthermore, M. genitalium can increase the susceptibility to several sexually transmitted pathogens, which significantly complicates the persistence and chronicity of M. genitalium infection. This review aimed to discuss the virulence factors of M. genitalium to shed light on its complex pathogenicity and pathogenesis of the infection.
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Affiliation(s)
- Wu Yueyue
- Institute of Pathogenic Biology, Hengyang Medical School; Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control; Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, China
| | - Xiu Feichen
- Institute of Pathogenic Biology, Hengyang Medical School; Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control; Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, China
| | - Xi Yixuan
- Institute of Pathogenic Biology, Hengyang Medical School; Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control; Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, China
| | - Liu Lu
- Institute of Pathogenic Biology, Hengyang Medical School; Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control; Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, China
| | - Chen Yiwen
- Institute of Pathogenic Biology, Hengyang Medical School; Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control; Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, China
| | - You Xiaoxing
- Institute of Pathogenic Biology, Hengyang Medical School; Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control; Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, China
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3
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Rodríguez-Vázquez R, Mouzo D, Zapata C. Phosphoproteome Analysis Using Two-Dimensional Electrophoresis Coupled with Chemical Dephosphorylation. Foods 2022; 11:3119. [PMID: 36230195 PMCID: PMC9562008 DOI: 10.3390/foods11193119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 09/26/2022] [Accepted: 10/04/2022] [Indexed: 11/22/2022] Open
Abstract
Protein phosphorylation is a reversible post-translational modification (PTM) with major regulatory roles in many cellular processes. However, the analysis of phosphoproteins remains the most challenging barrier in the prevailing proteome research. Recent technological advances in two-dimensional electrophoresis (2-DE) coupled to mass spectrometry (MS) have enabled the identification, characterization, and quantification of protein phosphorylation on a global scale. Most research on phosphoproteins with 2-DE has been conducted using phosphostains. Nevertheless, low-abundant and low-phosphorylated phosphoproteins are not necessarily detected using phosphostains and/or MS. In this study, we report a comparative analysis of 2-DE phosphoproteome profiles using Pro-Q Diamond phosphoprotein stain (Pro-Q DPS) and chemical dephosphorylation of proteins with HF-P from longissimus thoracis (LT) muscle samples of the Rubia Gallega cattle breed. We found statistically significant differences in the number of identified phosphoproteins between methods. More specifically, we found a three-fold increase in phosphoprotein detection with the HF-P method. Unlike Pro-Q DPS, phosphoprotein spots with low volume and phosphorylation rate were identified by HF-P technique. This is the first approach to assess meat phosphoproteome maps using HF-P at a global scale. The results open a new window for 2-DE gel-based phosphoproteome analysis.
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Affiliation(s)
- Raquel Rodríguez-Vázquez
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15872 Santiago de Compostela, Spain
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4
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Robertsson C, Svensäter G, Blum Z, Wickström C. Intracellular Ser/Thr/Tyr phosphoproteome of the oral commensal Streptococcus gordonii DL1. BMC Microbiol 2020; 20:280. [PMID: 32928109 PMCID: PMC7488673 DOI: 10.1186/s12866-020-01944-y] [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: 06/26/2020] [Accepted: 08/11/2020] [Indexed: 12/28/2022] Open
Abstract
Background To respond and adapt to environmental challenges, prokaryotes regulate cellular processes rapidly and reversibly through protein phosphorylation and dephosphorylation. This study investigates the intracellular proteome and Ser/Thr/Tyr phosphoproteome of the oral commensal Streptococcus gordonii. Intracellular proteins from planktonic cells of S. gordonii DL1 were extracted and subjected to 2D-gel electrophoresis. Proteins in general were visualized using Coomassie Brilliant Blue and T-Rex staining. Phosphorylated proteins were visualized with Pro-Q Diamond Phosphoprotein Gel Stain. Proteins were identified by LC-MS/MS and sequence analysis. Results In total, sixty-one intracellular proteins were identified in S. gordonii DL1, many of which occurred at multiple isoelectric points. Nineteen of these proteins were present as one or more Ser/Thr/Tyr phosphorylated form. The identified phosphoproteins turned out to be involved in a variety of cellular processes. Conclusion Nineteen phosphoproteins involved in various cellular functions were identified in S. gordonii. This is the first time the global intracellular Ser/Thr/Tyr phosphorylation profile has been analysed in an oral streptococcus. Comparison with phosphoproteomes of other species from previous studies showed many similarities. Proteins that are consistently found in a phosphorylated state across several species and growth conditions may represent a core phosphoproteome profile shared by many bacteria.
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Affiliation(s)
- Carolina Robertsson
- Department of Oral Biology and Pathology, Faculty of Odontology, Malmö University, 20506, Malmö, Sweden.
| | - Gunnel Svensäter
- Department of Oral Biology and Pathology, Faculty of Odontology, Malmö University, 20506, Malmö, Sweden
| | - Zoltan Blum
- Department of Biomedical Science, Malmö University, 20506, Malmö, Sweden
| | - Claes Wickström
- Department of Oral Biology and Pathology, Faculty of Odontology, Malmö University, 20506, Malmö, Sweden
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5
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Thingholm TE, Rönnstrand L, Rosenberg PA. Why and how to investigate the role of protein phosphorylation in ZIP and ZnT zinc transporter activity and regulation. Cell Mol Life Sci 2020; 77:3085-3102. [PMID: 32076742 PMCID: PMC7391401 DOI: 10.1007/s00018-020-03473-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 01/13/2020] [Accepted: 01/28/2020] [Indexed: 12/20/2022]
Abstract
Zinc is required for the regulation of proliferation, metabolism, and cell signaling. It is an intracellular second messenger, and the cellular level of ionic, mobile zinc is strictly controlled by zinc transporters. In mammals, zinc homeostasis is primarily regulated by ZIP and ZnT zinc transporters. The importance of these transporters is underscored by the list of diseases resulting from changes in transporter expression and activity. However, despite numerous structural studies of the transporters revealing both zinc binding sites and motifs important for transporter function, the exact molecular mechanisms regulating ZIP and ZnT activities are still not clear. For example, protein phosphorylation was found to regulate ZIP7 activity resulting in the release of Zn2+ from intracellular stores leading to phosphorylation of tyrosine kinases and activation of signaling pathways. In addition, sequence analyses predict all 24 human zinc transporters to be phosphorylated suggesting that protein phosphorylation is important for regulation of transporter function. This review describes how zinc transporters are implicated in a number of important human diseases. It summarizes the current knowledge regarding ZIP and ZnT transporter structures and points to how protein phosphorylation seems to be important for the regulation of zinc transporter activity. The review addresses the need to investigate the role of protein phosphorylation in zinc transporter function and regulation, and argues for a pressing need to introduce quantitative phosphoproteomics to specifically target zinc transporters and proteins involved in zinc signaling. Finally, different quantitative phosphoproteomic strategies are suggested.
