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Micaletto M, Fleurier S, Dion S, Denamur E, Matic I. The protein carboxymethyltransferase-dependent aspartate salvage pathway plays a crucial role in the intricate metabolic network of Escherichia coli. SCIENCE ADVANCES 2024; 10:eadj0767. [PMID: 38335294 PMCID: PMC10857468 DOI: 10.1126/sciadv.adj0767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 01/11/2024] [Indexed: 02/12/2024]
Abstract
Protein carboxymethyltransferase (Pcm) is a highly evolutionarily conserved enzyme that initiates the conversion of abnormal isoaspartate to aspartate residues. While it is commonly believed that Pcm facilitates the repair of damaged proteins, a number of observations suggest that it may have another role in cell functioning. We investigated whether Pcm provides a means for Escherichia coli to recycle aspartate, which is essential for protein synthesis and other cellular processes. We showed that Pcm is required for the energy production, the maintenance of cellular redox potential and of S-adenosylmethionine synthesis, which are critical for the proper functioning of many metabolic pathways. Pcm contributes to the full growth capacity both under aerobic and anaerobic conditions. Last, we showed that Pcm enhances the robustness of bacteria when exposed to sublethal antibiotic treatments and improves their fitness in the mammalian urinary tract. We propose that Pcm plays a crucial role in E. coli metabolism by ensuring a steady supply of aspartate.
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Affiliation(s)
- Maureen Micaletto
- Institut Cochin, Université Paris Cité, INSERM U1016, CNRS UMR 8104, 75014 Paris, France
| | - Sebastien Fleurier
- Institut Cochin, Université Paris Cité, INSERM U1016, CNRS UMR 8104, 75014 Paris, France
| | - Sara Dion
- IAME, Université de Paris, INSERM U1137, Université Sorbonne Paris Nord, 75018 Paris, France
| | - Erick Denamur
- IAME, Université de Paris, INSERM U1137, Université Sorbonne Paris Nord, 75018 Paris, France
- AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, 75018 Paris, France
| | - Ivan Matic
- Institut Cochin, Université Paris Cité, INSERM U1016, CNRS UMR 8104, 75014 Paris, France
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2
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Fereshteh S, Noori Goodarzi N, Sepehr A, Shafiei M, Ajdary S, Badmasti F. In Silico Analyses of Extracellular Proteins of Acinetobacter baumannii as Immunogenic Candidates. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH 2022; 21:e126559. [PMID: 36060914 PMCID: PMC9420209 DOI: 10.5812/ijpr-126559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/11/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022]
Abstract
Background: Acinetobacter baumannii is an important nosocomial pathogen causing high morbidity and mortality in immunocompromised patients with prolonged hospitalization. Multidrug-resistant A. baumannii infections are on the rise worldwide. Therefore, the discovery of an effective vaccine against this bacterium seems necessary as a cost-effective and preventive strategy. Methods: In this present study, 35 genomes of A. baumannii strains were considered, and the extracellular proteins were selected, maximally having one transmembrane helix with high adhesion probability and no similarity to host proteins, as immunogenic candidates using the web tool Vaxign. Subsequently, the role of these selected proteins in bacterial pathogenesis was investigated using VICMpred. Then, the major histocompatibility complex class II, linear B-cell epitopes, and conservation of epitopes were identified using the Immune Epitope Database, BepiPred, and Epitope Conservancy Analysis, respectively. Finally, the B-cell discontinuous epitopes of each protein were predicted using ElliPro and plotted on the three-dimensional structure (3D) of the proteins. The role of the unknown proteins was predicted using the STRING database. Results: In this study, eight acceptable immunogenic candidates, including FilF, FimA, putative acid phosphatase, putative exported protein, subtilisin-like serine protease, and three uncharacterized proteins, were identified in A. baumannii. Conclusions: The results of the STRING database showed that these three uncharacterized proteins play a role in nutrition (heme utilization), peptide bond cleavage (serine peptidases), and cellular processes (MlaD protein). Extracellular proteins might play a catalyst role in the outer membrane protein-based vaccine of A. baumannii. Furthermore, this study proposed a list of potent immunogenic candidates of extracellular proteins.
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Affiliation(s)
| | | | - Amin Sepehr
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Morvarid Shafiei
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Soheila Ajdary
- Department of Immunology, Pasteur Institute of Iran, Tehran, Iran
| | - Farzad Badmasti
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
- Corresponding Author: Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran.
