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Feng Y, Wang Z, Chien KY, Chen HL, Liang YH, Hua X, Chiu CH. "Pseudo-pseudogenes" in bacterial genomes: Proteogenomics reveals a wide but low protein expression of pseudogenes in Salmonella enterica. Nucleic Acids Res 2022; 50:5158-5170. [PMID: 35489061 PMCID: PMC9122581 DOI: 10.1093/nar/gkac302] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/11/2022] [Accepted: 04/14/2022] [Indexed: 12/03/2022] Open
Abstract
Pseudogenes (genes disrupted by frameshift or in-frame stop codons) are ubiquitously present in the bacterial genome and considered as nonfunctional fossil. Here, we used RNA-seq and mass-spectrometry technologies to measure the transcriptomes and proteomes of Salmonella enterica serovars Paratyphi A and Typhi. All pseudogenes’ mRNA sequences remained disrupted, and were present at comparable levels to their intact homologs. At the protein level, however, 101 out of 161 pseudogenes suggested successful translation, with their low expression regardless of growth conditions, genetic background and pseudogenization causes. The majority of frameshifting detected was compensatory for -1 frameshift mutations. Readthrough of in-frame stop codons primarily involved UAG; and cytosine was the most frequent base adjacent to the codon. Using a fluorescence reporter system, fifteen pseudogenes were confirmed to express successfully in vivo in Escherichia coli. Expression of the intact copy of the fifteen pseudogenes in S. Typhi affected bacterial pathogenesis as revealed in human macrophage and epithelial cell infection models. The above findings suggest the need to revisit the nonstandard translation mechanism as well as the biological role of pseudogenes in the bacterial genome.
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Affiliation(s)
- Ye Feng
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Zeyu Wang
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Kun-Yi Chien
- Graduate Institute of Biomedical Sciences, Chang Gung University College of Medicine, Taoyuan, Republic of China
| | - Hsiu-Ling Chen
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Republic of China
| | - Yi-Hua Liang
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Republic of China
| | - Xiaoting Hua
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Cheng-Hsun Chiu
- Graduate Institute of Biomedical Sciences, Chang Gung University College of Medicine, Taoyuan, Republic of China.,Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Republic of China.,Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Republic of China
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Analysis of In Vivo Transcriptome of Intracellular Bacterial Pathogen Salmonella enterica serovar Typhmurium Isolated from Mouse Spleen. Pathogens 2021; 10:pathogens10070823. [PMID: 34209260 PMCID: PMC8308634 DOI: 10.3390/pathogens10070823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/28/2021] [Accepted: 06/28/2021] [Indexed: 11/16/2022] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) is an important intracellular pathogen that poses a health threat to humans. This study tries to clarify the mechanism of Salmonella survival and reproduction in the host. In this study, high-throughput sequencing analysis was performed on RNA extracted from the strains isolated from infected mouse spleens and an S. Typhimurium reference strain (ATCC 14028) based on the BGISEQ-500 platform. A total of 1340 significant differentially expressed genes (DEGs) were screened. Functional annotation revealed DEGs associated with regulation, metabolism, transport and binding, pathogenesis, and motility. Through data mining and literature retrieval, 26 of the 58 upregulated DEGs (FPKM > 10) were not reported to be related to the adaptation to intracellular survival and were classified as candidate key genes (CKGs) for survival and proliferation in vivo. Our data contribute to our understanding of the mechanisms used by Salmonella to regulate virulence gene expression whilst replicating inside mammalian cells.