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Affiliation(s)
- T E Thingholm
- Department of Molecular Medicine, Cancer and Inflammation Research, University of Southern Denmark, J.B. Winsløws Vej 25, 3, 5000, Odense C, Denmark.
| | - L Rönnstrand
- Division of Translational Cancer Research, Lund University, Medicon Village, Building 404, Scheelevägen 2, Lund, Sweden
- Lund Stem Cell Center, Lund University, Medicon Village, Building 404, Scheelevägen 2, Lund, Sweden
- Division of Oncology, Skåne University Hospital, Lund, Sweden
| | - P A Rosenberg
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children's Hospital, 300 Longwood Ave, Boston, MA, 02115, USA
- Department of Neurology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
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6
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Harvey KL, Jarocki VM, Charles IG, Djordjevic SP. The Diverse Functional Roles of Elongation Factor Tu (EF-Tu) in Microbial Pathogenesis. Front Microbiol 2019; 10:2351. [PMID: 31708880 PMCID: PMC6822514 DOI: 10.3389/fmicb.2019.02351] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/27/2019] [Indexed: 12/25/2022] Open
Abstract
Elongation factor thermal unstable Tu (EF-Tu) is a G protein that catalyzes the binding of aminoacyl-tRNA to the A-site of the ribosome inside living cells. Structural and biochemical studies have described the complex interactions needed to effect canonical function. However, EF-Tu has evolved the capacity to execute diverse functions on the extracellular surface of both eukaryote and prokaryote cells. EF-Tu can traffic to, and is retained on, cell surfaces where can interact with membrane receptors and with extracellular matrix on the surface of plant and animal cells. Our structural studies indicate that short linear motifs (SLiMs) in surface exposed, non-conserved regions of the molecule may play a key role in the moonlighting functions ascribed to this ancient, highly abundant protein. Here we explore the diverse moonlighting functions relating to pathogenesis of EF-Tu in bacteria and examine putative SLiMs on surface-exposed regions of the molecule.
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Affiliation(s)
- Kate L Harvey
- The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Veronica M Jarocki
- The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Ian G Charles
- Quadram Institute, Norwich, United Kingdom.,Norwich Medical School, Norwich, United Kingdom
| | - Steven P Djordjevic
- The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
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7
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Lau BYC, Othman A, Ramli US. Application of Proteomics Technologies in Oil Palm Research. Protein J 2018; 37:473-499. [DOI: 10.1007/s10930-018-9802-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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8
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Diaz MH, Winchell JM. The Evolution of Advanced Molecular Diagnostics for the Detection and Characterization of Mycoplasma pneumoniae. Front Microbiol 2016; 7:232. [PMID: 27014191 PMCID: PMC4781879 DOI: 10.3389/fmicb.2016.00232] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 02/15/2016] [Indexed: 12/12/2022] Open
Abstract
Over the past decade there have been significant advancements in the methods used for detecting and characterizing Mycoplasma pneumoniae, a common cause of respiratory illness and community-acquired pneumonia worldwide. The repertoire of available molecular diagnostics has greatly expanded from nucleic acid amplification techniques (NAATs) that encompass a variety of chemistries used for detection, to more sophisticated characterizing methods such as multi-locus variable-number tandem-repeat analysis (MLVA), Multi-locus sequence typing (MLST), matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), single nucleotide polymorphism typing, and numerous macrolide susceptibility profiling methods, among others. These many molecular-based approaches have been developed and employed to continually increase the level of discrimination and characterization in order to better understand the epidemiology and biology of M. pneumoniae. This review will summarize recent molecular techniques and procedures and lend perspective to how each has enhanced the current understanding of this organism and will emphasize how Next Generation Sequencing may serve as a resource for researchers to gain a more comprehensive understanding of the genomic complexities of this insidious pathogen.
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Affiliation(s)
| | - Jonas M. Winchell
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, AtlantaGA, USA
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9
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Posttranslational Modifications. Atherosclerosis 2015. [DOI: 10.1002/9781118828533.ch34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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10
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Vishnyakov IE, Borchsenius SN. Mycoplasma heat shock proteins and their genes. Microbiology (Reading) 2014. [DOI: 10.1134/s002626171306012x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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11
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Kraskouskaya D, Bancerz M, Soor HS, Gardiner JE, Gunning PT. An Excimer-Based, Turn-On Fluorescent Sensor for the Selective Detection of Diphosphorylated Proteins in Aqueous Solution and Polyacrylamide Gels. J Am Chem Soc 2014; 136:1234-7. [DOI: 10.1021/ja411492k] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Dziyana Kraskouskaya
- Department of Chemistry and
Department of Chemical and Physical Sciences, University of Toronto, Mississauga, 3359 Mississauga Road North, Mississauga, Ontario, Canada L5L1C6
| | - Matthew Bancerz
- Department of Chemistry and
Department of Chemical and Physical Sciences, University of Toronto, Mississauga, 3359 Mississauga Road North, Mississauga, Ontario, Canada L5L1C6
| | - Harjeet S. Soor
- Department of Chemistry and
Department of Chemical and Physical Sciences, University of Toronto, Mississauga, 3359 Mississauga Road North, Mississauga, Ontario, Canada L5L1C6
| | - Jordan E. Gardiner
- Department of Chemistry and
Department of Chemical and Physical Sciences, University of Toronto, Mississauga, 3359 Mississauga Road North, Mississauga, Ontario, Canada L5L1C6
| | - Patrick T. Gunning
- Department of Chemistry and
Department of Chemical and Physical Sciences, University of Toronto, Mississauga, 3359 Mississauga Road North, Mississauga, Ontario, Canada L5L1C6
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12
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Raymond BBA, Tacchi JL, Jarocki VM, Minion FC, Padula MP, Djordjevic SP. P159 from Mycoplasma hyopneumoniae Binds Porcine Cilia and Heparin and Is Cleaved in a Manner Akin to Ectodomain Shedding. J Proteome Res 2013; 12:5891-903. [DOI: 10.1021/pr400903s] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Benjamin B. A. Raymond
- The
ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Jessica L. Tacchi
- The
ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Veronica M. Jarocki
- The
ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - F. Chris Minion
- Department
of Preventive and Veterinary Medicine, Iowa State University, 2180
Veterinary Medicine, Ames, Iowa 50011, United States
| | - Matthew P. Padula
- The
ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Steven P. Djordjevic
- The
ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
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13
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Rakhmatullina MR, Kirichenko SV. Current concepts of genetic variability of genital mycoplasmas and their role in the development of inflammatory diseases of the urogenital system. VESTNIK DERMATOLOGII I VENEROLOGII 2013. [DOI: 10.25208/vdv583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
The authors disclose current concepts of the taxonomic and morphologic characteristics of genital mycoplasmas and their role in the development of inflammatory urogenital diseases and reproductive disorders. They also discuss such issues as genetic variability of genital mycoplasmas and possible interrelation with different variants of the clinical course of inflammatory processes in the urogenital tract.