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3
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Huang PJ, Huang CY, Li YX, Liu YC, Chu LJ, Yeh YM, Cheng WH, Chen RM, Lee CC, Chen LC, Lin HC, Chiu SF, Lin WN, Lyu PC, Tang P, Huang KY. Dissecting the Transcriptomes of Multiple Metronidazole-Resistant and Sensitive Trichomonas vaginalis Strains Identified Distinct Genes and Pathways Associated with Drug Resistance and Cell Death. Biomedicines 2021; 9:biomedicines9121817. [PMID: 34944632 PMCID: PMC8698965 DOI: 10.3390/biomedicines9121817] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/25/2021] [Accepted: 11/30/2021] [Indexed: 12/20/2022] Open
Abstract
Trichomonas vaginalis is the causative agent of trichomoniasis, the most prevalent non-viral sexually transmitted infection worldwide. Metronidazole (MTZ) is the mainstay of anti-trichomonal chemotherapy; however, drug resistance has become an increasingly worrying issue. Additionally, the molecular events of MTZ-induced cell death in T. vaginalis remain elusive. To gain insight into the differential expression of genes related to MTZ resistance and cell death, we conducted RNA-sequencing of three paired MTZ-resistant (MTZ-R) and MTZ-sensitive (MTZ-S) T. vaginalis strains treated with or without MTZ. Comparative transcriptomes analysis identified that several putative drug-resistant genes were exclusively upregulated in different MTZ-R strains, such as ATP-binding cassette (ABC) transporters and multidrug resistance pumps. Additionally, several shared upregulated genes among all the MTZ-R transcriptomes were not previously identified in T. vaginalis, such as 5′-nucleotidase surE and Na+-driven multidrug efflux pump, which are a potential stress response protein and a multidrug and toxic compound extrusion (MATE)-like protein, respectively. Functional enrichment analysis revealed that purine and pyrimidine metabolisms were suppressed in MTZ-S parasites upon drug treatment, whereas the endoplasmic reticulum-associated degradation (ERAD) pathway, proteasome, and ubiquitin-mediated proteolysis were strikingly activated, highlighting the novel pathways responsible for drug-induced stress. Our work presents the most detailed analysis of the transcriptional changes and the regulatory networks associated with MTZ resistance and MTZ-induced signaling, providing insights into MTZ resistance and cell death mechanisms in trichomonads.
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Affiliation(s)
- Po-Jung Huang
- Department of Biomedical Sciences, Chang Gung University, Taoyuan City 333, Taiwan;
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taoyuan City 333, Taiwan; (Y.-M.Y.); (C.-C.L.)
| | - Ching-Yun Huang
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei City 114, Taiwan; (C.-Y.H.); (S.-F.C.)
- Host-Parasite Interactions Laboratory, National Defense Medical Center, Taipei City 114, Taiwan
| | - Yu-Xuan Li
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan City 333, Taiwan; (Y.-X.L.); (L.-J.C.); (P.T.)
| | - Yi-Chung Liu
- Institute of Bioinformatics and Structural Biology, Department of Life Science, National Tsing Hua University, Hsinchu 300, Taiwan; (Y.-C.L.); (P.-C.L.)
| | - Lichieh-Julie Chu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan City 333, Taiwan; (Y.-X.L.); (L.-J.C.); (P.T.)
- Molecular Medicine Research Center, Chang Gung University, Taoyuan City 333, Taiwan
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan City 333, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taoyuan City 333, Taiwan; (Y.-M.Y.); (C.-C.L.)
| | - Wei-Hung Cheng
- Department of Medical Laboratory Science, College of Medicine, I-Shou University, Kaohsiung City 824, Taiwan;
| | - Ruei-Ming Chen
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei City 114, Taiwan; (R.-M.C.); (H.-C.L.)
| | - Chi-Ching Lee
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taoyuan City 333, Taiwan; (Y.-M.Y.); (C.-C.L.)
- Department of Computer Science and Information Engineering, Chang Gung University, Taoyuan City 333, Taiwan
| | - Lih-Chyang Chen
- Department of Medicine, Mackay Medical College, New Taipei City 252, Taiwan;
| | - Hsin-Chung Lin
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei City 114, Taiwan; (R.-M.C.); (H.-C.L.)
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei City 114, Taiwan
| | - Shu-Fang Chiu
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei City 114, Taiwan; (C.-Y.H.); (S.-F.C.)
- Host-Parasite Interactions Laboratory, National Defense Medical Center, Taipei City 114, Taiwan
- Department of Inspection, Taipei City Hospital, Renai Branch, Taipei City 114, Taiwan
| | - Wei-Ning Lin
- Graduate Institute of Biomedical and Pharmaceutical Science, Fu Jen Catholic University, New Taipei City 242, Taiwan;
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, Department of Life Science, National Tsing Hua University, Hsinchu 300, Taiwan; (Y.-C.L.); (P.-C.L.)
| | - Petrus Tang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan City 333, Taiwan; (Y.-X.L.); (L.-J.C.); (P.T.)
