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Kolodziejek AM, Hovde CJ, Minnich SA. Contributions of Yersinia pestis outer membrane protein Ail to plague pathogenesis. Curr Opin Infect Dis 2022; 35:188-195. [PMID: 35665712 PMCID: PMC9186061 DOI: 10.1097/qco.0000000000000830] [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] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Pathogenic Yersinia have been a productive model system for studying bacterial pathogenesis. Hallmark contributions of Yersinia research to medical microbiology are legion and include: (i) the first identification of the role of plasmids in virulence, (ii) the important mechanism of iron acquisition from the host, (iii) the first identification of bacterial surface proteins required for host cell invasion, (iv) the archetypical type III secretion system, and (v) elucidation of the role of genomic reduction in the evolutionary trajectory from a fairly innocuous pathogen to a highly virulent species. RECENT FINDINGS The outer membrane (OM) protein Ail (attachment invasion locus) was identified over 30 years ago as an invasin-like protein. Recent work on Ail continues to provide insights into Gram-negative pathogenesis. This review is a synopsis of the role of Ail in invasion, serum resistance, OM stability, thermosensing, and vaccine development. SUMMARY Ail is shown to be an essential virulence factor with multiple roles in pathogenesis. The recent adaptation of Yersinia pestis to high virulence, which included genomic reduction to eliminate redundant protein functions, is a model to understand the emergence of new bacterial pathogens.
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Affiliation(s)
- Anna M. Kolodziejek
- Department of Animal, Veterinary, and Food Science, University of Idaho, Moscow, Idaho, USA
| | - Carolyn J. Hovde
- Department of Animal, Veterinary, and Food Science, University of Idaho, Moscow, Idaho, USA
| | - Scott A. Minnich
- Department of Animal, Veterinary, and Food Science, University of Idaho, Moscow, Idaho, USA
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Tanaka M, Ueno Y, Miyake T, Sakuma T, Okochi M. Enrichment of membrane curvature-sensing proteins from Escherichia coli using spherical supported lipid bilayers. J Biosci Bioeng 2021; 133:98-104. [PMID: 34776361 DOI: 10.1016/j.jbiosc.2021.10.003] [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: 07/26/2021] [Revised: 10/07/2021] [Accepted: 10/12/2021] [Indexed: 10/19/2022]
Abstract
Bacteria display dynamically organized curved membrane structures, especially during cell division. The importance of membrane curvature-sensing (MCS) proteins for the recognition and regulation of biological membrane morphologies has predominately been investigated in eukaryotic cells. Recently, a technique for screening MCS proteins from solutions that contain peripheral membrane proteins was developed, and MCS protein candidates were identified from mammalian cells. The technique uses differently sized spherical supported lipid bilayers (SSLBs), which consist of spherical SiO2 particles covered with a lipid bilayer. To discriminate between proteins possessing the MCS property, SSLBs with the same surface area were used in a comparative sedimentation assay with shotgun proteome analysis. In this study, to prove that the technique could be applied to other samples, MCS proteins in Escherichia coli were investigated. Through a comparative proteomic study, 35 and 47 proteins were enriched as candidate MCS proteins preferentially bound to SSLBs of 100 nm and 1000 nm, respectively. Among the identified MCS candidate proteins, FtsZ and SecA were further examined for their MCS properties using the two SSLB sizes, which revealed a high binding affinity for the low membrane curvature (large SSLB). This is the first study to explore MCS proteins in prokaryotic cells and the MCS property of the SecA protein. The results demonstrate a method to enrich MCS proteins that could be utilized to better elucidate membrane dynamics and protein function expression on curved membrane structures in prokaryotic cells.
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Affiliation(s)
- Masayoshi Tanaka
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Yu Ueno
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Takahiro Miyake
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Takahiro Sakuma
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Mina Okochi
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8552, Japan.
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Fijalkowska D, Fijalkowski I, Willems P, Van Damme P. Bacterial riboproteogenomics: the era of N-terminal proteoform existence revealed. FEMS Microbiol Rev 2021; 44:418-431. [PMID: 32386204 DOI: 10.1093/femsre/fuaa013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 05/07/2020] [Indexed: 12/17/2022] Open
Abstract
With the rapid increase in the number of sequenced prokaryotic genomes, relying on automated gene annotation became a necessity. Multiple lines of evidence, however, suggest that current bacterial genome annotations may contain inconsistencies and are incomplete, even for so-called well-annotated genomes. We here discuss underexplored sources of protein diversity and new methodologies for high-throughput genome reannotation. The expression of multiple molecular forms of proteins (proteoforms) from a single gene, particularly driven by alternative translation initiation, is gaining interest as a prominent contributor to bacterial protein diversity. In consequence, riboproteogenomic pipelines were proposed to comprehensively capture proteoform expression in prokaryotes by the complementary use of (positional) proteomics and the direct readout of translated genomic regions using ribosome profiling. To complement these discoveries, tailored strategies are required for the functional characterization of newly discovered bacterial proteoforms.
