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Lopandić Z, Dragačević L, Popović D, Andjelković U, Minić R, Gavrović-Jankulović M. BanLec-eGFP Chimera as a Tool for Evaluation of Lectin Binding to High-Mannose Glycans on Microorganisms. Biomolecules 2021; 11:180. [PMID: 33525574 PMCID: PMC7912117 DOI: 10.3390/biom11020180] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/11/2022] Open
Abstract
Fluorescently labeled lectins are useful tools for in vivo and in vitro studies of the structure and function of tissues and various pathogens such as viruses, bacteria, and fungi. For the evaluation of high-mannose glycans present on various glycoproteins, a three-dimensional (3D) model of the chimera was designed from the crystal structures of recombinant banana lectin (BanLec, Protein Data Bank entry (PDB): 5EXG) and an enhanced green fluorescent protein (eGFP, PDB 4EUL) by applying molecular modeling and molecular mechanics and expressed in Escherichia coli. BanLec-eGFP, produced as a soluble cytosolic protein of about 42 kDa, revealed β-sheets (41%) as the predominant secondary structures, with the emission peak maximum detected at 509 nm (excitation wavelength 488 nm). More than 65% of the primary structure was confirmed by mass spectrometry. Competitive BanLec-eGFP binding to high mannose glycans of the influenza vaccine (Vaxigrip®) was shown in a fluorescence-linked lectin sorbent assay (FLLSA) with monosaccharides (mannose and glucose) and wild type BanLec and H84T BanLec mutant. BanLec-eGFP exhibited binding to mannose residues on different strains of Salmonella in flow cytometry, with especially pronounced binding to a Salmonella Typhi clinical isolate. BanLec-eGFP can be a useful tool for screening high-mannose glycosylation sites on different microorganisms.
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Affiliation(s)
- Zorana Lopandić
- Department of Biochemistry, Faculty of Chemistry, University of Belgrade, 11000 Belgrade, Serbia;
| | - Luka Dragačević
- Institute of Virology, Vaccines and Sera, 11152 Belgrade, Serbia; (L.D.); (R.M.)
| | - Dragan Popović
- Institute of Chemistry, Technology and Metallurgy, National Institute of the Republic of Serbia, University of Belgrade, 11000 Belgrade, Serbia; (D.P.); (U.A.)
| | - Uros Andjelković
- Institute of Chemistry, Technology and Metallurgy, National Institute of the Republic of Serbia, University of Belgrade, 11000 Belgrade, Serbia; (D.P.); (U.A.)
- Department of Biotechnology, University of Rijeka, 5100 Rijeka, Croatia
| | - Rajna Minić
- Institute of Virology, Vaccines and Sera, 11152 Belgrade, Serbia; (L.D.); (R.M.)
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2
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Martínez-Flores I, Pérez-Morales D, Sánchez-Pérez M, Paredes CC, Collado-Vides J, Salgado H, Bustamante VH. In silico clustering of Salmonella global gene expression data reveals novel genes co-regulated with the SPI-1 virulence genes through HilD. Sci Rep 2016; 6:37858. [PMID: 27886269 PMCID: PMC5122947 DOI: 10.1038/srep37858] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/02/2016] [Indexed: 01/04/2023] Open
Abstract
A wide variety of Salmonella enterica serovars cause intestinal and systemic infections to humans and animals. Salmonella Patogenicity Island 1 (SPI-1) is a chromosomal region containing 39 genes that have crucial virulence roles. The AraC-like transcriptional regulator HilD, encoded in SPI-1, positively controls the expression of the SPI-1 genes, as well as of several other virulence genes located outside SPI-1. In this study, we applied a clustering method to the global gene expression data of S. enterica serovar Typhimurium from the COLOMBOS database; thus genes that show an expression pattern similar to that of SPI-1 genes were selected. This analysis revealed nine novel genes that are co-expressed with SPI-1, which are located in different chromosomal regions. Expression analyses and protein-DNA interaction assays showed regulation by HilD for six of these genes: gtgE, phoH, sinR, SL1263 (lpxR) and SL4247 were regulated directly, whereas SL1896 was regulated indirectly. Interestingly, phoH is an ancestral gene conserved in most of bacteria, whereas the other genes show characteristics of genes acquired by Salmonella. A role in virulence has been previously demonstrated for gtgE, lpxR and sinR. Our results further expand the regulon of HilD and thus identify novel possible Salmonella virulence genes.