| | - Kuo-Yang Huang
- Host-Parasite Interactions Laboratory, National Defense Medical Center, Taipei City 114, Taiwan
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei City 114, Taiwan
- Correspondence: ; Tel.: +886-2-87923100 (ext. 18564)
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Tan Y, Wang C, Schneider T, Li H, de Souza RF, Tang X, Swisher Grimm KD, Hsieh TF, Wang X, Li X, Zhang D. Comparative Phylogenomic Analysis Reveals Evolutionary Genomic Changes and Novel Toxin Families in Endophytic Liberibacter Pathogens. Microbiol Spectr 2021; 9:e0050921. [PMID: 34523996 PMCID: PMC8557891 DOI: 10.1128/spectrum.00509-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/10/2021] [Indexed: 01/02/2023] Open
Abstract
Liberibacter pathogens are the causative agents of several severe crop diseases worldwide, including citrus Huanglongbing and potato zebra chip. These bacteria are endophytic and nonculturable, which makes experimental approaches challenging and highlights the need for bioinformatic analysis in advancing our understanding about Liberibacter pathogenesis. Here, we performed an in-depth comparative phylogenomic analysis of the Liberibacter pathogens and their free-living, nonpathogenic, ancestral species, aiming to identify major genomic changes and determinants associated with their evolutionary transitions in living habitats and pathogenicity. Using gene neighborhood analysis and phylogenetic classification, we systematically uncovered, annotated, and classified all prophage loci into four types, including one previously unrecognized group. We showed that these prophages originated through independent gene transfers at different evolutionary stages of Liberibacter and only the SC-type prophage was associated with the emergence of the pathogens. Using ortholog clustering, we vigorously identified two additional sets of genomic genes, which were either lost or gained in the ancestor of the pathogens. Consistent with the habitat change, the lost genes were enriched for biosynthesis of cellular building blocks. Importantly, among the gained genes, we uncovered several previously unrecognized toxins, including new toxins homologous to the EspG/VirA effectors, a YdjM phospholipase toxin, and a secreted endonuclease/exonuclease/phosphatase (EEP) protein. Our results substantially extend the knowledge of the evolutionary events and potential determinants leading to the emergence of endophytic, pathogenic Liberibacter species, which will facilitate the design of functional experiments and the development of new methods for detection and blockage of these pathogens. IMPORTANCELiberibacter pathogens are associated with several severe crop diseases, including citrus Huanglongbing, the most destructive disease to the citrus industry. Currently, no effective cure or treatments are available, and no resistant citrus variety has been found. The fact that these obligate endophytic pathogens are not culturable has made it extremely challenging to experimentally uncover the genes/proteins important to Liberibacter pathogenesis. Further, earlier bioinformatics studies failed to identify key genomic determinants, such as toxins and effector proteins, that underlie the pathogenicity of the bacteria. In this study, an in-depth comparative genomic analysis of Liberibacter pathogens along with their ancestral nonpathogenic species identified the prophage loci and several novel toxins that are evolutionarily associated with the emergence of the pathogens. These results shed new light on the disease mechanism of Liberibacter pathogens and will facilitate the development of new detection and blockage methods targeting the toxins.
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Affiliation(s)
- Yongjun Tan
- Department of Biology, College of Arts & Sciences, Saint Louis University, St. Louis, Missouri, USA
| | - Cindy Wang
- Department of Biology, College of Arts & Sciences, Saint Louis University, St. Louis, Missouri, USA
| | - Theresa Schneider
- Department of Biology, College of Arts & Sciences, Saint Louis University, St. Louis, Missouri, USA
| | - Huan Li
- Department of Biology, College of Arts & Sciences, Saint Louis University, St. Louis, Missouri, USA
| | - Robson Francisco de Souza
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Xueming Tang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Kylie D. Swisher Grimm
- United States Department of Agriculture—Agricultural Research Service, Temperate Tree Fruit and Vegetable Research Unit, Prosser, Washington, USA
| | - Tzung-Fu Hsieh
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
- Plants for Human Health Institute, North Carolina State University, Kannapolis, North Carolina, USA
| | - Xu Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, Alabama, USA
- Alabama Agricultural Experiment Station, Auburn University, Auburn, Alabama, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Xu Li
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
- Plants for Human Health Institute, North Carolina State University, Kannapolis, North Carolina, USA
| | - Dapeng Zhang
- Department of Biology, College of Arts & Sciences, Saint Louis University, St. Louis, Missouri, USA
- Bioinformatics and Computational Biology Program, College of Arts & Sciences, Saint Louis University, St. Louis, Missouri, USA
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5
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Machado ATP, Fonseca EMB, Reis MAD, Saraiva AM, Santos CAD, de Toledo MAS, Polikarpov I, de Souza AP, Aparicio R, Iulek J. Conformational variability of the stationary phase survival protein E from Xylella fastidiosa revealed by X-ray crystallography, small-angle X-ray scattering studies, and normal mode analysis. Proteins 2017; 85:1931-1943. [PMID: 28677327 DOI: 10.1002/prot.25347] [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: 01/10/2017] [Revised: 06/07/2017] [Accepted: 07/02/2017] [Indexed: 11/05/2022]
Abstract
Xylella fastidiosa is a xylem-limited bacterium that infects a wide variety of plants. Stationary phase survival protein E is classified as a nucleotidase, which is expressed when bacterial cells are in the stationary growth phase and subjected to environmental stresses. Here, we report four refined X-ray structures of this protein from X. fastidiosa in four different crystal forms in the presence and/or absence of the substrate 3'-AMP. In all chains, the conserved loop verified in family members assumes a closed conformation in either condition. Therefore, the enzymatic mechanism for the target protein might be different of its homologs. Two crystal forms exhibit two monomers whereas the other two show four monomers in the asymmetric unit. While the biological unit has been characterized as a tetramer, differences of their sizes and symmetry are remarkable. Four conformers identified by Small-Angle X-ray Scattering (SAXS) in a ligand-free solution are related to the low frequency normal modes of the crystallographic structures associated with rigid body-like protomer arrangements responsible for the longitudinal and symmetric adjustments between tetramers. When the substrate is present in solution, only two conformers are selected. The most prominent conformer for each case is associated to a normal mode able to elongate the protein by moving apart two dimers. To our knowledge, this work was the first investigation based on the normal modes that analyzed the quaternary structure variability for an enzyme of the SurE family followed by crystallography and SAXS validation. The combined results raise new directions to study allosteric features of XfSurE protein.