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14
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Martinez MA, Das K, Saikolappan S, Materon LA, Dhandayuthapani S. A serine/threonine phosphatase encoded by MG_207 of Mycoplasma genitalium is critical for its virulence. BMC Microbiol 2013; 13:44. [PMID: 23432936 PMCID: PMC3639085 DOI: 10.1186/1471-2180-13-44] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 02/19/2013] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Bacterial signal transduction systems like two component system (TCS) and Serine/Threonine kinase (STK) and Serine/Threonine phosphatase (STP) play important roles in the virulence and pathogenesis of bacterial pathogens. Mycoplasma genitalium, a mollicute that causes the urogenital diseases urethritis and cervicitis in men and women, respectively, is a pathogen which lacks TCS but possesses STK/STP. In this study, we investigated the biochemical and virulence properties of an STP protein encoded by the gene MG_207 of this species. RESULTS We overexpressed MG207 in Escherichia coli overexpression system as a recombinant His10MG207 protein and purified it with affinity chromatography. This recombinant protein readily hydrolyzed the substrate p-nitrophenyl phosphate (pNPP) in a dose-dependent manner. Additional studies using synthetic peptides as substrates revealed that the recombinant protein was able to hydrolyze the threonine phosphate. Further, a transposon insertion mutant strain of M. genitalium (TIM207) that lacks the protein MG207 showed differentially phosphorylated proteins when compared to the wild type G37 strain. Mass spectrometry revealed that some of the key proteins differentially phosphorylated in TIM207 strain were putative cytoskeletal protein encoded by the gene MG_328 and pyruvate dehydrogenase E1 α chain encoded by the gene MG_274. In addition, TIM207 was noticed to be less cytotoxic to HeLa cells and this correlated with the production of less hydrogen peroxide by this strain. This strain was also less efficient in inducing the differentiation of THP-1 cell line as compared to wild type M. genitalium. CONCLUSIONS The results of the study suggest that MG207 is an important signaling protein of M. genitalium and its presence may be crucial for the virulence of this species.
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Affiliation(s)
- Mario A Martinez
- Regional Academic Health Center and Department of Microbiology and Immunology, University of Texas Health Science Center at San Antonio, Edinburg, TX 78541, USA
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15
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Borràs E, Espadas G, Mancuso FM, Maier T, Chiva C, Sabidó E. Integrative quantitation enables a comprehensive proteome comparison of two Mycoplasma pneumoniae genetic perturbations. MOLECULAR BIOSYSTEMS 2013; 9:1249-56. [DOI: 10.1039/c3mb25581f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Guo G, Lv D, Yan X, Subburaj S, Ge P, Li X, Hu Y, Yan Y. Proteome characterization of developing grains in bread wheat cultivars (Triticum aestivum L.). BMC PLANT BIOLOGY 2012. [PMID: 22900893 DOI: 10.86/1471-2229-12-147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
BACKGROUND The analyses of protein synthesis, accumulation and regulation during grain development in wheat are more complex because of its larger genome size compared to model plants such as Arabidopsis and rice. In this study, grains from two wheat cultivars Jimai 20 and Zhoumai 16 with different gluten quality properties were harvested at five development stages, and were used to displayed variable expression patterns of grain proteins. RESULTS Proteome characterization during grain development in Chinese bread wheat cultivars Jimai 20 and Zhoumai 16 with different quality properties was investigated by 2-DE and tandem MALDI-TOF/TOF-MS. Identification of 117 differentially accumulated protein spots representing 82 unique proteins and five main expression patterns enabled a chronological description of wheat grain formation. Significant proteome expression differences between the two cultivars were found; these included 14 protein spots that accumulated in both cultivars but with different patterns and 27 cultivar-different spots. Among the cultivar-different protein spots, 14 accumulated in higher abundance in Jimai 20 than in Zhoumai 16, and included NAD-dependent isocitrate dehydrogenase, triticin precursor, LMW-s glutenin subunit and replication factor C-like protein. These proteins are likely to be associated with superior gluten quality. In addition, some proteins such as class II chitinase and peroxidase 1 with isoforms in developing grains were shown to be phosphorylated by Pro-Q Diamond staining and phosphorprotein site prediction. Phosphorylation could have important roles in wheat grain development. qRT-PCR analysis demonstrated that transcriptional and translational expression patterns of many genes were significantly different. CONCLUSIONS Wheat grain proteins displayed variable expression patterns at different developmental stages and a considerable number of protein spots showed differential accumulation between two cultivars. Differences in seed storage proteins were considered to be related to different quality performance of the flour from these wheat cultivars. Some proteins with isoforms were phosphorylated, and this may reflect their importance in grain development. Our results provide new insights into proteome characterization during grain development in different wheat genotypes.
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Affiliation(s)
- Guangfang Guo
- College of Life Science, Capital Normal University, Beijing 100048, China
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17
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Guo G, Lv D, Yan X, Subburaj S, Ge P, Li X, Hu Y, Yan Y. Proteome characterization of developing grains in bread wheat cultivars (Triticum aestivum L.). BMC PLANT BIOLOGY 2012; 12:147. [PMID: 22900893 PMCID: PMC3480910 DOI: 10.1186/1471-2229-12-147] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 08/16/2012] [Indexed: 05/20/2023]
Abstract
BACKGROUND The analyses of protein synthesis, accumulation and regulation during grain development in wheat are more complex because of its larger genome size compared to model plants such as Arabidopsis and rice. In this study, grains from two wheat cultivars Jimai 20 and Zhoumai 16 with different gluten quality properties were harvested at five development stages, and were used to displayed variable expression patterns of grain proteins. RESULTS Proteome characterization during grain development in Chinese bread wheat cultivars Jimai 20 and Zhoumai 16 with different quality properties was investigated by 2-DE and tandem MALDI-TOF/TOF-MS. Identification of 117 differentially accumulated protein spots representing 82 unique proteins and five main expression patterns enabled a chronological description of wheat grain formation. Significant proteome expression differences between the two cultivars were found; these included 14 protein spots that accumulated in both cultivars but with different patterns and 27 cultivar-different spots. Among the cultivar-different protein spots, 14 accumulated in higher abundance in Jimai 20 than in Zhoumai 16, and included NAD-dependent isocitrate dehydrogenase, triticin precursor, LMW-s glutenin subunit and replication factor C-like protein. These proteins are likely to be associated with superior gluten quality. In addition, some proteins such as class II chitinase and peroxidase 1 with isoforms in developing grains were shown to be phosphorylated by Pro-Q Diamond staining and phosphorprotein site prediction. Phosphorylation could have important roles in wheat grain development. qRT-PCR analysis demonstrated that transcriptional and translational expression patterns of many genes were significantly different. CONCLUSIONS Wheat grain proteins displayed variable expression patterns at different developmental stages and a considerable number of protein spots showed differential accumulation between two cultivars. Differences in seed storage proteins were considered to be related to different quality performance of the flour from these wheat cultivars. Some proteins with isoforms were phosphorylated, and this may reflect their importance in grain development. Our results provide new insights into proteome characterization during grain development in different wheat genotypes.