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Röder J, Felgner P, Hensel M. Comprehensive Single Cell Analyses of the Nutritional Environment of Intracellular Salmonella enterica. Front Cell Infect Microbiol 2021; 11:624650. [PMID: 33834004 PMCID: PMC8021861 DOI: 10.3389/fcimb.2021.624650] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 01/25/2021] [Indexed: 12/11/2022] Open
Abstract
The facultative intracellular pathogen Salmonella enterica Typhimurium (STM) resides in a specific membrane-bound compartment termed the Salmonella-containing vacuole (SCV). STM is able to obtain all nutrients required for rapid proliferation, although being separated from direct access to host cell metabolites. The formation of specific tubular membrane compartments, called Salmonella-induced filaments (SIFs) are known to provides bacterial nutrition by giving STM access to endocytosed material and enabling proliferation. Additionally, STM expresses a range of nutrient uptake system for growth in nutrient limited environments to overcome the nutrition depletion inside the host. By utilizing dual fluorescence reporters, we shed light on the nutritional environment of intracellular STM in various host cells and distinct intracellular niches. We showed that STM uses nutrients of the host cell and adapts uniquely to the different nutrient conditions. In addition, we provide further evidence for improved nutrient supply by SIF formation or presence in the cytosol of epithelial cells, and the correlation of nutrient supply to bacterial proliferation.
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Affiliation(s)
- Jennifer Röder
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Pascal Felgner
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Michael Hensel
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
- CellNanOs – Center of Cellular Nanoanalytics, Fachbereich Biologie/Chemie, Universität Osnabrück, Osnabrück, Germany
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Novel DNA Binding and Regulatory Activities for σ 54 (RpoN) in Salmonella enterica Serovar Typhimurium 14028s. J Bacteriol 2017; 199:JB.00816-16. [PMID: 28373272 DOI: 10.1128/jb.00816-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 03/27/2017] [Indexed: 01/13/2023] Open
Abstract
The variable sigma (σ) subunit of the bacterial RNA polymerase (RNAP) holoenzyme, which is responsible for promoter specificity and open complex formation, plays a strategic role in the response to environmental changes. Salmonella enterica serovar Typhimurium utilizes the housekeeping σ70 and five alternative sigma factors, including σ54 The σ54-RNAP differs from other σ-RNAP holoenzymes in that it forms a stable closed complex with the promoter and requires ATP hydrolysis by an activated cognate bacterial enhancer binding protein (bEBP) to transition to an open complex and initiate transcription. In S. Typhimurium, σ54-dependent promoters normally respond to one of 13 different bEBPs, each of which is activated under a specific growth condition. Here, we utilized a constitutively active, promiscuous bEBP to perform a genome-wide identification of σ54-RNAP DNA binding sites and the transcriptome of the σ54 regulon of S. Typhimurium. The position and context of many of the identified σ54 RNAP DNA binding sites suggest regulatory roles for σ54-RNAP that connect the σ54 regulon to regulons of other σ factors to provide a dynamic response to rapidly changing environmental conditions.IMPORTANCE The alternative sigma factor σ54 (RpoN) is required for expression of genes involved in processes with significance in agriculture, bioenergy production, bioremediation, and host-microbe interactions. The characterization of the σ54 regulon of the versatile pathogen S. Typhimurium has expanded our understanding of the scope of the σ54 regulon and how it links to other σ regulons within the complex regulatory network for gene expression in bacteria.
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Tran TK, Han QQ, Shi Y, Guo L. A comparative proteomic analysis of Salmonella typhimurium under the regulation of the RstA/RstB and PhoP/PhoQ systems. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1686-1695. [PMID: 27618760 DOI: 10.1016/j.bbapap.2016.09.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 08/23/2016] [Accepted: 09/08/2016] [Indexed: 11/17/2022]
Abstract
In pathogenic bacteria, the two-component regulatory systems (TCSs) play important roles in signal transduction and regulation of their pathogenesis. Here, we used quantitative proteomic methods to comparatively analyze functional networks under the control of the RstA/RstB system versus the PhoP/PhoQ system in Salmonella typhimurium. By comparing the proteomic profile from a wild-type strain to that from a ΔrstB strain or a ΔphoPQ strain under a condition known to activate these TCSs, we found that the levels of 159 proteins representing 6.92% of the 2297 proteins identified from the ΔrstB strain and 341 proteins representing 14.9% of the 2288 proteins identified from the ΔphoPQ strain were significantly changed, respectively. Bioinformatics analysis revealed that the RstA/RstB system and the PhoP/PhoQ system coordinated with regard to the regulation of specific proteins as well as metabolic processes. Our observations suggested that the regulatory networks controlled by the PhoP/PhoQ system were much more extensive than those by the RstA/RstB system, whereas the RstA/RstB system specifically regulated expression of the constituents participating in pyrimidine metabolism and iron acquisition. Additional results also suggested that the RstA/RstB system was required for regulation of Salmonella motility and invasion.