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Affiliation(s)
| | | | - Marcelo Augusto Dos Reis
- Institute of Chemistry, University of Campinas, São Paulo, Brazil.,Federal Institute of Education, Science and Technology of South of Minas Gerais, Inconfidentes, Minas Gerais, Brazil
| | - Antonio Marcos Saraiva
- Molecular Biology and Genetic Engineering Centre, University of Campinas, São Paulo, Brazil
| | | | | | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo, Brazil
| | - Anete Pereira de Souza
- Molecular Biology and Genetic Engineering Centre, University of Campinas, São Paulo, Brazil.,Department of Plant Biology, Biology Institute, University of Campinas, São Paulo, Brazil
| | - Ricardo Aparicio
- Institute of Chemistry, University of Campinas, São Paulo, Brazil
| | - Jorge Iulek
- Department of Chemistry, State University of Ponta Grossa, Brazil
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6
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Mathiharan YK, Pappachan A, Savithri HS, Murthy MRN. Dramatic structural changes resulting from the loss of a crucial hydrogen bond in the hinge region involved in C-terminal helix swapping in SurE: a survival protein from Salmonella typhimurium. PLoS One 2013; 8:e55978. [PMID: 23409101 PMCID: PMC3567009 DOI: 10.1371/journal.pone.0055978] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 01/04/2013] [Indexed: 11/30/2022] Open
Abstract
Domain swapping is an interesting feature of some oligomeric proteins in which each protomer of the oligomer provides an identical surface for exclusive interaction with a segment or domain belonging to another protomer. Here we report results of mutagenesis experiments on the structure of C-terminal helix swapped dimer of a stationary phase survival protein from Salmonella typhimurium (StSurE). Wild type StSurE is a dimer in which a large helical segment at the C-terminus and a tetramerization loop comprising two β strands are swapped between the protomers. Key residues in StSurE that might promote C-terminal helix swapping were identified by sequence and structural comparisons. Three mutants in which the helix swapping is likely to be avoided were constructed and expressed in E. coli. Three-dimensional X-ray crystal structures of the mutants H234A and D230A/H234A could be determined at 2.1 Å and 2.35 Å resolutions, respectively. Contrary to expectations, helix swapping was mostly retained in both the mutants. The loss of the crucial D230 OD2– H234 NE2 hydrogen bond (2.89 Å in the wild type structure) in the hinge region was compensated by new inter and intra-chain interactions. However, the two fold molecular symmetry was lost and there were large conformational changes throughout the polypeptide. In spite of these changes, the dimeric structure and an approximate tetrameric organization were retained, probably due to the interactions involving the tetramerization loop. Mutants were mostly functionally inactive, highlighting the importance of precise inter-subunit interactions for the symmetry and function of StSurE.
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Affiliation(s)
| | - Anju Pappachan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - H. S. Savithri
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Mathur R. N. Murthy
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- * E-mail:
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7
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dos Reis MA, Saraiva AM, dos Santos ML, de Souza AP, Aparicio R. Crystallization and preliminary X-ray analysis of stationary phase survival protein E (SurE) from Xylella fastidiosa in two crystal forms. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:464-7. [PMID: 22505421 PMCID: PMC3325821 DOI: 10.1107/s1744309112007129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 02/16/2012] [Indexed: 11/10/2022]
Abstract
The bacterium Xylella fastidiosa is a phytopathogenic organism that causes citrus variegated chlorosis, a disease which attacks economically important crops, mainly oranges. In this communication, the crystallization and preliminary X-ray crystallographic analysis of XfSurE, a survival protein E from X. fastidiosa, are reported. Data were collected for two crystal forms, I and II, to 1.93 and 2.9 Å resolution, respectively. Crystal form I belonged to space group C2, with unit-cell parameters a = 172.36, b = 84.18, c = 87.24 Å, α = γ = 90, β = 96.59°, whereas crystal form II belonged to space group C2, with unit-cell parameters a = 88.05, b = 81.26, c = 72.84 Å, α = γ = 90, β = 94.76°.
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Affiliation(s)
- Marcelo Augusto dos Reis
- Laboratory of Structural Biology and Crystallography, Institute of Chemistry, University of Campinas, CP 6154, 13084-862 Campinas-SP, Brazil
| | - Antonio Marcos Saraiva
- Plant Biology Department, Biology Institute, University of Campinas, CP 6010, 13083-875 Campinas-SP, Brazil
| | - Marcelo Leite dos Santos
- Laboratory of Structural Biology and Crystallography, Institute of Chemistry, University of Campinas, CP 6154, 13084-862 Campinas-SP, Brazil
| | - Anete Pereira de Souza
- Plant Biology Department, Biology Institute, University of Campinas, CP 6010, 13083-875 Campinas-SP, Brazil
- Genetic and Molecular Analysis Laboratory, Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas, CP 6010, 13083-970 Campinas-SP, Brazil
| | - Ricardo Aparicio
- Laboratory of Structural Biology and Crystallography, Institute of Chemistry, University of Campinas, CP 6154, 13084-862 Campinas-SP, Brazil
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Lau SK, Fan RY, Ho TC, Wong GK, Tsang AK, Teng JL, Chen W, Watt RM, Curreem SO, Tse H, Yuen KY, Woo PC. Environmental adaptability and stress tolerance of Laribacter hongkongensis: a genome-wide analysis. Cell Biosci 2011; 1:22. [PMID: 21711489 PMCID: PMC3135505 DOI: 10.1186/2045-3701-1-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 06/14/2011] [Indexed: 12/31/2022] Open
Abstract
Background Laribacter hongkongensis is associated with community-acquired gastroenteritis and traveler's diarrhea and it can reside in human, fish, frogs and water. In this study, we performed an in-depth annotation of the genes in its genome related to adaptation to the various environmental niches. Results L. hongkongensis possessed genes for DNA repair and recombination, basal transcription, alternative σ-factors and 109 putative transcription factors, allowing DNA repair and global changes in gene expression in response to different environmental stresses. For acid stress, it possessed a urease gene cassette and two arc gene clusters. For alkaline stress, it possessed six CDSs for transporters of the monovalent cation/proton antiporter-2 and NhaC Na+:H+ antiporter families. For heavy metals acquisition and tolerance, it possessed CDSs for iron and nickel transport and efflux pumps for other metals. For temperature stress, it possessed genes related to chaperones and chaperonins, heat shock proteins and cold shock proteins. For osmotic stress, 25 CDSs were observed, mostly related to regulators for potassium ion, proline and glutamate transport. For oxidative and UV light stress, genes for oxidant-resistant dehydratase, superoxide scavenging, hydrogen peroxide scavenging, exclusion and export of redox-cycling antibiotics, redox balancing, DNA repair, reduction of disulfide bonds, limitation of iron availability and reduction of iron-sulfur clusters are present. For starvation, it possessed phosphorus and, despite being asaccharolytic, carbon starvation-related CDSs. Conclusions The L. hongkongensis genome possessed a high variety of genes for adaptation to acid, alkaline, temperature, osmotic, oxidative, UV light and starvation stresses and acquisition of and tolerance to heavy metals.