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Affiliation(s)
- Guangfang Guo
- College of Life Science, Capital Normal University, Beijing 100048, China
| | - Dongwen Lv
- College of Life Science, Capital Normal University, Beijing 100048, China
| | - Xing Yan
- College of Life Science, Capital Normal University, Beijing 100048, China
| | | | - Pei Ge
- College of Life Science, Capital Normal University, Beijing 100048, China
| | - Xiaohui Li
- College of Life Science, Capital Normal University, Beijing 100048, China
| | - Yingkao Hu
- College of Life Science, Capital Normal University, Beijing 100048, China
| | - Yueming Yan
- College of Life Science, Capital Normal University, Beijing 100048, China
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18
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Párraga-Niño N, Colomé-Calls N, Canals F, Querol E, Ferrer-Navarro M. A comprehensive proteome of Mycoplasma genitalium. J Proteome Res 2012; 11:3305-16. [PMID: 22582988 DOI: 10.1021/pr300084c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mycoplasma genitalium is a human pathogen associated with several sexually transmitted diseases. Proteomic technologies, along with other methods for global gene expression analysis, play a key role in understanding the mechanisms of bacterial pathogenesis and physiology. The proteome of M. genitalium, model of a minimal cell, has been extended using a combination of different proteomic approaches and technologies. The total proteome of this microorganism has been analyzed using gel-based and gel-free approaches, achieving the identification of 85.3% of the predicted ORFs. In addition, a comprehensive analysis of membrane subproteome has been performed. For this purpose, the TX-114 soluble fraction has been analyzed as well as the surface proteins, using cell-surface protein labeling with CyDye. Finally, the serological response of M. genitalium-infected patients and healthy donors has been analyzed to identify proteins that trigger immunological response. Here, we present the most extensive M. genitalium proteome analysis (85.3% of predicted ORFs), a comprehensive M. genitalium membrane analysis, and a study of the human serological response to M. genitalium.
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Affiliation(s)
- Noemí Párraga-Niño
- Institut de Biotecnologia i de Biomedicina (IBB) and Dpt Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona (UAB), E-08193 Cerdanyola del Vallès (Barcelona), Spain
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Tichy A, Salovska B, Rehulka P, Klimentova J, Vavrova J, Stulik J, Hernychova L. Phosphoproteomics: Searching for a needle in a haystack. J Proteomics 2011; 74:2786-97. [DOI: 10.1016/j.jprot.2011.07.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 07/13/2011] [Accepted: 07/22/2011] [Indexed: 11/27/2022]
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The proteome of Mycoplasma pneumoniae
, a supposedly “simple” cell. Proteomics 2011; 11:3614-32. [DOI: 10.1002/pmic.201100076] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 05/09/2011] [Accepted: 06/15/2011] [Indexed: 11/07/2022]
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Abstract
We present the complete genome sequence and proteogenomic map for Acholeplasma laidlawii PG-8A (class Mollicutes, order Acholeplasmatales, family Acholeplasmataceae). The genome of A. laidlawii is represented by a single 1,496,992-bp circular chromosome with an average G+C content of 31 mol%. This is the longest genome among the Mollicutes with a known nucleotide sequence. It contains genes of polymerase type I, SOS response, and signal transduction systems, as well as RNA regulatory elements, riboswitches, and T boxes. This demonstrates a significant capability for the regulation of gene expression and mutagenic response to stress. Acholeplasma laidlawii and phytoplasmas are the only Mollicutes known to use the universal genetic code, in which UGA is a stop codon. Within the Mollicutes group, only the sterol-nonrequiring Acholeplasma has the capacity to synthesize saturated fatty acids de novo. Proteomic data were used in the primary annotation of the genome, validating expression of many predicted proteins. We also detected posttranslational modifications of A. laidlawii proteins: phosphorylation and acylation. Seventy-four candidate phosphorylated proteins were found: 16 candidates are proteins unique to A. laidlawii, and 11 of them are surface-anchored or integral membrane proteins, which implies the presence of active signaling pathways. Among 20 acylated proteins, 14 contained palmitic chains, and six contained stearic chains. No residue of linoleic or oleic acid was observed. Acylated proteins were components of mainly sugar and inorganic ion transport systems and were surface-anchored proteins with unknown functions.
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Quantification of mRNA and protein and integration with protein turnover in a bacterium. Mol Syst Biol 2011; 7:511. [PMID: 21772259 PMCID: PMC3159969 DOI: 10.1038/msb.2011.38] [Citation(s) in RCA: 218] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 05/20/2011] [Indexed: 12/12/2022] Open
Abstract
Determination of the average cellular copy number of 400 proteins under different growth conditions and integration with protein turnover and absolute mRNA levels reveals the dynamics of protein expression in the genome-reduced bacterium Mycoplasma pneumoniae. Our study provides a fine-grained, quantitative picture to unprecedented detail in an established model organism for systems-wide studies. Our integrative approach reveals a novel, dynamic view on the processes, interactions and regulations underlying the central dogma pathway and the composition of protein complexes. Simulations using our quantitative data on mRNA, protein and turnover show how an organism copes with stochastic noise in gene expression in vivo. Our data serve as an important resource for colleagues both within our field of research and in related disciplines.