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Affiliation(s)
- Trung-Kien Tran
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China; Hung Vuong University, Phu Tho, Vietnam
| | - Qiang-Qiang Han
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yixin Shi
- The School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA; The Center for Infectious Diseases and Vaccinology at the Biodesign Institute, Arizona State University, Tempe, AZ 85287-4501, USA.
| | - Lin Guo
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China.
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Proteomic Analyses of Intracellular Salmonella enterica Serovar Typhimurium Reveal Extensive Bacterial Adaptations to Infected Host Epithelial Cells. Infect Immun 2015; 83:2897-906. [PMID: 25939512 DOI: 10.1128/iai.02882-14] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 04/27/2015] [Indexed: 12/22/2022] Open
Abstract
Salmonella species can gain access into nonphagocytic cells, where the bacterium proliferates in a unique membrane-bounded compartment. In order to reveal bacterial adaptations to their intracellular niche, here we conducted the first comprehensive proteomic survey of Salmonella isolated from infected epithelial cells. Among ∼ 3,300 identified bacterial proteins, we found that about 100 proteins were significantly altered at the onset of Salmonella intracellular replication. In addition to substantially increased iron-uptake capacities, bacterial high-affinity manganese and zinc transporters were also upregulated, suggesting an overall limitation of metal ions in host epithelial cells. We also found that Salmonella induced multiple phosphate utilization pathways. Furthermore, our data suggested upregulation of the two-component PhoPQ system as well as of many downstream virulence factors under its regulation. Our survey also revealed that intracellular Salmonella has increased needs for certain amino acids and biotin. In contrast, Salmonella downregulated glycerol and maltose utilization as well as chemotaxis pathways.
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Mass spectrometry-based proteomic approaches to study pathogenic bacteria-host interactions. Protein Cell 2015; 6:265-74. [PMID: 25722051 PMCID: PMC4383758 DOI: 10.1007/s13238-015-0136-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 01/21/2015] [Indexed: 02/08/2023] Open
Abstract
Elucidation of molecular mechanisms underlying host-pathogen interactions is important for control and treatment of infectious diseases worldwide. Within the last decade, mass spectrometry (MS)-based proteomics has become a powerful and effective approach to better understand complex and dynamic host-pathogen interactions at the protein level. Herein we will review the recent progress in proteomic analyses towards bacterial infection of their mammalian host with a particular focus on enteric pathogens. Large-scale studies of dynamic proteomic alterations during infection will be discussed from the perspective of both pathogenic bacteria and host cells.