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Affiliation(s)
- Susanna Kp Lau
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,Carol Yu Centre of Infection, The University of Hong Kong, Hong Kong.,Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Rachel Yy Fan
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Tom Cc Ho
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Gilman Km Wong
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Alan Kl Tsang
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Jade Ll Teng
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Wenyang Chen
- Faculty of Dentistry, The University of Hong Kong, Hong Kong
| | - Rory M Watt
- Faculty of Dentistry, The University of Hong Kong, Hong Kong
| | | | - Herman Tse
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,Carol Yu Centre of Infection, The University of Hong Kong, Hong Kong.,Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,Carol Yu Centre of Infection, The University of Hong Kong, Hong Kong.,Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Patrick Cy Woo
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,Carol Yu Centre of Infection, The University of Hong Kong, Hong Kong.,Department of Microbiology, The University of Hong Kong, Hong Kong
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9
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Antonyuk SV, Ellis MJ, Strange RW, Bessho Y, Kuramitsu S, Shinkai A, Yokoyama S, Hasnain SS. Structure of SurE protein from Aquifex aeolicus VF5 at 1.5 A resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:1204-8. [PMID: 20054112 DOI: 10.1107/s1744309109043814] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Accepted: 10/22/2009] [Indexed: 11/10/2022]
Abstract
SurE is a stationary-phase survival protein found in bacteria, eukaryotes and archaea that exhibits a divalent-metal-ion-dependent phosphatase activity and acts as a nucleotidase and polyphosphate phosphohydrolase. The structure of the SurE protein from the hyperthermophile Aquifex aeolicus has been solved at 1.5 A resolution using molecular replacement with one dimer in the asymmetric unit and refined to an R factor of 15.6%. The crystal packing reveals that two dimers assemble to form a tetramer, although gel-filtration chromatography showed the presence of only a dimer in solution. The phosphatase active-site pocket was occupied by sulfate ions from the crystallization medium.
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Affiliation(s)
- Svetlana V Antonyuk
- Molecular Biophysics Group, School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
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10
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Saraiva AM, Reis MA, Tada SF, Rosselli-Murai LK, Schneider DRS, Pelloso AC, Toledo MAS, Giles C, Aparicio R, de Souza AP. Functional and small-angle X-ray scattering studies of a new stationary phase survival protein E (SurE) from Xylella fastidiosa--evidence of allosteric behaviour. FEBS J 2009; 276:6751-62. [PMID: 19843181 DOI: 10.1111/j.1742-4658.2009.07390.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The genome data of bacterium Xylella fastidiosa strain 9a5c has identified several orfs related to its phytopathogenic adaptation and survival. Among these genes, the surE codifies a survival protein E (XfSurE) whose function is not so well understood, but functional assays in Escherichia coli revealed nucleotidase and exopolyphosphate activity. In the present study, we report the XfSurE protein overexpression in E. coli and its purification. The overall secondary structure was analyzed by CD. Small-angle X-ray scattering and gel filtration techniques demonstrated that the oligomeric state of the protein in solution is a tetramer. In addition, functional kinetics experiments were carried out with several monophosphate nucleoside substrates and revealed a highly positive cooperativity. An allosteric mechanism involving torsion movements in solution is proposed to explain the cooperative behaviour of XfSurE. This is the first characterization of a SurE enzyme from a phytopathogen organism and, to our knowledge, the first solution structure of a SurE protein to be described.