A hallmark of Systems Biology is the integration of diverse, large quantitative data sets with the aim to gain novel insights into how biological processes work. We measured individual mRNA and protein abundances as well as protein turnover in the bacterium Mycoplasma pneumoniae. This human pathogen is an ideal model organism for organism-wide studies. It can be readily cultured under laboratory conditions and it has a very small genome with only 690 protein-coding genes. This comparably low complexity allows for the exhaustive analysis of major cellular biomolecules avoiding constrains introduced by limitations of available analysis techniques. Using a recently developed mass spectrometry-based approach, we determined the average cellular copy number for over 400 individual proteins under different growth and stress conditions. The 20 most abundant proteins, including Elongation factor Tu, cellular chaperones, and proteins involved in metabolizing glucose, the major energy source of M. pneumoniae account for nearly 44% of the total cellular protein mass. We observed abundance changes of many expected and several unexpected proteins in response to cellular stress, such as heat shock, DNA damage and osmotic stress, as well as along batch culture growth over 4 days. Integration of the protein abundance data with quantitative mRNA measurements revealed a modest correlation between these two classes of biomolecules. However, for several classical stress-induced proteins, we observed a correlated induction of mRNA and protein in response to heat shock. A focused analysis of mRNA–protein abundance dynamics during batch culture growth suggested that the regulation of gene expression is largely decoupled from protein dynamics in M. pneumoniae, indicating extensive post-transcriptional and post-translational regulation influencing the cellular mRNA–protein ratios. To investigate the factors influencing the cellular protein abundance, we measured individual protein turnover rates by mass spectrometry using a label-chase approach involving stable isotope-labelled amino acids. The average half-life of a protein in M. pneumoniae is 23 h. Based on the measured quantitative mRNA data, the protein abundances and their half-lives, we established an ordinary differential equations model for the estimation of individual in vivo protein degradation and translation efficiency rates. We found out that translation efficiency rather than protein turnover is the dominating factor influencing protein abundance. Using our abundance and turnover data, we additionally performed stochastic simulations of gene expression. We observed that long protein half-life and low translational efficiency buffers gene expression noise propagating from low cellular mRNA levels in vivo. We compared the abundance ratios of proteins associating into complexes in vivo with their expected functional stoichiometries. We observed that for stable protein complexes, such as the GroEL/ES chaperonin or DNA gyrase, our measured abundance ratios reflected the expected subunit stoichiometries. More dynamic protein complexes, such as the DnaK/J/GrpE chaperone system or RNA polymerase, showed several unusual subunit ratios, pointing towards transient interaction of sub-stoichiometric subunits for function. A detailed, quantitative analysis of the ribosome, the largest cellular protein complex, revealed large abundance differences of the 51 subunits. This observation indicates a multi-functionality for several, abundant ribosomal proteins. Finally, a comparison of the determined average cellular protein abundances with a different pathogenic bacterium, Leptospira interrogans, revealed that cellular protein abundances closely reflect their respective lifestyles. Our study represents an organism-wide, quantitative analysis of cellular protein abundances. Integrating our proteomics data with determined mRNA levels and protein turnover rates reveals insights into the dynamic interplay and regulation of mRNA and proteins, the central biomolecules of a cell. Biological function and cellular responses to environmental perturbations are regulated by a complex interplay of DNA, RNA, proteins and metabolites inside cells. To understand these central processes in living systems at the molecular level, we integrated experimentally determined abundance data for mRNA, proteins, as well as individual protein half-lives from the genome-reduced bacterium Mycoplasma pneumoniae. We provide a fine-grained, quantitative analysis of basic intracellular processes under various external conditions. Proteome composition changes in response to cellular perturbations reveal specific stress response strategies. The regulation of gene expression is largely decoupled from protein dynamics and translation efficiency has a higher regulatory impact on protein abundance than protein turnover. Stochastic simulations using in vivo data show how low translation efficiency and long protein half-lives effectively reduce biological noise in gene expression. Protein abundances are regulated in functional units, such as complexes or pathways, and reflect cellular lifestyles. Our study provides a detailed integrative analysis of average cellular protein abundances and the dynamic interplay of mRNA and proteins, the central biomolecules of a cell.
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Bernardini G, Laschi M, Serchi T, Arena S, D'Ambrosio C, Braconi D, Scaloni A, Santucci A. Mapping phosphoproteins in Neisseria meningitidis serogroup A. Proteomics 2011; 11:1351-8. [PMID: 21365747 DOI: 10.1002/pmic.201000406] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 11/08/2010] [Accepted: 12/29/2010] [Indexed: 11/10/2022]
Abstract
To investigate the phosphorylation capability of serogroup A Neisseria meningitidis (MenA) and to implement our knowledge in meningococcal biology and in bacterial post-translational modifications, cell extracts were separated by 2-DE and 51 novel phosphoproteins were revealed by the use of the highly specific Ser/Thr/Tyr-phosphorylated proteins staining by Pro-Q Diamond and identified by MALDI-ToF/MS. Our results indicate that phosphorylation in MenA is comparable to that of other bacterial species. A first functional characterization of the identified modified proteins was also given, in order to understand their role in meningococcal physiopathology.
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Affiliation(s)
- Giulia Bernardini
- Dipartimento di Biologia Molecolare, Università degli Studi di Siena, via Fiorentina, Siena, Italy
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The interplay of the EIIA(Ntr) component of the nitrogen-related phosphotransferase system (PTS(Ntr)) of Pseudomonas putida with pyruvate dehydrogenase. Biochim Biophys Acta Gen Subj 2011; 1810:995-1005. [PMID: 21236318 DOI: 10.1016/j.bbagen.2011.01.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Revised: 01/05/2011] [Accepted: 01/06/2011] [Indexed: 11/20/2022]
Abstract
BACKGROUND Pseudomonas putida KT2440 is endowed with a variant of the phosphoenolpyruvate-carbohydrate phosphotransferase system (PTS(Ntr)), which is not related to sugar transport but believed to rule the metabolic balance of carbon vs. nitrogen. The metabolic targets of such a system are largely unknown. METHODS Dielectric breakdown of P. putida cells grown in rich medium revealed the presence of forms of the EIIA(Ntr) (PtsN) component of PTS(Ntr), which were strongly associated to other cytoplasmic proteins. To investigate such intracellular partners of EIIA(Ntr), a soluble protein extract of bacteria bearing an E epitope tagged version of PtsN was immunoprecipitated with a monoclonal anti-E antibody and the pulled-down proteins identified by mass spectrometry. RESULTS The E1 subunit of the pyruvate dehydrogenase (PDH) complex, the product of the aceE gene, was identified as a major interaction partner of EIIA(Ntr). To examine the effect of EIIA(Ntr) on PDH, the enzyme activity was measured in extracts of isogenic ptsN(+)/ptsN(-)P. putida strains and the role of phosphorylation was determined. Expression of PtsN and AceE proteins fused to different fluorescent moieties and confocal laser microscopy indicated a significant co-localization of the two proteins in the bacterial cytoplasm. CONCLUSION EIIA(Ntr) down-regulates PDH activity. Both genetic and biochemical evidence revealed that the non-phosphorylated form of PtsN is the protein species that inhibits PDH. GENERAL SIGNIFICANCE EIIA(Ntr) takes part in the node of C metabolism that checks the flux of carbon from carbohydrates into the Krebs cycle by means of direct protein-protein interactions with AceE. This type of control might connect metabolism to many other cellular functions. This article is part of a Special Issue entitled: Systems Biology of Microorganisms.