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Correia S, Nunes-Miranda JD, Pinto L, Santos HM, de Toro M, Sáenz Y, Torres C, Capelo JL, Poeta P, Igrejas G. Complete proteome of a quinolone-resistant Salmonella Typhimurium phage type DT104B clinical strain. Int J Mol Sci 2014; 15:14191-219. [PMID: 25196519 PMCID: PMC4159846 DOI: 10.3390/ijms150814191] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 06/27/2014] [Accepted: 07/25/2014] [Indexed: 11/26/2022] Open
Abstract
Salmonellosis is one of the most common and widely distributed foodborne diseases. The emergence of Salmonella strains that are resistant to a variety of antimicrobials is a serious global public health concern. Salmonella enterica serovar Typhimurium definitive phage type 104 (DT104) is one of these emerging epidemic multidrug resistant strains. Here we collate information from the diverse and comprehensive range of experiments on Salmonella proteomes that have been published. We then present a new study of the proteome of the quinolone-resistant Se20 strain (phage type DT104B), recovered after ciprofloxacin treatment and compared it to the proteome of reference strain SL1344. A total of 186 and 219 protein spots were recovered from Se20 and SL1344 protein extracts, respectively, after two-dimensional gel electrophoresis. The signatures of 94% of the protein spots were successfully identified through matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS). Three antimicrobial resistance related proteins, whose genes were previously detected by polymerase chain reaction (PCR), were identified in the clinical strain. The presence of these proteins, dihydropteroate synthase type-2 (sul2 gene), aminoglycoside resistance protein A (strA gene) and aminoglycoside 6'-N-acetyltransferase type Ib-cr4 (aac(6')-Ib-cr4 gene), was confirmed in the DT104B clinical strain. The aac(6')-Ib-cr4 gene is responsible for plasmid-mediated aminoglycoside and quinolone resistance. This is a preliminary analysis of the proteome of these two S. Typhimurium strains and further work is being developed to better understand how antimicrobial resistance is developing in this pathogen.
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Affiliation(s)
- Susana Correia
- Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal.
| | - Júlio D Nunes-Miranda
- Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal.
| | - Luís Pinto
- Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal.
| | - Hugo M Santos
- BIOSCOPE group, REQUIMTE-CQFB, Chemistry Department, Faculty of Science and Technology, University NOVA of Lisbon, 2829-516 Monte de Caparica, Portugal.
| | - María de Toro
- Departamento de Biología Molecular (Universidad de Cantabria) and Instituto de Biomedicina y Biotecnología de Cantabria IBBTEC (UC-SODERCAN-CSIC), Santander 39011, Spain.
| | - Yolanda Sáenz
- Microbiología Molecular, Centro de Investigación Biomédica de La Rioja, C/Piqueras 98, 26006 Logroño, La Rioja, Spain.
| | - Carmen Torres
- Microbiología Molecular, Centro de Investigación Biomédica de La Rioja, C/Piqueras 98, 26006 Logroño, La Rioja, Spain.
| | - José Luis Capelo
- BIOSCOPE group, REQUIMTE-CQFB, Chemistry Department, Faculty of Science and Technology, University NOVA of Lisbon, 2829-516 Monte de Caparica, Portugal.
| | - Patrícia Poeta
- Centre of Studies of Animal and Veterinary Sciences, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal.
| | - Gilberto Igrejas
- Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal.
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9
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Ramachandran VK, Shearer N, Thompson A. The primary transcriptome of Salmonella enterica Serovar Typhimurium and its dependence on ppGpp during late stationary phase. PLoS One 2014; 9:e92690. [PMID: 24664308 PMCID: PMC3963941 DOI: 10.1371/journal.pone.0092690] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 02/24/2014] [Indexed: 12/01/2022] Open
Abstract
We have used differential RNA-seq (dRNA-seq) to characterise the transcriptomic architecture of S. Typhimurium SL1344, and its dependence on the bacterial alarmone, guanosine tetraphosphate (ppGpp) during late stationary phase, (LSP). Under LSP conditions we were able to identify the transcriptional start sites (TSSs) for 53% of the S. Typhimurium open reading frames (ORFs) and discovered 282 candidate non-coding RNAs (ncRNAs). The mapping of LSP TSSs enabled a detailed comparison with a previous dRNA-seq study of the early stationary phase (ESP) transcriptional architecture of S. Typhimurium SL1344 and its dependence on ppGpp. For the purposes of this study, LSP was defined as an aerobic LB culture grown to a later optical density reading (OD600 = 3.6) compared to ESP (OD600 = 2.3). The precise nucleotide positions of the majority of S. Typhimurium TSSs at LSP agreed closely with those identified at ESP. However, the identification of TSSs at different positions, or where additional or fewer TSSs were found at LSP compared to ESP enabled the genome-wide categorisation of growth phase dependent changes in promoter structure, the first time such an analysis has been done on this scale. Comparison of the ppGpp-dependency LSP and ESP TSSs for mRNAs and ncRNAs revealed a similar breadth of ppGpp-activation and repression. However, we note several ncRNAs previously shown to be involved in virulence were highly ppGpp-dependent at LSP. Finally, although SPI1 was expressed at ESP, we found SPI1 was not as highly expressed at LSP, instead we observed elevated expression of SPI2 encoded genes. We therefore also report an analysis of SPI2 transcriptional architecture at LSP resulting in localisation of SsrB binding sites and identification of a previously unreported SPI2 TSS. We also show that ppGpp is required for nearly all of SPI2 expression at LSP as well as for expression of SPI1 at ESP.