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Affiliation(s)
- Antonio M Saraiva
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, Campinas São Paulo, Brazil
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11
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Tidhar A, Flashner Y, Cohen S, Levi Y, Zauberman A, Gur D, Aftalion M, Elhanany E, Zvi A, Shafferman A, Mamroud E. The NlpD lipoprotein is a novel Yersinia pestis virulence factor essential for the development of plague. PLoS One 2009; 4:e7023. [PMID: 19759820 PMCID: PMC2736372 DOI: 10.1371/journal.pone.0007023] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Accepted: 08/13/2009] [Indexed: 12/22/2022] Open
Abstract
Yersinia pestis is the causative agent of plague. Previously we have isolated an attenuated Y. pestis transposon insertion mutant in which the pcm gene was disrupted. In the present study, we investigated the expression and the role of pcm locus genes in Y. pestis pathogenesis using a set of isogenic surE, pcm, nlpD and rpoS mutants of the fully virulent Kimberley53 strain. We show that in Y. pestis, nlpD expression is controlled from elements residing within the upstream genes surE and pcm. The NlpD lipoprotein is the only factor encoded from the pcm locus that is essential for Y. pestis virulence. A chromosomal deletion of the nlpD gene sequence resulted in a drastic reduction in virulence to an LD(50) of at least 10(7) cfu for subcutaneous and airway routes of infection. The mutant was unable to colonize mouse organs following infection. The filamented morphology of the nlpD mutant indicates that NlpD is involved in cell separation; however, deletion of nlpD did not affect in vitro growth rate. Trans-complementation experiments with the Y. pestis nlpD gene restored virulence and all other phenotypic defects. Finally, we demonstrated that subcutaneous administration of the nlpD mutant could protect animals against bubonic and primary pneumonic plague. Taken together, these results demonstrate that Y. pestis NlpD is a novel virulence factor essential for the development of bubonic and pneumonic plague. Further, the nlpD mutant is superior to the EV76 prototype live vaccine strain in immunogenicity and in conferring effective protective immunity. Thus it could serve as a basis for a very potent live vaccine against bubonic and pneumonic plague.
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Affiliation(s)
- Avital Tidhar
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Yehuda Flashner
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Sara Cohen
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Yinon Levi
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Ayelet Zauberman
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - David Gur
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Moshe Aftalion
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Eytan Elhanany
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Anat Zvi
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Avigdor Shafferman
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Emanuelle Mamroud
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
- * E-mail:
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12
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Gonçalves AMD, Rêgo AT, Thomaz M, Enguita FJ, Carrondo MA. Expression, purification, crystallization and preliminary X-ray characterization of two crystal forms of stationary-phase survival E protein from Campylobacter jejuni. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:213-6. [PMID: 18323612 PMCID: PMC2374147 DOI: 10.1107/s1744309108003096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2007] [Accepted: 01/28/2008] [Indexed: 11/10/2022]
Abstract
Survival E (SurE) protein from Campylobacter jejuni, a Gram-negative mesophile, has been overexpressed in Escherichia coli as a soluble protein, successfully purified and crystallized in two distinct crystal forms. The first form belongs to space group P2(1)2(1)2(1), with a tetramer in the asymmetric unit and unit-cell parameters a = 80.5, b = 119.0, c = 135.3 A. The second form belongs to space group C2, with unit-cell parameters a = 121.4, b = 47.1, c = 97.8 A, and contains a dimer in the asymmetric unit. Diffraction data have been collected from these crystal forms to 2.5 and 2.95 A resolution, respectively.
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Affiliation(s)
- A. M. D. Gonçalves
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras, Portugal
| | - A. T. Rêgo
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras, Portugal
| | - M. Thomaz
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2748-901 Oeiras, Portugal
| | - F. J. Enguita
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras, Portugal
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - M. A. Carrondo
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras, Portugal
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13
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Iwasaki W, Miki K. Crystal structure of the stationary phase survival protein SurE with metal ion and AMP. J Mol Biol 2007; 371:123-36. [PMID: 17561111 DOI: 10.1016/j.jmb.2007.05.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Revised: 04/28/2007] [Accepted: 05/03/2007] [Indexed: 11/30/2022]
Abstract
The stationary phase survival protein SurE is a metal ion-dependent phosphatase distributed among eubacteria, archaea, and eukaryotes. In Escherichia coli, SurE has activities as nucleotidase and exopolyphosphatase, and is thought to be involved in stress response. However, its physiological role and reaction mechanism are unclear. We report here the crystal structures of the tetramer of SurE from Thermus thermophilus HB8 (TtSurE) both alone and crystallized with Mn(2+) and substrate AMP. In the presence of Mn(2+) and AMP, differences between the protomers were observed in the active site and in the loop located near the active site; AMP-bound active sites with the loops in a novel open conformation were found in the two protomers, and AMP-free active sites with the loops in a conventional closed conformation were found in the other two protomers. The two loops in the open conformation are entwined with each other, and this entwining is suggested to be required for enzymatic activity by site-directed mutagenesis. TtSurE exists as an equilibrium mixture of dimer and tetramer in solution. The loop-entwined structure indicates that SurE acts as a tetramer. The structural features and the absence of negative cooperativity imply the half-of-the-sites reactivity mechanism resulting from a pre-existing tendency toward structural asymmetry.