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Su HC, Ramkissoon K, Doolittle J, Clark M, Khatun J, Secrest A, Wolfgang MC, Giddings MC. The development of ciprofloxacin resistance in Pseudomonas aeruginosa involves multiple response stages and multiple proteins. Antimicrob Agents Chemother 2010; 54:4626-35. [PMID: 20696867 PMCID: PMC2976116 DOI: 10.1128/aac.00762-10] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Revised: 07/14/2010] [Accepted: 07/30/2010] [Indexed: 01/17/2023] Open
Abstract
Microbes have developed resistance to nearly every antibiotic, yet the steps leading to drug resistance remain unclear. Here we report a multistage process by which Pseudomonas aeruginosa acquires drug resistance following exposure to ciprofloxacin at levels ranging from 0.5× to 8× the initial MIC. In stage I, susceptible cells are killed en masse by the exposure. In stage II, a small, slow to nongrowing population survives antibiotic exposure that does not exhibit significantly increased resistance according to the MIC measure. In stage III, exhibited at 0.5× to 4× the MIC, a growing population emerges to reconstitute the population, and these cells display heritable increases in drug resistance of up to 50 times the original level. We studied the stage III cells by proteomic methods to uncover differences in the regulatory pathways that are involved in this phenotype, revealing upregulation of phosphorylation on two proteins, succinate-semialdehyde dehydrogenase (SSADH) and methylmalonate-semialdehyde dehydrogenase (MMSADH), and also revealing upregulation of a highly conserved protein of unknown function. Transposon disruption in the encoding genes for each of these targets substantially dampened the ability of cells to develop the stage III phenotype. Considering these results in combination with computational models of resistance and genomic sequencing results, we postulate that stage III heritable resistance develops from a combination of both genomic mutations and modulation of one or more preexisting cellular pathways.
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Affiliation(s)
- Hsun-Cheng Su
- Department of Microbiology and Immunology, Curriculum in Bioinformatics and Computational Biology, Cystic Fibrosis/Pulmonary Research and Treatment Center, Department of Biomedical Engineering, Department of Computer Science, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Kevin Ramkissoon
- Department of Microbiology and Immunology, Curriculum in Bioinformatics and Computational Biology, Cystic Fibrosis/Pulmonary Research and Treatment Center, Department of Biomedical Engineering, Department of Computer Science, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Janet Doolittle
- Department of Microbiology and Immunology, Curriculum in Bioinformatics and Computational Biology, Cystic Fibrosis/Pulmonary Research and Treatment Center, Department of Biomedical Engineering, Department of Computer Science, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Martha Clark
- Department of Microbiology and Immunology, Curriculum in Bioinformatics and Computational Biology, Cystic Fibrosis/Pulmonary Research and Treatment Center, Department of Biomedical Engineering, Department of Computer Science, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Jainab Khatun
- Department of Microbiology and Immunology, Curriculum in Bioinformatics and Computational Biology, Cystic Fibrosis/Pulmonary Research and Treatment Center, Department of Biomedical Engineering, Department of Computer Science, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Ashley Secrest
- Department of Microbiology and Immunology, Curriculum in Bioinformatics and Computational Biology, Cystic Fibrosis/Pulmonary Research and Treatment Center, Department of Biomedical Engineering, Department of Computer Science, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Matthew C. Wolfgang
- Department of Microbiology and Immunology, Curriculum in Bioinformatics and Computational Biology, Cystic Fibrosis/Pulmonary Research and Treatment Center, Department of Biomedical Engineering, Department of Computer Science, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Morgan C. Giddings
- Department of Microbiology and Immunology, Curriculum in Bioinformatics and Computational Biology, Cystic Fibrosis/Pulmonary Research and Treatment Center, Department of Biomedical Engineering, Department of Computer Science, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
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Abstract
GroEL is a chaperone thought of as essential for bacterial life. However, some species of Mollicutes are missing GroEL. We use phylogenetic analysis to show that the presence of GroEL is polyphyletic among the Mollicutes, and that there is evidence for lateral gene transfer of GroEL to Mycoplasma penetrans from the Proteobacteria. Furthermore, we propose that the presence of GroEL in Mycoplasma may be required for invasion of host tissue, suggesting that GroEL may act as an adhesin-invasin.
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Affiliation(s)
- Gregory W Clark
- Ontario Cancer Institute, University Health Network and Department of Medical Biophysics, University of Toronto, 5-354 MaRS TMDT, 101 College St., Toronto, ON M5G 1L7, Canada
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First partial proteome of the poultry pathogen Mycoplasma synoviae. Vet Microbiol 2010; 145:134-41. [DOI: 10.1016/j.vetmic.2010.03.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 03/03/2010] [Accepted: 03/08/2010] [Indexed: 02/04/2023]
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Schmidl SR, Gronau K, Pietack N, Hecker M, Becher D, Stülke J. The phosphoproteome of the minimal bacterium Mycoplasma pneumoniae: analysis of the complete known Ser/Thr kinome suggests the existence of novel kinases. Mol Cell Proteomics 2010; 9:1228-42. [PMID: 20097688 DOI: 10.1074/mcp.m900267-mcp200] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mycoplasma pneumoniae belongs to the Mollicutes, the group of organisms with the smallest genomes that are capable of host-independent life. These bacteria show little regulation in gene expression, suggesting an important role for the control of protein activities. We have studied protein phosphorylation in M. pneumoniae to identify phosphorylated proteins. Two-dimensional gel electrophoresis and mass spectrometry allowed the detection of 63 phosphorylated proteins, many of them enzymes of central carbon metabolism and proteins related to host cell adhesion. We identified 16 phosphorylation sites, among them 8 serine and 8 threonine residues, respectively. A phosphoproteome analysis with mutants affected in the two annotated protein kinase genes or in the single known protein phosphatase gene suggested that only one protein (HPr) is phosphorylated by the HPr kinase, HPrK, whereas four adhesion-related or surface proteins were targets of the protein kinase C, PrkC. A comparison with the phosphoproteomes of other bacteria revealed that protein phosphorylation is evolutionarily only poorly conserved. Only one single protein with an identified phosphorylation site, a phosphosugar mutase (ManB in M. pneumoniae), is phosphorylated on a conserved serine residue in all studied organisms from archaea and bacteria to man. We demonstrate that this protein undergoes autophosphorylation. This explains the strong conservation of this phosphorylation event. For most other proteins, even if they are phosphorylated in different species, the actual phosphorylation sites are different. This suggests that protein phosphorylation is a form of adaptation of the bacteria to the specific needs of their particular ecological niche.