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Affiliation(s)
- Daria Fijalkowska
- Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Igor Fijalkowski
- Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Patrick Willems
- Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Petra Van Damme
- Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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Cao S, Chen Y, Yan Y, Zhu S, Tan Y, Wang T, Song Y, Deng H, Yang R, Du Z. Secretome and Comparative Proteomics of Yersinia pestis Identify Two Novel E3 Ubiquitin Ligases That Contribute to Plague Virulence. Mol Cell Proteomics 2021; 20:100066. [PMID: 33631294 PMCID: PMC7994543 DOI: 10.1016/j.mcpro.2021.100066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 02/12/2021] [Indexed: 11/21/2022] Open
Abstract
Plague is a zoonotic disease that primarily infects rodents via fleabite. Transmission from flea to host niches requires rapid adaption of Yersinia pestis to the outer environments to establish infection. Here, quantitative proteome and secretome analyses of Y. pestis grown under conditions mimicking the two typical niches, i.e., the mammalian host (Mh) and the flea vector (Fv), were performed to understand the adaption strategies of this deadly pathogen. A secretome of Y. pestis containing 308 proteins has been identified using TMT-labeling mass spectrometry analysis. Although some proteins are known to be secreted, such as the type III secretion substrates, PsaA and F1 antigen, most of them were found to be secretory proteins for the first time. Comparative proteomic analysis showed that membrane proteins, chaperonins and stress response proteins are significantly upregulated under the Mh condition, among which the previously uncharacterized proteins YP_3416∼YP_3418 are remarkable because they cannot only be secreted but also translocated into HeLa cells by Y. pestis. We further demonstrated that the purified YP_3416 and YP_3418 exhibited E3 ubiquitin ligase activity in in vitro ubiquitination assay and yp_3416∼3418 deletion mutant of Y. pestis showed significant virulence attenuation in mice. Taken together, our results represent the first Y. pestis secretome, which will promote the better understanding of Y. pestis pathogenesis, as well as the development of new strategies for treatment and prevention of plague.
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Affiliation(s)
- Shiyang Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yuling Chen
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yanfeng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Songbiao Zhu
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yafang Tan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tong Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
| | - Zongmin Du
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
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Tanaka M, Komikawa T, Yanai K, Okochi M. Proteomic Exploration of Membrane Curvature Sensors Using a Series of Spherical Supported Lipid Bilayers. Anal Chem 2020; 92:16197-16203. [DOI: 10.1021/acs.analchem.0c04039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Masayoshi Tanaka
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Takumi Komikawa
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Kentaro Yanai
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Mina Okochi
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8552, Japan
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Lye PY, Noor SM, Shohaimi SA, Junoh NF, Tan SC, Iwamoto S, Kotani E, Norazmi MN, Nagamine T, Mori H, Liew MW. Process development for quantitation and vaccine efficacy assessment of recombinant hemagglutinin-neuraminidase. Process Biochem 2020. [DOI: 10.1016/j.procbio.2019.11.018] [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: 11/16/2022]
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Koch L, Poyot T, Schnetterle M, Guillier S, Soulé E, Nolent F, Gorgé O, Neulat-Ripoll F, Valade E, Sebbane F, Biot F. Transcriptomic studies and assessment of Yersinia pestis reference genes in various conditions. Sci Rep 2019; 9:2501. [PMID: 30792499 PMCID: PMC6385181 DOI: 10.1038/s41598-019-39072-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/14/2018] [Indexed: 12/27/2022] Open
Abstract
Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is a very sensitive widespread technique considered as the gold standard to explore transcriptional variations. While a particular methodology has to be followed to provide accurate results many published studies are likely to misinterpret results due to lack of minimal quality requirements. Yersinia pestis is a highly pathogenic bacterium responsible for plague. It has been used to propose a ready-to-use and complete approach to mitigate the risk of technical biases in transcriptomic studies. The selection of suitable reference genes (RGs) among 29 candidates was performed using four different methods (GeNorm, NormFinder, BestKeeper and the Delta-Ct method). An overall comprehensive ranking revealed that 12 following candidate RGs are suitable for accurate normalization: gmk, proC, fabD, rpoD, nadB, rho, thrA, ribD, mutL, rpoB, adk and tmk. Some frequently used genes like 16S RNA had even been found as unsuitable to study Y. pestis. This methodology allowed us to demonstrate, under different temperatures and states of growth, significant transcriptional changes of six efflux pumps genes involved in physiological aspects as antimicrobial resistance or virulence. Previous transcriptomic studies done under comparable conditions had not been able to highlight these transcriptional modifications. These results highlight the importance of validating RGs prior to the normalization of transcriptional expression levels of targeted genes. This accurate methodology can be extended to any gene of interest in Y. pestis. More generally, the same workflow can be applied to identify and validate appropriate RGs in other bacteria to study transcriptional variations.
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Affiliation(s)
- Lionel Koch
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny-sur-Orge, France
- Ecole du Val de Grace (EVDG), Paris, France
- Aix Marseille University, INSERM, SSA, IRBA, MCT, Marseille, France
| | - Thomas Poyot
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny-sur-Orge, France
| | - Marine Schnetterle
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny-sur-Orge, France
- Aix Marseille University, INSERM, SSA, IRBA, MCT, Marseille, France
| | - Sophie Guillier
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny-sur-Orge, France
- Aix Marseille University, INSERM, SSA, IRBA, MCT, Marseille, France
| | - Estelle Soulé
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny-sur-Orge, France
- Aix Marseille University, INSERM, SSA, IRBA, MCT, Marseille, France
| | - Flora Nolent
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny-sur-Orge, France
- Aix Marseille University, INSERM, SSA, IRBA, MCT, Marseille, France
| | - Olivier Gorgé
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny-sur-Orge, France
- Aix Marseille University, INSERM, SSA, IRBA, MCT, Marseille, France
| | - Fabienne Neulat-Ripoll
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny-sur-Orge, France
- Aix Marseille University, INSERM, SSA, IRBA, MCT, Marseille, France
| | - Eric Valade
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny-sur-Orge, France
- Ecole du Val de Grace (EVDG), Paris, France
- Aix Marseille University, INSERM, SSA, IRBA, MCT, Marseille, France
| | - Florent Sebbane
- Inserm, University of Lille, CNRS, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL-Center for Infection and Immunity of Lille, Lille, France
| | - Fabrice Biot
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny-sur-Orge, France.