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Affiliation(s)
| | - Neil Shearer
- Institute of Food Research, Norwich, United Kingdom
| | - Arthur Thompson
- Institute of Food Research, Norwich, United Kingdom
- * E-mail:
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Wang Y, Huang KY, Huo Y. Proteomic comparison between Salmonella Typhimurium and Salmonella Typhi. J Microbiol 2014; 52:71-6. [PMID: 24390840 DOI: 10.1007/s12275-014-3204-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 07/30/2013] [Accepted: 08/05/2013] [Indexed: 11/26/2022]
Abstract
The genus Salmonella contains more than 2500 serovars. While most cause the self-limiting gastroenteritis, a few serovars can elicit typhoid fever, a severe systemic infection. S. enterica subsp. enterica serovar Typhimurium and S. Typhi are the representatives of the gastroenteritis and typhoid fever types of Salmonella. In this study, we adopted Stable Isotope Labeling with Amino acids in Cell culture (SILAC) technology to quantitatively compare the proteomes of the two serovars. We found several proteins with serovar-specific expression, which could be developed as new biomarkers for clinical serotype diagnosis. We found that flagella and chemotaxis genes were down-regulated in S. Typhi in comparison with S. Typhimurium. We attributed this observation to the fact that the smooth cellular structure of S. Typhi may better fit its systemic lifestyle. Instead of known virulence factors that were located within Salmonella Pathogenecity Islands, a number of core genes, which were involved in metabolism and transport of carbohydrates and amino acids, showed differential expression between the two serovars. Further studies on the roles of these differentially-expressed genes in the pathogenesis should be undertaken.
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Affiliation(s)
- Yue Wang
- Department of Gynecology and Obstetrics, Women's Hospital School of Medicine Zhejiang University, Hangzhou, P. R. China
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Pieper R, Zhang Q, Clark DJ, Parmar PP, Alami H, Suh MJ, Kuntumalla S, Braisted JC, Huang ST, Tzipori S. Proteomic View of Interactions of Shiga Toxin-Producing Escherichia coli with the Intestinal Environment in Gnotobiotic Piglets. PLoS One 2013; 8:e66462. [PMID: 23840478 PMCID: PMC3686733 DOI: 10.1371/journal.pone.0066462] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 05/05/2013] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Shiga toxin (Stx)-producing Escherichia coli cause severe intestinal infections involving colonization of epithelial Peyer's patches and formation of attachment/effacement (A/E) lesions. These lesions trigger leukocyte infiltration followed by inflammation and intestinal hemorrhage. Systems biology, which explores the crosstalk of Stx-producing Escherichia coli with the in vivo host environment, may elucidate novel molecular pathogenesis aspects. METHODOLOGY/PRINCIPAL FINDINGS Enterohemorrhagic E. coli strain 86-24 produces Shiga toxin-2 and belongs to the serotype O157:H7. Bacterial cells were scrapped from stationary phase cultures (the in vitro condition) and used to infect gnotobiotic piglets via intestinal lavage. Bacterial cells isolated from the piglets' guts constituted the in vivo condition. Cell lysates were subjected to quantitative 2D gel and shotgun proteomic analyses, revealing metabolic shifts towards anaerobic energy generation, changes in carbon utilization, phosphate and ammonia starvation, and high activity of a glutamate decarboxylase acid resistance system in vivo. Increased