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Affiliation(s)
- Sebastian R Schmidl
- Department of General Microbiology, Georg-August-Universität Göttingen, Grisebachstrasse 8, D-37077 Göttingen, Germany
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Yus E, Maier T, Michalodimitrakis K, van Noort V, Yamada T, Chen WH, Wodke JAH, Güell M, Martínez S, Bourgeois R, Kühner S, Raineri E, Letunic I, Kalinina OV, Rode M, Herrmann R, Gutiérrez-Gallego R, Russell RB, Gavin AC, Bork P, Serrano L. Impact of genome reduction on bacterial metabolism and its regulation. Science 2009; 326:1263-8. [PMID: 19965476 DOI: 10.1126/science.1177263] [Citation(s) in RCA: 217] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
To understand basic principles of bacterial metabolism organization and regulation, but also the impact of genome size, we systematically studied one of the smallest bacteria, Mycoplasma pneumoniae. A manually curated metabolic network of 189 reactions catalyzed by 129 enzymes allowed the design of a defined, minimal medium with 19 essential nutrients. More than 1300 growth curves were recorded in the presence of various nutrient concentrations. Measurements of biomass indicators, metabolites, and 13C-glucose experiments provided information on directionality, fluxes, and energetics; integration with transcription profiling enabled the global analysis of metabolic regulation. Compared with more complex bacteria, the M. pneumoniae metabolic network has a more linear topology and contains a higher fraction of multifunctional enzymes; general features such as metabolite concentrations, cellular energetics, adaptability, and global gene expression responses are similar, however.
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Affiliation(s)
- Eva Yus
- Centre for Genomic Regulation (CRG) and Universitat Pompeu Fabra, Avenida Dr. Aiguader 88, 08003 Barcelona, Spain
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The stability of cytadherence proteins in Mycoplasma pneumoniae requires activity of the protein kinase PrkC. Infect Immun 2009; 78:184-92. [PMID: 19858294 DOI: 10.1128/iai.00958-09] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycoplasma pneumoniae belongs to the mollicutes, a group of bacteria that have strongly reduced genomes but that are nevertheless capable of independent life. With only three transcription factors, the regulatory features of these bacteria are very limited. Thus, posttranslational regulation might be important for M. pneumoniae. In addition to the highly specific HPr kinase, the M. pneumoniae prkC gene encodes the serine/threonine protein kinase C. In order to study the function(s) of this kinase, we isolated an M. pneumoniae mutant affected in PrkC. This mutation resulted in nonadherent growth and loss of cytotoxicity. Examination of the phosphorylation profile of the prkC mutant suggested that phosphorylation of cytadherence proteins was affected by the loss of this kinase. In contrast, inactivation of the prpC gene affecting the protein phosphatase that antagonizes PrkC-dependent phosphorylation resulted in more intensive phosphorylation of the cytadherence proteins HMW1 and HMW3 of the major adhesin P1 and of the surface protein MPN474. Moreover, loss of PrkC affects not only the phosphorylation state of the cytadherence proteins but also their intracellular accumulation. However, the expression of the corresponding genes was not affected by PrkC, suggesting that PrkC-dependent phosphorylation results in stabilization of the cytadherence proteins. The HMW proteins and P1 are part of the so-called terminal organelle of M. pneumoniae that is involved in gliding motility, cell division, and adhesion to host epithelial tissues. Our observations suggest that the posttranslational modification of cytadherence proteins by PrkC is essential for the development and function of the M. pneumoniae terminal organelle.
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Chalker VJ, Jordan K, Ali T, Ison C. Real-time PCR detection of the mg219 gene of unknown function of Mycoplasma genitalium in men with and without non-gonococcal urethritis and their female partners in England. J Med Microbiol 2009; 58:895-899. [DOI: 10.1099/jmm.0.009977-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Real-time PCR was employed to detect a region of the Mycoplasma genitalium
mg219 gene, a gene of unknown function, in clinical samples. Amplification of DNA and signal production from 15 other species of human mycoplasmas and 14 other bacteria and viruses did not occur. Using a panel of 208 genital and rectal samples, the sensitivity when compared to the modified mgpa gene (encoding the major surface protein MgPa) real-time PCR assay was found to be 100 % and the specificity of the assay 99.5 % with a positive predictive value of 80 % and a negative predictive value of 100 %. The mg219 gene was found to be in all strains of M. genitalium and was highly conserved. M. genitalium was detected in 3.9 % (11/280, 95 % CI 2.1–6.9) of all male specimens, in 7.7 % (10/130, 95 % CI 4.1–13.7) of patients with non-gonococcal urethritis (NGU) and in 0.7 % (1/150, 95 % CI <0.01–4.1) of patients without urethritis. The presence of M. genitalium was significantly associated with NGU (P ≤0.01; 95 % Cl 0.88–0.98) and non-chlamydial-non-gonococcal urethritis (P=0.0005; 95 % Cl 0.84–0.97).
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Affiliation(s)
- Victoria J. Chalker
- Sexually Transmitted Bacteria Reference Laboratory, Health Protection Agency Centre for Infections, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Karen Jordan
- Microbiology Laboratory, Northampton General Hospital Trust, Billing Road, Northampton NN1 5BD, UK
| | - Tahir Ali
- Sexually Transmitted Bacteria Reference Laboratory, Health Protection Agency Centre for Infections, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Cathy Ison
- Sexually Transmitted Bacteria Reference Laboratory, Health Protection Agency Centre for Infections, 61 Colindale Avenue, London NW9 5EQ, UK
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Amino acid changes in elongation factor Tu of Mycoplasma pneumoniae and Mycoplasma genitalium influence fibronectin binding. Infect Immun 2009; 77:3533-41. [PMID: 19546194 DOI: 10.1128/iai.00081-09] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycoplasma pneumoniae and Mycoplasma genitalium are closely related organisms that cause distinct clinical manifestations and possess different tissue predilections despite their high degree of genome homology. We reported earlier that surface-localized M. pneumoniae elongation factor Tu (EF-Tu(Mp)) mediates binding to the extracellular matrix component fibronectin (Fn) through the carboxyl region of EF-Tu. In this study, we demonstrate that surface-associated M. genitalium EF-Tu (EF-Tu(Mg)), in spite of sharing 96% identity with EF-Tu(Mp), does not bind Fn. We utilized this finding to identify the essential amino acids of EF-Tu(Mp) that mediate Fn interactions by generating modified recombinant EF-Tu proteins with amino acid changes corresponding to those of EF-Tu(Mg). Amino acid changes in serine 343, proline 345, and threonine 357 were sufficient to significantly reduce the Fn binding of EF-Tu(Mp). Synthetic peptides corresponding to this region of EF-Tu(Mp) (EF-Tu(Mp) 340-358) blocked both recombinant EF-Tu(Mp) and radiolabeled M. pneumoniae cell binding to Fn. In contrast, EF-Tu(Mg) 340-358 peptides exhibited minimal blocking activity, reinforcing the specificity of EF-Tu-Fn interactions as mediators of microbial colonization and tissue tropism.