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Affiliation(s)
- Wakana Iwasaki
- RIKEN SPring-8 Center at Harima Institute, Koto 1-1-1, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
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14
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Hicks WM, Kotlajich MV, Visick JE. Recovery from long-term stationary phase and stress survival in Escherichia coli require the L-isoaspartyl protein carboxyl methyltransferase at alkaline pH. MICROBIOLOGY-SGM 2005; 151:2151-2158. [PMID: 16000706 DOI: 10.1099/mic.0.27835-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The L-isoaspartyl protein carboxyl methyltransferase (pcm) can stimulate repair of isoaspartyl residues arising spontaneously in proteins to normal L-aspartyl residues. PCM is needed in Escherichia coli for maximal long-term survival when exposed to oxidative stress, osmotic stress, repeated heat stress or methanol. The effect of pH on a pcm mutant during long-term stationary phase was examined. PCM was not required for long-term survival of E. coli subjected to pH stress alone; however, PCM-deficient cells showed impaired resistance to paraquat and methanol only at elevated pH. The mutant also showed stress-survival phenotypes in minimal medium buffered to pH 9.0. Accumulation of isoaspartyl residues was accelerated at pH 8.0 or 9.0 in vivo, though PCM-deficient cells did not show higher levels of damage. However, the pcm mutant displayed an extended lag phase in recovering from stationary phase at pH 9.0. Protein repair by PCM thus plays a key role in long-term stress survival only at alkaline pH in E. coli, and it may function primarily to repair damage in cells that are recovering from nutrient limitation and in those cells that are able to divide during long-term stationary phase.
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Affiliation(s)
- Wade M Hicks
- Department of Biology, North Central College, Naperville, IL 60540, USA
| | | | - Jonathan E Visick
- Department of Biology, North Central College, Naperville, IL 60540, USA
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15
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Núñez C, Adams L, Childers S, Lovley DR. The RpoS sigma factor in the dissimilatory Fe(III)-reducing bacterium Geobacter sulfurreducens. J Bacteriol 2004; 186:5543-6. [PMID: 15292160 PMCID: PMC490870 DOI: 10.1128/jb.186.16.5543-5546.2004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Geobacter sulfurreducens RpoS sigma factor was shown to contribute to survival in stationary phase and upon oxygen exposure. Furthermore, a mutation in rpoS decreased the rate of reduction of insoluble Fe(III) but not of soluble forms of iron. This study suggests that RpoS plays a role in regulating metabolism of Geobacter under suboptimal conditions in subsurface environments.
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Affiliation(s)
- Cinthia Núñez
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003, USA.
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16
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Mura C, Katz JE, Clarke SG, Eisenberg D. Structure and function of an archaeal homolog of survival protein E (SurEalpha): an acid phosphatase with purine nucleotide specificity. J Mol Biol 2003; 326:1559-75. [PMID: 12595266 DOI: 10.1016/s0022-2836(03)00056-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The survival protein E (SurE) family was discovered by its correlation to stationary phase survival of Escherichia coli and various repair proteins involved in sustaining this and other stress-response phenotypes. In order to better understand this ancient and well-conserved protein family, we have determined the 2.0A resolution crystal structure of SurEalpha from the hyperthermophilic crenarchaeon Pyrobaculum aerophilum (Pae). This first structure of an archaeal SurE reveals significant similarities to and differences from the only other known SurE structure, that from the eubacterium Thermatoga maritima (Tma). Both SurE monomers adopt similar folds; however, unlike the Tma SurE dimer, crystalline Pae SurEalpha is predominantly non-domain swapped. Comparative structural analyses of Tma and Pae SurE suggest conformationally variant regions, such as a hinge loop that may be involved in domain swapping. The putative SurE active site is highly conserved, and implies a model for SurE bound to a potential substrate, guanosine-5'-monophosphate (GMP). Pae SurEalpha has optimal acid phosphatase activity at temperatures above 90 degrees C, and is less specific than Tma SurE in terms of metal ion requirements. Substrate specificity also differs between Pae and Tma SurE, with a more specific recognition of purine nucleotides by the archaeal enzyme. Analyses of the sequences, phylogenetic distribution, and genomic organization of the SurE family reveal examples of genomes encoding multiple surE genes, and suggest that SurE homologs constitute a broad family of enzymes with phosphatase-like activities.
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Affiliation(s)
- Cameron Mura
- Howard Hughes Medical Institute and UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, 201 Boyer Hall, Box 951570, Los Angeles, CA 90095-1570, USA
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17
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Testerman TL, Vazquez-Torres A, Xu Y, Jones-Carson J, Libby SJ, Fang FC. The alternative sigma factor sigmaE controls antioxidant defences required for Salmonella virulence and stationary-phase survival. Mol Microbiol 2002; 43:771-82. [PMID: 11929531 DOI: 10.1046/j.1365-2958.2002.02787.x] [Citation(s) in RCA: 143] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bacteria must contend with conditions of nutrient limitation in all natural environments. Complex programmes of gene expression, controlled in part by the alternative sigma factors sigmaS (sigma38, RpoS) and sigmaH (sigma32, RpoH), allow a number of bacterial species to survive conditions of partial or complete starvation. We show here that the alternative sigma factor sigmaE (sigma24, RpoE) also facilitates the survival of Salmonella typhimurium under conditions of nutrient deprivation. Expression of the sigmaE regulon is strongly induced upon entry of Salmonella into stationary phase. A Salmonella mutant lacking sigmaE has reduced survival during stationary phase as well as increased susceptibility to oxidative stress. A Salmonella strain lacking both sigmaE and sigmaS is non-viable after just 24 h in stationary phase, but survival of these mutants is completely preserved under anaerobic stationary-phase conditions, suggesting that oxidative injury is one of the major mechanisms of reduced microbial viability during periods of nutrient deprivation. Moreover, the attenuated virulence of sigmaE-deficient Salmonella for mice can be largely restored by genetic abrogation of the host phagocyte respiratory burst, suggesting that the sigmaE regulon plays an important antioxidant role during Salmonella infection of mammalian hosts.