- Aix Marseille University, INSERM, SSA, IRBA, MCT, Marseille, France.
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Abstract
Due to their physicochemical properties, membrane protein proteomics analyses often require extensive sample preparation protocols resulting in sample loss and introducing technical variation. Several methods for membrane proteomics have been described, designed to meet the needs of specific sample types and experimental designs. Here, we present a complete membrane proteomics pipeline starting from the membrane sample preparation to the protein identification/quantification and also discuss about annotation of proteomics data. The protocol has been developed using Escherichia coli samples but is directly adaptable to other bacteria including pathogens. We describe a method for the preparation of E. coli inner membrane vesicles (IMVs) central to our pipeline. IMVs are functional membrane vesicles that can also be used for biochemical studies. Next, we propose methods for membrane protein digestion and describe alternative experimental approaches that have been previously tested in our lab. We highlight a surface proteolysis protocol for the identification of inner membrane and membrane-bound proteins. This is a simple, fast, and reproducible method for the membrane sample characterization that has been previously used for the E. coli inner membrane proteome characterization (Papanastasiou et al., 2013) and the experimental validation of E. coli membrane proteome (Orfanoudaki & Economou, 2014). It provides a reduced load on MS-time and allows for multiple repeats. Then we discuss membrane protein quantification approaches and tools that can be used for the functional annotation of identified proteins. Overall, membrane proteome quantification can be fast, simplified, and reproducible; however, optimization steps should be performed for a given sample type.
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Nieckarz M, Raczkowska A, Dębski J, Kistowski M, Dadlez M, Heesemann J, Rossier O, Brzostek K. Impact of OmpR on the membrane proteome of Yersinia enterocolitica in different environments: repression of major adhesin YadA and heme receptor HemR. Environ Microbiol 2016; 18:997-1021. [PMID: 26627632 DOI: 10.1111/1462-2920.13165] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 11/26/2015] [Accepted: 11/29/2015] [Indexed: 01/22/2023]
Abstract
Enteropathogenic Yersinia enterocolitica is able to grow within or outside the mammalian host. Previous transcriptomic studies have indicated that the regulator OmpR plays a role in the expression of hundreds of genes in enterobacteria. Here, we have examined the impact of OmpR on the production of Y. enterocolitica membrane proteins upon changes in temperature, osmolarity and pH. Proteomic analysis indicated that the loss of OmpR affects the production of 120 proteins, a third of which are involved in uptake/transport, including several that participate in iron or heme acquisition. A set of proteins associated with virulence was also affected. The influence of OmpR on the abundance of adhesin YadA and heme receptor HemR was examined in more detail. OmpR was found to repress YadA production and bind to the yadA promoter, suggesting a direct regulatory effect. In contrast, the repression of hemR expression by OmpR appears to be indirect. These findings provide new insights into the role of OmpR in remodelling the cell surface and the adaptation of Y. enterocolitica to different environmental niches, including the host.
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Affiliation(s)
- Marta Nieckarz
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, Warsaw, 02-096, Poland
| | - Adrianna Raczkowska
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, Warsaw, 02-096, Poland
| | - Janusz Dębski
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
| | - Michał Kistowski
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
| | - Michał Dadlez
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawińskiego 5a, Warsaw, 02-106, Poland.,Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
| | - Jürgen Heesemann
- Max von Pettenkofer Institute for Hygiene and Medical Microbiology, Ludwig Maximilians University, Pettenkoferstrasse 9a, Munich, 80336, Germany
| | - Ombeline Rossier
- Max von Pettenkofer Institute for Hygiene and Medical Microbiology, Ludwig Maximilians University, Pettenkoferstrasse 9a, Munich, 80336, Germany
| | - Katarzyna Brzostek
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, Warsaw, 02-096, Poland
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Leiser OP, Merkley ED, Clowers BH, Deatherage Kaiser BL, Lin A, Hutchison JR, Melville AM, Wagner DM, Keim PS, Foster JT, Kreuzer HW. Investigation of Yersinia pestis Laboratory Adaptation through a Combined Genomics and Proteomics Approach. PLoS One 2015; 10:e0142997. [PMID: 26599979 PMCID: PMC4658026 DOI: 10.1371/journal.pone.0142997] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 10/29/2015] [Indexed: 11/19/2022] Open
Abstract
The bacterial pathogen Yersinia pestis, the cause of plague in humans and animals, normally has a sylvatic lifestyle, cycling between fleas and mammals. In contrast, laboratory-grown Y. pestis experiences a more constant environment and conditions that it would not normally encounter. The transition from the natural environment to the laboratory results in a vastly different set of selective pressures, and represents what could be considered domestication. Understanding the kinds of adaptations Y. pestis undergoes as it becomes domesticated will contribute to understanding the basic biology of this important pathogen. In this study, we performed a parallel serial passage experiment (PSPE) to explore the mechanisms by which Y. pestis adapts to laboratory conditions, hypothesizing that cells would undergo significant changes in virulence and nutrient acquisition systems. Two wild strains were serially passaged in 12 independent populations each for ~750 generations, after which each population was analyzed using whole-genome sequencing, LC-MS/MS proteomic analysis, and GC/MS metabolomics. We observed considerable parallel evolution in the endpoint populations, detecting multiple independent mutations in ail, pepA, and zwf, suggesting that specific selective pressures are shaping evolutionary responses. Complementary LC-MS/MS proteomic data provide physiological context to the observed mutations, and reveal regulatory changes not necessarily associated with specific mutations, including changes in amino acid metabolism and cell envelope biogenesis. Proteomic data support hypotheses generated by genomic data in addition to suggesting future mechanistic studies, indicating that future whole-genome sequencing studies be designed to leverage proteomics as a critical complement.