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Affiliation(s)
- Irma Martínez-Flores
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
| | - Deyanira Pérez-Morales
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
| | - Mishael Sánchez-Pérez
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
| | - Claudia C Paredes
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
| | - Julio Collado-Vides
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
| | - Heladia Salgado
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
| | - Víctor H Bustamante
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
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3
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Xu J, Nakamura S, Islam MS, Guo Y, Ihara K, Tomioka R, Masuda M, Yoneyama H, Isogai E. Mannose-Binding Lectin Inhibits the Motility of Pathogenic Salmonella by Affecting the Driving Forces of Motility and the Chemotactic Response. PLoS One 2016; 11:e0154165. [PMID: 27104738 PMCID: PMC4841586 DOI: 10.1371/journal.pone.0154165] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 04/08/2016] [Indexed: 01/05/2023] Open
Abstract
Mannose-binding lectin (MBL) is a key pattern recognition molecule in the lectin pathway of the complement system, an important component of innate immunity. MBL functions as an opsonin which enhances the sequential immune process such as phagocytosis. We here report an inhibitory effect of MBL on the motility of pathogenic bacteria, which occurs by affecting the energy source required for motility and the signaling pathway of chemotaxis. When Salmonella cells were treated with a physiological concentration of MBL, their motile fraction and free-swimming speed decreased. Rotation assays of a single flagellum showed that the flagellar rotation rate was significantly reduced by the addition of MBL. Measurements of the intracellular pH and membrane potential revealed that MBL affected a driving force for the Salmonella flagellum, the electrochemical potential difference of protons. We also found that MBL treatment increased the reversal frequency of Salmonella flagellar rotation, which interfered with the relative positive chemotaxis toward an attractive substrate. We thus propose that the motility inhibition effect of MBL may be secondarily involved in the attack against pathogens, potentially facilitating the primary role of MBL in the complement system.
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Affiliation(s)
- Jun Xu
- Department of Animal Microbiology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
- * E-mail: (SN); (JX)
| | - Shuichi Nakamura
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
- * E-mail: (SN); (JX)
| | - Md. Shafiqul Islam
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Yijie Guo
- Department of Immunobiology and Pathogenic Biology, Medical School of Xi’an Jiaotong University, Xi’an, China
| | - Kohei Ihara
- Department of Animal Microbiology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Rintaro Tomioka
- Department of Animal Microbiology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Mizuki Masuda
- Department of Animal Microbiology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Hiroshi Yoneyama
- Department of Animal Microbiology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Emiko Isogai
- Department of Animal Microbiology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
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4
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Hayward MR, Jansen VAA, Woodward MJ. Comparative genomics of Salmonella enterica serovars Derby and Mbandaka, two prevalent serovars associated with different livestock species in the UK. BMC Genomics 2013; 14:365. [PMID: 23725633 PMCID: PMC3680342 DOI: 10.1186/1471-2164-14-365] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 05/27/2013] [Indexed: 01/06/2023] Open
Abstract