abundance of pyridine nucleotide transhydrogenase (PntA and PntB) suggested in vivo shortage of intracellular NADPH. Abundance changes of proteins implicated in lipopolysaccharide biosynthesis (LpxC, ArnA, the predicted acyltransferase L7029) and outer membrane (OM) assembly (LptD, MlaA, MlaC) suggested bacterial cell surface modulation in response to activated host defenses. Indeed, there was evidence for interactions of innate immunity-associated proteins secreted into the intestines (GP340, REG3-γ, resistin, lithostathine, and trefoil factor 3) with the bacterial cell envelope. SIGNIFICANCE Proteomic analysis afforded insights into system-wide adaptations of strain 86-24 to a hostile intestinal milieu, including responses to limited nutrients and cofactor supplies, intracellular acidification, and reactive nitrogen and oxygen species-mediated stress. Protein and lipopolysaccharide compositions of the OM were altered. Enhanced expression of type III secretion system effectors correlated with a metabolic shift back to a more aerobic milieu in vivo. Apparent pathogen pattern recognition molecules from piglet intestinal secretions adhered strongly to the bacterial cell surface.
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Affiliation(s)
- Rembert Pieper
- J. Craig Venter Institute, Rockville, Maryland, United States of America
- * E-mail:
| | - Quanshun Zhang
- Division of Infectious Diseases, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | - David J. Clark
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | | | - Hamid Alami
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Moo-Jin Suh
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | | | - John C. Braisted
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Shih-Ting Huang
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Saul Tzipori
- Division of Infectious Diseases, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
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Denkel LA, Rhen M, Bange FC. Biotin sulfoxide reductase contributes to oxidative stress tolerance and virulence in Salmonella enterica serovar Typhimurium. MICROBIOLOGY-SGM 2013; 159:1447-1458. [PMID: 23657680 DOI: 10.1099/mic.0.067256-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Oxidative stress converts sulfur residues of molecules like biotin and methionine into their oxidized forms. Here we show that the biotin sulfoxide reductase BisC of Salmonella enterica serovar Typhimurium (S. Typhimurium) repairs both oxidized biotin and oxidized methionine. Exposure to H2O2 in vitro reduced survival of a S. Typhimurium ΔbisC mutant. Furthermore, replication of the ΔbisC mutant inside IFN-γ activated macrophages was reduced. In vitro tolerance of the mutant to H2O2 was restored by plasmids carrying either bisC or msrA; the latter encodes a methioinine sulfoxide reductase. In contrast, the proliferation defect inside IFN-γ activated macrophages was rescued by bisC but not by msrA. Thus growth of the ΔbisC mutant in IFN-γ activated macrophages required repair of oxidized biotin. Both the ΔbisC and a biotin auxotrophic (ΔbioB) mutant were attenuated in mice, suggesting that besides biotin biosynthesis, biotin repair was essential for virulence of S. Typhimurium in vivo. Attenuation of the ΔbisC mutant was more pronounced in 129 mice that produce a stronger oxidative response. These results show that BisC is essential for full virulence of Salmonella by contributing to the defence of S. Typhimurium against host-derived stress, and provides an attractive drug target since it is not present in mammals.