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Affiliation(s)
- Owen P. Leiser
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86001, United States of America
| | - Eric D. Merkley
- Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, Richland, WA, 99352, United States of America
| | - Brian H. Clowers
- Department of Chemistry, Washington State University, Pullman, WA, 99354, United States of America
| | - Brooke L. Deatherage Kaiser
- Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, Richland, WA, 99352, United States of America
| | - Andy Lin
- Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, Richland, WA, 99352, United States of America
| | - Janine R. Hutchison
- Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, Richland, WA, 99352, United States of America
| | - Angela M. Melville
- Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, Richland, WA, 99352, United States of America
| | - David M. Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86001, United States of America
| | - Paul S. Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86001, United States of America
| | - Jeffrey T. Foster
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86001, United States of America
| | - Helen W. Kreuzer
- Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, Richland, WA, 99352, United States of America
- * E-mail:
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Combinational deletion of three membrane protein-encoding genes highly attenuates yersinia pestis while retaining immunogenicity in a mouse model of pneumonic plague. Infect Immun 2015; 83:1318-38. [PMID: 25605764 DOI: 10.1128/iai.02778-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Previously, we showed that deletion of genes encoding Braun lipoprotein (Lpp) and MsbB attenuated Yersinia pestis CO92 in mouse and rat models of bubonic and pneumonic plague. While Lpp activates Toll-like receptor 2, the MsbB acyltransferase modifies lipopolysaccharide. Here, we deleted the ail gene (encoding the attachment-invasion locus) from wild-type (WT) strain CO92 or its lpp single and Δlpp ΔmsbB double mutants. While the Δail single mutant was minimally attenuated compared to the WT bacterium in a mouse model of pneumonic plague, the Δlpp Δail double mutant and the Δlpp ΔmsbB Δail triple mutant were increasingly attenuated, with the latter being unable to kill mice at a 50% lethal dose (LD50) equivalent to 6,800 LD50s of WT CO92. The mutant-infected animals developed balanced TH1- and TH2-based immune responses based on antibody isotyping. The triple mutant was cleared from mouse organs rapidly, with concurrent decreases in the production of various cytokines and histopathological lesions. When surviving animals infected with increasing doses of the triple mutant were subsequently challenged on day 24 with the bioluminescent WT CO92 strain (20 to 28 LD50s), 40 to 70% of the mice survived, with efficient clearing of the invading pathogen, as visualized in real time by in vivo imaging. The rapid clearance of the triple mutant, compared to that of WT CO92, from animals was related to the decreased adherence and invasion of human-derived HeLa and A549 alveolar epithelial cells and to its inability to survive intracellularly in these cells as well as in MH-S murine alveolar and primary human macrophages. An early burst of cytokine production in macrophages elicited by the triple mutant compared to WT CO92 and the mutant's sensitivity to the bactericidal effect of human serum would further augment bacterial clearance. Together, deletion of the ail gene from the Δlpp ΔmsbB double mutant severely attenuated Y. pestis CO92 to evoke pneumonic plague in a mouse model while retaining the required immunogenicity needed for subsequent protection against infection.
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Gao L, Ge H, Huang X, Liu K, Zhang Y, Xu W, Wang Y. Systematically ranking the tightness of membrane association for peripheral membrane proteins (PMPs). Mol Cell Proteomics 2014; 14:340-53. [PMID: 25505158 DOI: 10.1074/mcp.m114.044800] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Large-scale quantitative evaluation of the tightness of membrane association for nontransmembrane proteins is important for identifying true peripheral membrane proteins with functional significance. Herein, we simultaneously ranked more than 1000 proteins of the photosynthetic model organism Synechocystis sp. PCC 6803 for their relative tightness of membrane association using a proteomic approach. Using multiple precisely ranked and experimentally verified peripheral subunits of photosynthetic protein complexes as the landmarks, we found that proteins involved in two-component signal transduction systems and transporters are overall tightly associated with the membranes, whereas the associations of ribosomal proteins are much weaker. Moreover, we found that hypothetical proteins containing the same domains generally have similar tightness. This work provided a global view of the structural organization of the membrane proteome with respect to divergent functions, and built the foundation for future investigation of the dynamic membrane proteome reorganization in response to different environmental or internal stimuli.