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Demina IA, Serebryakova MV, Ladygina VG, Rogova MA, Zgoda VG, Korzhenevskyi DA, Govorun VM. Proteome of the bacterium Mycoplasma gallisepticum. BIOCHEMISTRY (MOSCOW) 2009; 74:165-74. [PMID: 19267672 DOI: 10.1134/s0006297909020072] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Using modern proteomic assays, we have identified the products of gene expression and posttranslational modifications of proteins of the bacterium Mycoplasma gallisepticum S6. Combinations of different technologies of protein separation by electrophoresis and mass-spectrometric analysis gave us a total of 446 proteins, i.e. 61% of the annotated proteins of this microorganism. The Pro-Q Diamond and Pro-Q Emerald dye technology was used for fluorescent detection of ten phosphoproteins and two glycoproteins. The acylation of proteins was studied by electrophoresis after in vivo labeling with different 14C-labeled fatty acids, followed by autoradiography. Sixteen acylated proteins were identified, with a quarter of them involved in plasma membrane construction and another quarter involved in cell energy metabolism.
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Affiliation(s)
- I A Demina
- Research Institute for Physical-Chemical Medicine, Ministry of Public Health of the Russian Federation, Moscow, Russia.
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Wilton J, Jenkins C, Cordwell SJ, Falconer L, Minion FC, Oneal DC, Djordjevic MA, Connolly A, Barchia I, Walker MJ, Djordjevic SP. Mhp493 (P216) is a proteolytically processed, cilium and heparin binding protein of Mycoplasma hyopneumoniae. Mol Microbiol 2008; 71:566-82. [PMID: 19040640 DOI: 10.1111/j.1365-2958.2008.06546.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Mycoplasma hyopneumoniae induces respiratory disease in swine by colonizing cilia causing ciliostasis, cilial loss and epithelial cell death. Heparin binds to M. hyopneumoniae cells in a dose-dependent manner and blocks its ability to adhere to porcine cilia. We show here that Mhp493 (P216), a paralogue of the cilium adhesin P97 (Mhp183), is cleaved between amino acids 1040 and 1089 generating surface-accessible, heparin-binding proteins P120 and P85. Antiphosphoserine antibodies recognized P85 in 2-D immunoblotting studies and TiO(2) chromatography of trypsin digests of P85 isolated a single peptide with an m/z of 917.3. A phosphoserine residue in the tryptic peptide (90)VSELpSFR(96) (position 94 in P85) was identified by MALDI-MS/MS. Polyhistidine fusion proteins (F1(P216), F2(P216), F3(P216)) spanning Mhp493 bound heparin with biologically significant Kd values, and heparin, fucoidan and mucin inhibited this interaction. Latex beads coated with F1(P216), F2(P216) and F3(P216) adhered to and entered porcine kidney epithelial-like (PK15) cell monolayers. Microtitre plate-based assays showed that sequences within P120 and P85 bind to porcine cilia and are recognized by serum antibodies elicited during infection by M. hyopneumoniae. Mhp493 contributes significantly to the surface architecture of M. hyopneumoniae and is the first cilium adhesin to be described that lacks an R1 cilium-binding domain.
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Affiliation(s)
- Jody Wilton
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Camden, NSW 2570, Australia
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Burgos R, Pich OQ, Querol E, Piñol J. Deletion of the Mycoplasma genitalium MG_217 gene modifies cell gliding behaviour by altering terminal organelle curvature. Mol Microbiol 2008; 69:1029-40. [PMID: 18573175 DOI: 10.1111/j.1365-2958.2008.06343.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Motility is often a virulence factor of pathogenic bacteria. Although recent works have identified genes involved in gliding motility of mycoplasmas, little is known about the mechanisms governing the cell gliding behaviour. Here, we report that Mycoplasma genitalium MG217 is a novel protein involved in the gliding apparatus of this organism and it is, at least, one of the genes that are directing cells to move in narrow circles when they glide. In the absence of MG_217 gene, cells are still able to glide but they mainly move drawing erratic or wide circular paths. This change in the gliding behaviour correlates with a rearrangement in the terminal organelle disposition, suggesting that the terminal organelle operates as a guide to steer the mycoplasma cell in a specific direction. Immunogold labelling reveals that MG217 protein is located intracellular at the distal end of the terminal organelle, between the cell membrane and the terminal button. Such location is consistent with the idea that MG217 could act as a modulator of the terminal organelle curvature, allowing cells to move in specific directions.
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Affiliation(s)
- Raul Burgos
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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Hegermann J, Halbedel S, Dumke R, Regula J, Gabdoulline RR, Mayer F, Stülke J, Herrmann R. The acidic, glutamine-rich Mpn474 protein of Mycoplasma pneumoniae is surface exposed and covers the complete cell. MICROBIOLOGY-SGM 2008; 154:1185-1192. [PMID: 18375811 DOI: 10.1099/mic.0.2007/013342-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The protein Mpn474 encoded by the mpn474 gene of the human-pathogenic Mycoplasma pneumoniae contains 1033 amino acids and has an isoelectric point of 4.79, which is caused by the large excess of glutamic acid residues (11 %). Although the protein lacks recognizable export signals we showed by immuno-electron microscopy that Mpn474 is surface exposed, covering the cell completely. By combining cross-linking and careful treatment of the bacterial cells with Triton X-100, we found that this protein is weakly bound to the cell surface, while the true transmembrane protein Mpn141 (adhesin P1) is firmly attached under the same experimental conditions. A transposon mutant in the mpn474 gene, which has no obvious phenotype, served as negative control for the immunodetection.
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Affiliation(s)
- Jan Hegermann
- Abteilung für Allgemeine Mikrobiologie, Institut für Mikrobiologie und Genetik, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Sven Halbedel
- Abteilung für Allgemeine Mikrobiologie, Institut für Mikrobiologie und Genetik, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Roger Dumke
- Institut für Medizinische Mikrobiologie und Hygiene, Technische Universität, Medizinische Fakultät Carl Gustav Carus, Fetscherstr. 74, D-01307 Dresden, Germany
| | - Jörg Regula
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Razif R Gabdoulline
- Molecular and Cellular Modeling Group, EML Research, Schloss-Wolfsbrunnenweg 33, D-69118 Heidelberg, Germany
| | - Frank Mayer
- Abteilung für Allgemeine Mikrobiologie, Institut für Mikrobiologie und Genetik, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Jörg Stülke
- Abteilung für Allgemeine Mikrobiologie, Institut für Mikrobiologie und Genetik, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Richard Herrmann
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
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