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Affiliation(s)
- Luisa A Denkel
- Dept. of Medical Microbiology and Hospital Epidemiology, Medical School Hannover, 30625 Hannover, Germany
| | - Mikael Rhen
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, 17177 Stockholm, Sweden
| | - Franz-Christoph Bange
- Dept. of Medical Microbiology and Hospital Epidemiology, Medical School Hannover, 30625 Hannover, Germany
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A Comprehensive Subcellular Proteomic Survey of Salmonella Grown under Phagosome-Mimicking versus Standard Laboratory Conditions. INTERNATIONAL JOURNAL OF PROTEOMICS 2012; 2012:123076. [PMID: 22900174 PMCID: PMC3410353 DOI: 10.1155/2012/123076] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 06/06/2012] [Indexed: 11/17/2022]
Abstract
Towards developing a systems-level pathobiological understanding of Salmonella enterica, we performed a subcellular proteomic analysis of this pathogen grown under standard laboratory and phagosome-mimicking conditions in vitro. Analysis of proteins from cytoplasmic, inner membrane, periplasmic, and outer membrane fractions yielded coverage of 25% of the theoretical proteome. Confident subcellular location could be assigned to over 1000 proteins, with good agreement between experimentally observed location and predicted/known protein properties. Comparison of protein location under the different environmental conditions provided insight into dynamic protein localization and possible moonlighting (multiple function) activities. Notable examples of dynamic localization were the response regulators of two-component regulatory systems (e.g., ArcB and PhoQ). The DNA-binding protein Dps that is generally regarded as cytoplasmic was significantly enriched in the outer membrane for all growth conditions examined, suggestive of moonlighting activities. These observations imply the existence of unknown transport mechanisms and novel functions for a subset of Salmonella proteins. Overall, this work provides a catalog of experimentally verified subcellular protein locations for Salmonella and a framework for further investigations using computational modeling.
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14
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Role of antigens and virulence factors of Salmonella enterica serovar Typhi in its pathogenesis. Microbiol Res 2012; 167:199-210. [DOI: 10.1016/j.micres.2011.08.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 08/05/2011] [Accepted: 08/08/2011] [Indexed: 12/25/2022]
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Collado-Romero M, Martins RP, Arce C, Moreno Á, Lucena C, Carvajal A, Garrido JJ. An in vivo proteomic study of the interaction between Salmonella Typhimurium and porcine ileum mucosa. J Proteomics 2012; 75:2015-26. [DOI: 10.1016/j.jprot.2012.01.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 12/08/2011] [Accepted: 01/01/2012] [Indexed: 11/29/2022]
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16
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Cooper B, Chen R, Garrett WM, Murphy C, Chang C, Tucker ML, Bhagwat AA. Proteomic Pleiotropy of OpgGH, an Operon Necessary for Efficient Growth of Salmonella enterica serovar Typhimurium under Low-Osmotic Conditions. J Proteome Res 2012; 11:1720-7. [DOI: 10.1021/pr200933d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
| | - Ruiqiang Chen
- Department of Cell Biology and
Molecular Genetics, University of Maryland, College Park, Maryland 20742, United States
| | | | | | - Caren Chang
- Department of Cell Biology and
Molecular Genetics, University of Maryland, College Park, Maryland 20742, United States
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17
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Ansong C, Tolić N, Purvine SO, Porwollik S, Jones M, Yoon H, Payne SH, Martin JL, Burnet MC, Monroe ME, Venepally P, Smith RD, Peterson SN, Heffron F, McClelland M, Adkins JN. Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium. BMC Genomics 2011; 12:433. [PMID: 21867535 PMCID: PMC3174948 DOI: 10.1186/1471-2164-12-433] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 08/25/2011] [Indexed: 12/22/2022] Open
Abstract
Background Complete and accurate genome annotation is crucial for comprehensive and systematic studies of biological systems. However, determining protein-coding genes for most new genomes is almost completely performed by inference using computational predictions with significant documented error rates (> 15%). Furthermore, gene prediction programs provide no information on biologically important post-translational processing events critical for protein function. Results We experimentally annotated the bacterial pathogen Salmonella Typhimurium 14028, using "shotgun" proteomics to accurately uncover the translational landscape and post-translational features. The data provide protein-level experimental validation for approximately half of the predicted protein-coding genes in Salmonella and suggest revisions to several genes that appear to have incorrectly assigned translational start sites, including a potential novel alternate start codon. Additionally, we uncovered 12 non-annotated genes missed by gene prediction programs, as well as evidence suggesting a role for one of these novel ORFs in Salmonella pathogenesis. We also characterized post-translational features in the Salmonella genome, including chemical modifications and proteolytic cleavages. We find that bacteria have a much larger and more complex repertoire of chemical modifications than previously thought including several novel modifications. Our in vivo proteolysis data identified more than 130 signal peptide and N-terminal methionine cleavage events critical for protein function. Conclusion This work highlights several ways in which application of proteomics data can improve the quality of genome annotations to facilitate novel biological insights and provides a comprehensive proteome map of Salmonella as a resource for systems analysis.