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Affiliation(s)
- Liyan Gao
- From the ‡State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China
| | - Haitao Ge
- §State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
| | - Xiahe Huang
- From the ‡State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China
| | - Kehui Liu
- From the ‡State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China
| | - Yuanya Zhang
- From the ‡State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China
| | - Wu Xu
- ¶Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana 70504
| | - Yingchun Wang
- From the ‡State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China;
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Merritt PM, Nero T, Bohman L, Felek S, Krukonis ES, Marketon MM. Yersinia pestis targets neutrophils via complement receptor 3. Cell Microbiol 2014; 17:666-87. [PMID: 25359083 DOI: 10.1111/cmi.12391] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Revised: 10/18/2014] [Accepted: 10/28/2014] [Indexed: 01/20/2023]
Abstract
Yersinia species display a tropism for lymphoid tissues during infection, and the bacteria select innate immune cells for delivery of cytotoxic effectors by the type III secretion system. Yet, the mechanism for target cell selection remains a mystery. Here we investigate the interaction of Yersinia pestis with murine splenocytes to identify factors that participate in the targeting process. We find that interactions with primary immune cells rely on multiple factors. First, the bacterial adhesin Ail is required for efficient targeting of neutrophils in vivo. However, Ail does not appear to directly mediate binding to a specific cell type. Instead, we find that host serum factors direct Y. pestis to specific innate immune cells, particularly neutrophils. Importantly, specificity towards neutrophils was increased in the absence of bacterial adhesins because of reduced targeting of other cell types, but this phenotype was only visible in the presence of mouse serum. Addition of antibodies against complement receptor 3 and CD14 blocked target cell selection, suggesting that a combination of host factors participate in steering bacteria towards neutrophils during plague infection.
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Affiliation(s)
- Peter M Merritt
- Department of Biology, Indiana University, Bloomington, IN, USA
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Production of outer membrane vesicles by the plague pathogen Yersinia pestis. PLoS One 2014; 9:e107002. [PMID: 25198697 PMCID: PMC4157834 DOI: 10.1371/journal.pone.0107002] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 08/04/2014] [Indexed: 12/24/2022] Open
Abstract
Many Gram-negative bacteria produce outer membrane vesicles (OMVs) during cell growth and division, and some bacterial pathogens deliver virulence factors to the host via the release of OMVs during infection. Here we show that Yersinia pestis, the causative agent of the disease plague, produces and releases native OMVs under physiological conditions. These OMVs, approximately 100 nm in diameter, contain multiple virulence-associated outer membrane proteins including the adhesin Ail, the F1 outer fimbrial antigen, and the protease Pla. We found that OMVs released by Y. pestis contain catalytically active Pla that is competent for plasminogen activation and α2-antiplasmin degradation. The abundance of OMV-associated proteins released by Y. pestis is significantly elevated at 37°C compared to 26°C and is increased in response to membrane stress and mutations in RseA, Hfq, and the major Braun lipoprotein (Lpp). In addition, we show that Y. pestis OMVs are able to bind to components of the extracellular matrix such as fibronectin and laminin. These data suggest that Y. pestis may produce OMVs during mammalian infection and we propose that dispersal of Pla via OMV release may influence the outcome of infection through interactions with Pla substrates such as plasminogen and Fas ligand.
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15
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Walukiewicz HE, Tohidifar P, Ordal GW, Rao CV. Interactions among the three adaptation systems of Bacillus subtilis chemotaxis as revealed by an in vitro receptor-kinase assay. Mol Microbiol 2014; 93:1104-18. [PMID: 25039821 DOI: 10.1111/mmi.12721] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2014] [Indexed: 01/03/2023]
Abstract
The Bacillus subtilis chemotaxis pathway employs three systems for sensory adaptation: the methylation system, the CheC/CheD/CheYp system, and the CheV system. Little is known in general about how these three adaptation systems contribute to chemotaxis in B. subtilis and whether they interact with one another. To further understand these three adaptation systems, we employed a quantitative in vitro receptor-kinase assay. Using this assay, we were able to determine how CheD and CheV affect receptor-kinase activity as a function of the receptor modification state. CheD was found to increase receptor-kinase activity, where the magnitude of the increase depends on the modification state of the receptor. The principal new findings concern CheV. Little was known about this protein before now. Our data suggest that this protein has two roles depending on the modification state of the receptor, one for sensory adaptation when the receptors are modified (methylated) and the other for signal amplification when they are unmodified (unmethylated). In addition, our data suggest that methylation of site 630 tunes the strength of the CheV adaptation system. Collectively, our results provide new insight regarding the integrated function of the three adaptation systems in B. subtilis.