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Affiliation(s)
- Traci L Testerman
- Department of Medicine, University of Colorado Health Sciences Center, Denver, CO 80262, USA
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18
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Zhang RG, Skarina T, Katz J, Beasley S, Khachatryan A, Vyas S, Arrowsmith C, Clarke S, Edwards A, Joachimiak A, Savchenko A. Structure of Thermotoga maritima stationary phase survival protein SurE: a novel acid phosphatase. Structure 2001; 9:1095-106. [PMID: 11709173 PMCID: PMC2792002 DOI: 10.1016/s0969-2126(01)00675-x] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
BACKGROUND The rpoS, nlpD, pcm, and surE genes are among many whose expression is induced during the stationary phase of bacterial growth. rpoS codes for the stationary-phase RNA polymerase sigma subunit, and nlpD codes for a lipoprotein. The pcm gene product repairs damaged proteins by converting the atypical isoaspartyl residues back to L-aspartyls. The physiological and biochemical functions of surE are unknown, but its importance in stress is supported by the duplication of the surE gene in E. coli subjected to high-temperature growth. The pcm and surE genes are highly conserved in bacteria, archaea, and plants. RESULTS The structure of SurE from Thermotoga maritima was determined at 2.0 A. The SurE monomer is composed of two domains; a conserved N-terminal domain, a Rossman fold, and a C-terminal oligomerization domain, a new fold. Monomers form a dimer that assembles into a tetramer. Biochemical analysis suggests that SurE is an acid phosphatase, with an optimum pH of 5.5-6.2. The active site was identified in the N-terminal domain through analysis of conserved residues. Structure-based site-directed point mutations abolished phosphatase activity. T. maritima SurE intra- and intersubunit salt bridges were identified that may explain the SurE thermostability. CONCLUSIONS The structure of SurE provided information about the protein's fold, oligomeric state, and active site. The protein possessed magnesium-dependent acid phosphatase activity, but the physiologically relevant substrate(s) remains to be identified. The importance of three of the assigned active site residues in catalysis was confirmed by site-directed mutagenesis.
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Affiliation(s)
- R.-G. Zhang
- Biosciences Division and Structural Biology Center, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, Illinois 60439
| | - T. Skarina
- Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
| | - J.E. Katz
- Department of Chemistry and Biochemistry and The Molecular Biology Institute, University of California, Los Angeles, California, 90024
| | - S. Beasley
- Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
| | - A. Khachatryan
- Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
| | - S. Vyas
- Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
| | - C.H. Arrowsmith
- Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
| | - S. Clarke
- Department of Chemistry and Biochemistry and The Molecular Biology Institute, University of California, Los Angeles, California, 90024
- Correspondence: (A.J.), (A.E.), (S.C.)
| | - A. Edwards
- Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
- Clinical Genomics Centre/Proteomics, University Health Network, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Correspondence: (A.J.), (A.E.), (S.C.)
| | - A. Joachimiak
- Biosciences Division and Structural Biology Center, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, Illinois 60439
- Correspondence: (A.J.), (A.E.), (S.C.)
| | - A. Savchenko
- Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
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Weichart DH, Kell DB. Characterization of an autostimulatory substance produced by Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2001; 147:1875-1885. [PMID: 11429464 DOI: 10.1099/00221287-147-7-1875] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The recovery of dilute populations of stationary phase cells of Escherichia coli was studied using an automatic growth analyser. The addition of 30% supernatant from 2-d-old stationary phase cells of the organism reproducibly shortened the apparent lag times by 22-57.5%, depending on the age of the inoculum. True lag times, as determined by colony counts, of stationary phase cells were reduced by supernatant addition by 41-62%. The growth-stimulating substance was characterized and partly purified from supernatants: the active material was shown to be dialysable, heat-stable, acid- and alkali-stable and protease-resistant. Extraction with ethyl acetate or ion-exchange resins was not successful, but the active material could be quantitatively extracted with ethanol after saturation with salt. It is concluded that the active substance is a small, non-proteinaceous, non-ionic organic molecule. Separation of extracts by HPLC indicated that the stimulatory substance is weakly hydrophobic and has retention times similar to those of uracil. So far, however, the exact chemical identity of the active substance has not been elucidated.
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Affiliation(s)
- Dieter H Weichart
- Institute of Biological Sciences, Cledwyn Building, University of Wales, Aberystwyth SY23 3DD, UK1
| | - Douglas B Kell
- Institute of Biological Sciences, Cledwyn Building, University of Wales, Aberystwyth SY23 3DD, UK1
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20
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Abstract
We present a summary of recent progress in understanding Escherichia coli K-12 gene and protein functions. New information has come both from classical biological experimentation and from using the analytical tools of functional genomics. The content of the E. coli genome can clearly be seen to contain elements acquired by horizontal transfer. Nevertheless, there is probably a large, stable core of >3500 genes that are shared among all E. coli strains. The gene-enzyme relationship is examined, and, in many cases, it exhibits complexity beyond a simple one-to-one relationship. Also, the E. coli genome can now be seen to contain many multiple enzymes that carry out the same or closely similar reactions. Some are similar in sequence and may share common ancestry; some are not. We discuss the concept of a minimal genome as being variable among organisms and obligatorily linked to their life styles and defined environmental conditions. We also address classification of functions of gene products and avenues of insight into the history of protein evolution.
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Affiliation(s)
- M Riley
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA. ,
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