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Affiliation(s)
- Charles Ansong
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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18
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McDermott JE, Yoon H, Nakayasu ES, Metz TO, Hyduke DR, Kidwai AS, Palsson BO, Adkins JN, Heffron F. Technologies and approaches to elucidate and model the virulence program of salmonella. Front Microbiol 2011; 2:121. [PMID: 21687430 PMCID: PMC3108385 DOI: 10.3389/fmicb.2011.00121] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 05/15/2011] [Indexed: 11/13/2022] Open
Abstract
Salmonella is a primary cause of enteric diseases in a variety of animals. During its evolution into a pathogenic bacterium, Salmonella acquired an elaborate regulatory network that responds to multiple environmental stimuli within host animals and integrates them resulting in fine regulation of the virulence program. The coordinated action by this regulatory network involves numerous virulence regulators, necessitating genome-wide profiling analysis to assess and combine efforts from multiple regulons. In this review we discuss recent high-throughput analytic approaches used to understand the regulatory network of Salmonella that controls virulence processes. Application of high-throughput analyses have generated large amounts of data and necessitated the development of computational approaches for data integration. Therefore, we also cover computer-aided network analyses to infer regulatory networks, and demonstrate how genome-scale data can be used to construct regulatory and metabolic systems models of Salmonella pathogenesis. Genes that are coordinately controlled by multiple virulence regulators under infectious conditions are more likely to be important for pathogenesis. Thus, reconstructing the global regulatory network during infection or, at the very least, under conditions that mimic the host cellular environment not only provides a bird's eye view of Salmonella survival strategy in response to hostile host environments but also serves as an efficient means to identify novel virulence factors that are essential for Salmonella to accomplish systemic infection in the host.
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Affiliation(s)
- Jason E. McDermott
- Computational Biology and Bioinformatics Group, Pacific Northwest National LaboratoryRichland, WA, USA
| | - Hyunjin Yoon
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences UniversityPortland, OR, USA
| | - Ernesto S. Nakayasu
- Biological Separations and Mass Spectroscopy Group, Pacific Northwest National LaboratoryRichland WA, USA
| | - Thomas O. Metz
- Biological Separations and Mass Spectroscopy Group, Pacific Northwest National LaboratoryRichland WA, USA
| | - Daniel R. Hyduke
- Systems Biology, University of California San DiegoSan Diego, CA, USA
| | - Afshan S. Kidwai
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences UniversityPortland, OR, USA
| | | | - Joshua N. Adkins
- Biological Separations and Mass Spectroscopy Group, Pacific Northwest National LaboratoryRichland WA, USA
| | - Fred Heffron
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences UniversityPortland, OR, USA
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19
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Yu JL, Guo L. Quantitative Proteomic Analysis of Salmonella enterica Serovar Typhimurium under PhoP/PhoQ Activation Conditions. J Proteome Res 2011; 10:2992-3002. [DOI: 10.1021/pr101177g] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Jian-Lan Yu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, P. R. China
| | - Lin Guo
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, P. R. China
- Key Laboratory of Analytical Chemistry for Biology, Medicine (Ministry of Education), Wuhan University, Wuhan, P. R. China
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