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Affiliation(s)
- Hanna E Walukiewicz
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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Stekhoven DJ, Omasits U, Quebatte M, Dehio C, Ahrens CH. Proteome-wide identification of predominant subcellular protein localizations in a bacterial model organism. J Proteomics 2014; 99:123-37. [PMID: 24486812 DOI: 10.1016/j.jprot.2014.01.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 01/12/2014] [Accepted: 01/15/2014] [Indexed: 01/04/2023]
Abstract
UNLABELLED Proteomics data provide unique insights into biological systems, including the predominant subcellular localization (SCL) of proteins, which can reveal important clues about their functions. Here we analyzed data of a complete prokaryotic proteome expressed under two conditions mimicking interaction of the emerging pathogen Bartonella henselae with its mammalian host. Normalized spectral count data from cytoplasmic, total membrane, inner and outer membrane fractions allowed us to identify the predominant SCL for 82% of the identified proteins. The spectral count proportion of total membrane versus cytoplasmic fractions indicated the propensity of cytoplasmic proteins to co-fractionate with the inner membrane, and enabled us to distinguish cytoplasmic, peripheral inner membrane and bona fide inner membrane proteins. Principal component analysis and k-nearest neighbor classification training on selected marker proteins or predominantly localized proteins, allowed us to determine an extensive catalog of at least 74 expressed outer membrane proteins, and to extend the SCL assignment to 94% of the identified proteins, including 18% where in silico methods gave no prediction. Suitable experimental proteomics data combined with straightforward computational approaches can thus identify the predominant SCL on a proteome-wide scale. Finally, we present a conceptual approach to identify proteins potentially changing their SCL in a condition-dependent fashion. BIOLOGICAL SIGNIFICANCE The work presented here describes the first prokaryotic proteome-wide subcellular localization (SCL) dataset for the emerging pathogen B. henselae (Bhen). The study indicates that suitable subcellular fractionation experiments combined with straight-forward computational analysis approaches assessing the proportion of spectral counts observed in different subcellular fractions are powerful for determining the predominant SCL of a large percentage of the experimentally observed proteins. This includes numerous cases where in silico prediction methods do not provide any prediction. Avoiding a treatment with harsh conditions, cytoplasmic proteins tend to co-fractionate with proteins of the inner membrane fraction, indicative of close functional interactions. The spectral count proportion (SCP) of total membrane versus cytoplasmic fractions allowed us to obtain a good indication about the relative proximity of individual protein complex members to the inner membrane. Using principal component analysis and k-nearest neighbor approaches, we were able to extend the percentage of proteins with a predominant experimental localization to over 90% of all expressed proteins and identified a set of at least 74 outer membrane (OM) proteins. In general, OM proteins represent a rich source of candidates for the development of urgently needed new therapeutics in combat of resurgence of infectious disease and multi-drug resistant bacteria. Finally, by comparing the data from two infection biology relevant conditions, we conceptually explore methods to identify and visualize potential candidates that may partially change their SCL in these different conditions. The data are made available to researchers as a SCL compendium for Bhen and as an assistance in further improving in silico SCL prediction algorithms.
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Affiliation(s)
- Daniel J Stekhoven
- Quantitative Model Organism Proteomics (Q-MOP), Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
| | - Ulrich Omasits
- Quantitative Model Organism Proteomics (Q-MOP), Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland
| | - Maxime Quebatte
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Christoph Dehio
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Christian H Ahrens
- Quantitative Model Organism Proteomics (Q-MOP), Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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Papanastasiou M, Orfanoudaki G, Koukaki M, Kountourakis N, Sardis MF, Aivaliotis M, Karamanou S, Economou A. The Escherichia coli peripheral inner membrane proteome. Mol Cell Proteomics 2012; 12:599-610. [PMID: 23230279 DOI: 10.1074/mcp.m112.024711] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Biological membranes are essential for cell viability. Their functional characteristics strongly depend on their protein content, which consists of transmembrane (integral) and peripherally associated membrane proteins. Both integral and peripheral inner membrane proteins mediate a plethora of biological processes. Whereas transmembrane proteins have characteristic hydrophobic stretches and can be predicted using bioinformatics approaches, peripheral inner membrane proteins are hydrophilic, exist in equilibria with soluble pools, and carry no discernible membrane targeting signals. We experimentally determined the cytoplasmic peripheral inner membrane proteome of the model organism Escherichia coli using a multidisciplinary approach. Initially, we extensively re-annotated the theoretical proteome regarding subcellular localization using literature searches, manual curation, and multi-combinatorial bioinformatics searches of the available databases. Next we used sequential biochemical fractionations coupled to direct identification of individual proteins and protein complexes using high resolution mass spectrometry. We determined that the proposed cytoplasmic peripheral inner membrane proteome occupies a previously unsuspected ∼19% of the basic E. coli BL21(DE3) proteome, and the detected peripheral inner membrane proteome occupies ∼25% of the estimated expressed proteome of this cell grown in LB medium to mid-log phase. This value might increase when fleeting interactions, not studied here, are taken into account. Several proteins previously regarded as exclusively cytoplasmic bind membranes avidly. Many of these proteins are organized in functional or/and structural oligomeric complexes that bind to the membrane with multiple interactions. Identified proteins cover the full spectrum of biological activities, and more than half of them are essential. Our data suggest that the cytoplasmic proteome displays remarkably dynamic and extensive communication with biological membrane surfaces that we are only beginning to decipher.
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Rakin A, Schneider L, Podladchikova O. Hunger for iron: the alternative siderophore iron scavenging systems in highly virulent Yersinia. Front Cell Infect Microbiol 2012; 2:151. [PMID: 23226687 PMCID: PMC3510459 DOI: 10.3389/fcimb.2012.00151] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Accepted: 11/13/2012] [Indexed: 11/16/2022] Open
Abstract
Low molecular weight siderophores are used by many living organisms to scavenge scarcely available ferric iron. Presence of at least a single siderophore-based iron acquisition system is usually acknowledged as a virulence-associated trait and a pre-requisite to become an efficient and successful pathogen. Currently, it is assumed that yersiniabactin (Ybt) is the solely functional endogenous siderophore iron uptake system in highly virulent Yersinia (Yersinia pestis, Y. pseudotuberculosis, and Y. enterocolitica biotype 1B). Genes responsible for biosynthesis, transport, and regulation of the yersiniabactin (ybt) production are clustered on a mobile genetic element, the High-Pathogenicity Island (HPI) that is responsible for broad dissemination of the ybt genes in Enterobacteriaceae. However, the ybt gene cluster is absent from nearly half of Y. pseudotuberculosis O3 isolates and epidemic Y. pseudotuberculosis O1 isolates responsible for the Far East Scarlet-like Fever. Several potential siderophore-mediated iron uptake gene clusters are documented in Yersinia genomes, however, neither of them have been proven to be functional. It has been suggested that at least two siderophores alternative to Ybt may operate in the highly virulent Yersinia pestis/Y. pseudotuberculosis group, and are referred to as pseudochelin (Pch) and yersiniachelin (Ych). Furthermore, most sporadic Y. pseudotuberculosis O1 strains possess gene clusters encoding all three iron scavenging systems. Thus, the Ybt system appears not to be the sole endogenous siderophore iron uptake system in the highly virulent yersiniae and may be efficiently substituted and/or supplemented by alternative iron siderophore scavenging systems.
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Affiliation(s)
- Alexander Rakin
- Phylogenomics of the Enteropathogenic Yersinia, Max von Pettenkofer-Institute, LMU Munich, Germany.
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Kolodziejek AM, Hovde CJ, Minnich SA. Yersinia pestis Ail: multiple roles of a single protein. Front Cell Infect Microbiol 2012; 2:103. [PMID: 22919692 PMCID: PMC3417512 DOI: 10.3389/fcimb.2012.00103] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 07/14/2012] [Indexed: 01/03/2023] Open
Abstract
Yersinia pestis is one of the most virulent bacteria identified. It is the causative agent of plague—a systemic disease that has claimed millions of human lives throughout history. Y. pestis survival in insect and mammalian host species requires fine-tuning to sense and respond to varying environmental cues. Multiple Y. pestis attributes participate in this process and contribute to its pathogenicity and highly efficient transmission between hosts. These include factors inherited from its enteric predecessors; Y. enterocolitica and Y. pseudotuberculosis, as well as phenotypes acquired or lost during Y. pestis speciation. Representatives of a large Enterobacteriaceae Ail/OmpX/PagC/Lom family of outer membrane proteins (OMPs) are found in the genomes of all pathogenic Yersiniae. This review describes the current knowledge regarding the role of Ail in Y. pestis pathogenesis and virulence. The pronounced role of Ail in the following areas are discussed (1) inhibition of the bactericidal properties of complement, (2) attachment and Yersinia outer proteins (Yop) delivery to host tissue, (3) prevention of PMNL recruitment to the lymph nodes, and (4) inhibition of the inflammatory response. Finally, Ail homologs in Y. enterocolitica and Y. pseudotuberculosis are compared to illustrate differences that may have contributed to the drastic bacterial lifestyle change that shifted Y. pestis from an enteric to a vector-born systemic pathogen.
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Affiliation(s)
- Anna M Kolodziejek
- School of Food Science, University of Idaho Moscow, ID, USA. akolodziejek@ vandals.uidaho.edu
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Tiwari V, Vashistt J, Kapil A, Moganty RR. Comparative proteomics of inner membrane fraction from carbapenem-resistant Acinetobacter baumannii with a reference strain. PLoS One 2012; 7:e39451. [PMID: 22761799 PMCID: PMC3383706 DOI: 10.1371/journal.pone.0039451] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 05/21/2012] [Indexed: 12/31/2022] Open
Abstract
Acinetobacter baumannii has been identified by the Infectious Diseases Society of America as one of the six pathogens that cause majority of hospital infections. Increased resistance of A.baumannii even to the latest generation of β-lactams like carbapenem is an immediate threat to mankind. As inner-membrane fraction plays a significant role in survival of A.baumannii, we investigated the inner-membrane fraction proteome of carbapenem-resistant strain of A.baumannii using Differential In-Gel Electrophoresis (DIGE) followed by DeCyder, Progenesis and LC-MS/MS analysis. We identified 19 over-expressed and 4 down-regulated proteins (fold change>2, p<0.05) in resistant strain as compared to reference strain. Some of the upregulated proteins in resistant strain and their association with carbapenem resistance in A.baumannii are: i) β-lactamases, AmpC and OXA-51: cleave and inactivate carbapenem ii) metabolic enzymes, ATP synthase, malate dehydrogenase and 2-oxoglutarate dehydrogenase: help in increased energy production for the survival and iii) elongation factor Tu and ribosomal proteins: help in the overall protein production. Further, entry of carbapenem perhaps is limited by controlled production of OmpW and low levels of surface antigen help to evade host defence mechanism in developing resistance in A.baumannii. Present results support a model for the importance of proteins of inner-membrane fraction and their synergistic effect in the mediation of resistance of A.baumannii to carbapenem.
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Affiliation(s)
- Vishvanath Tiwari
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Jitendraa Vashistt
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Arti Kapil
- Department of Microbiology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Rajeswari R. Moganty
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
- * E-mail:
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Bochet P, Rügheimer F, Guina T, Brooks P, Goodlett D, Clote P, Schwikowski B. Fragmentation-free LC-MS can identify hundreds of proteins. Proteomics 2010; 11:22-32. [DOI: 10.1002/pmic.200900765] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Revised: 09/02/2010] [Accepted: 09/20/2010] [Indexed: 11/09/2022]
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Payne SH, Huang ST, Pieper R. A proteogenomic update to Yersinia: enhancing genome annotation. BMC Genomics 2010; 11:460. [PMID: 20687929 PMCID: PMC3091656 DOI: 10.1186/1471-2164-11-460] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 08/05/2010] [Indexed: 01/18/2023] Open
Abstract
Background Modern biomedical research depends on a complete and accurate proteome. With the widespread adoption of new sequencing technologies, genome sequences are generated at a near exponential rate, diminishing the time and effort that can be invested in genome annotation. The resulting gene set contains numerous errors in even the most basic form of annotation: the primary structure of the proteins. Results The application of experimental proteomics data to genome annotation, called proteogenomics, can quickly and efficiently discover misannotations, yielding a more accurate and complete genome annotation. We present a comprehensive proteogenomic analysis of the plague bacterium, Yersinia pestis KIM. We discover non-annotated genes, correct protein boundaries, remove spuriously annotated ORFs, and make major advances towards accurate identification of signal peptides. Finally, we apply our data to 21 other Yersinia genomes, correcting and enhancing their annotations. Conclusions In total, 141 gene models were altered and have been updated in RefSeq and Genbank, which can be accessed seamlessly through any NCBI tool (e.g. blast) or downloaded directly. Along with the improved gene models we discover new, more accurate means of identifying signal peptides in proteomics data.
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Affiliation(s)
- Samuel H Payne
- J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.
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Global gene expression profiling of Yersinia pestis replicating inside macrophages reveals the roles of a putative stress-induced operon in regulating type III secretion and intracellular cell division. Infect Immun 2010; 78:3700-15. [PMID: 20566693 DOI: 10.1128/iai.00062-10] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yersinia pestis, the causative agent of plague, is a facultative intracellular pathogen. Previous studies have indicated that the ability of Y. pestis to survive inside macrophages may be critical during the early stages of plague pathogenesis. To gain insights into the biology of intracellular Y. pestis and its environment following phagocytosis, we determined the genome-wide transcriptional profile of Y. pestis KIM5 replicating inside J774.1 macrophage-like cells using DNA microarrays. At 1.5, 4, and 8 h postinfection, a total of 801, 464, and 416 Y. pestis genes were differentially regulated, respectively, compared to the level of gene expression of control bacteria grown in tissue culture medium. A number of stress-response genes, including those involved in detoxification of reactive oxygen species, as well as several metabolic genes involved in macromolecule synthesis, were significantly induced in intracellular Y. pestis, consistent with the presence of oxidative stress and nutrient starvation inside Yersinia-containing vacuoles. A putative stress-induced operon consisting of y2313, y2315, and y2316 (y2313-y2316), and a previously unidentified open reading frame, orfX, was studied further on the basis of its high level of intracellular expression. Mutant strains harboring either deletion, Deltay2313-y2316 or DeltaorfX, exhibited diverse phenotypes, including reduced effector secretion by the type III secretion system, increased intracellular replication, and filamentous morphology of the bacteria growing inside macrophages. The results suggest a possible role for these genes in regulating cell envelope characteristics in the intracellular environment.
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Pieper R, Huang ST, Parmar PP, Clark DJ, Alami H, Fleischmann RD, Perry RD, Peterson SN. Proteomic analysis of iron acquisition, metabolic and regulatory responses of Yersinia pestis to iron starvation. BMC Microbiol 2010; 10:30. [PMID: 20113483 PMCID: PMC2835676 DOI: 10.1186/1471-2180-10-30] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Accepted: 01/29/2010] [Indexed: 11/29/2022] Open
Abstract
Background The Gram-negative bacterium Yersinia pestis is the causative agent of the bubonic plague. Efficient iron acquisition systems are critical to the ability of Y. pestis to infect, spread and grow in mammalian hosts, because iron is sequestered and is considered part of the innate host immune defence against invading pathogens. We used a proteomic approach to determine expression changes of iron uptake systems and intracellular consequences of iron deficiency in the Y. pestis strain KIM6+ at two physiologically relevant temperatures (26°C and 37°C). Results Differential protein display was performed for three Y. pestis subcellular fractions. Five characterized Y. pestis iron/siderophore acquisition systems (Ybt, Yfe, Yfu, Yiu and Hmu) and a putative iron/chelate outer membrane receptor (Y0850) were increased in abundance in iron-starved cells. The iron-sulfur (Fe-S) cluster assembly system Suf, adapted to oxidative stress and iron starvation in E. coli, was also more abundant, suggesting functional activity of Suf in Y. pestis under iron-limiting conditions. Metabolic and reactive oxygen-deactivating enzymes dependent on Fe-S clusters or other iron cofactors were decreased in abundance in iron-depleted cells. This data was consistent with lower activities of aconitase and catalase in iron-starved vs. iron-rich cells. In contrast, pyruvate oxidase B which metabolizes pyruvate via electron transfer to ubiquinone-8 for direct utilization in the respiratory chain was strongly increased in abundance and activity in iron-depleted cells. Conclusions Many protein abundance differences were indicative of the important regulatory role of the ferric uptake regulator Fur. Iron deficiency seems to result in a coordinated shift from iron-utilizing to iron-independent biochemical pathways in the cytoplasm of Y. pestis. With growth temperature as an additional variable in proteomic comparisons of the Y. pestis fractions (26°C and 37°C), there was little evidence for temperature-specific adaptation processes to iron starvation.
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Affiliation(s)
- Rembert Pieper
- J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.
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