Background Despite the frequent isolation of Salmonella enterica sub. enterica serovars Derby and Mbandaka from livestock in the UK and USA little is known about the biological processes maintaining their prevalence. Statistics for Salmonella isolations from livestock production in the UK show that S. Derby is most commonly associated with pigs and turkeys and S. Mbandaka with cattle and chickens. Here we compare the first sequenced genomes of S. Derby and S. Mbandaka as a basis for further analysis of the potential host adaptations that contribute to their distinct host species distributions. Results Comparative functional genomics using the RAST annotation system showed that predominantly mechanisms that relate to metabolite utilisation, in vivo and ex vivo persistence and pathogenesis distinguish S. Derby from S. Mbandaka. Alignment of the genome nucleotide sequences of S. Derby D1 and D2 and S. Mbandaka M1 and M2 with Salmonella pathogenicity islands (SPI) identified unique complements of genes associated with host adaptation. We also describe a new genomic island with a putative role in pathogenesis, SPI-23. SPI-23 is present in several S. enterica serovars, including S. Agona, S. Dublin and S. Gallinarum, it is absent in its entirety from S. Mbandaka. Conclusions We discovered a new 37 Kb genomic island, SPI-23, in the chromosome sequence of S. Derby, encoding 42 ORFS, ten of which are putative TTSS effector proteins. We infer from full-genome synonymous SNP analysis that these two serovars diverged, between 182kya and 625kya coinciding with the divergence of domestic pigs. The differences between the genomes of these serovars suggest they have been exposed to different stresses including, phage, transposons and prolonged externalisation. The two serovars possess distinct complements of metabolic genes; many of which cluster into pathways for catabolism of carbon sources.
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Affiliation(s)
- Matthew R Hayward
- Animal Health and Veterinary Laboratories Agency, Woodham Lane, New Haw, Addlestone, Surrey, UK.
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Prajapat MK, Saini S. Interplay between Fur and HNS in controlling virulence gene expression in Salmonella typhimurium. Comput Biol Med 2012; 42:1133-40. [PMID: 23040276 DOI: 10.1016/j.compbiomed.2012.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 09/08/2012] [Accepted: 09/11/2012] [Indexed: 01/04/2023]
Abstract
Salmonella enterica is responsible for a large number of diseases in a wide-range of hosts. Two of the global regulators involved in controlling gene expression during the infection cycle of the bacterium are Fur and HNS. In this paper, we demonstrate computationally that Fur and HNS have disproportionately high density of binding sites in the Pathogenicity Islands on the Salmonella chromosome. Moreover, the frequency of binding sites for the two proteins is correlated throughout the genome of the organism. These results indicate a complex interplay between Fur and HNS in regulating cellular global behavior.
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Affiliation(s)
- Mahendra Kumar Prajapat
- Chemical Engineering, Indian Institute of Technology Gandhinagar, VGEC Campus, Chandkheda, Ahmedabad, Gujarat 382424, India
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6
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Thioredoxin 1 participates in the activity of the Salmonella enterica serovar Typhimurium pathogenicity island 2 type III secretion system. J Bacteriol 2009; 191:6918-27. [PMID: 19767428 DOI: 10.1128/jb.00532-09] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The facultative intracellular pathogen Salmonella enterica serovar Typhimurium relies on its Salmonella pathogenicity island 2 (SPI2) type III secretion system (T3SS) for intracellular replication and virulence. We report that the oxidoreductase thioredoxin 1 (TrxA) and SPI2 are coinduced for expression under in vitro conditions that mimic an intravacuolar environment, that TrxA is needed for proper SPI2 activity under these conditions, and that TrxA is indispensable for SPI2 activity in both phagocytic and epithelial cells. Infection experiments in mice demonstrated that SPI2 strongly contributed to virulence in a TrxA-proficient background whereas SPI2 did not affect virulence in a trxA mutant. Complementation analyses using wild-type trxA or a genetically engineered trxA coding for noncatalytic TrxA showed that the catalytic activity of TrxA is essential for SPI2 activity in phagocytic cells whereas a noncatalytic variant of TrxA partially sustained SPI2 activity in epithelial cells and virulence in mice. These results show that TrxA is needed for the intracellular induction of SPI2 and provide new insights into the functional integration between catalytic and noncatalytic activities of TrxA and a bacterial T3SS in different settings of intracellular infections.
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Rodland KD, Adkins JN, Ansong C, Chowdhury S, Manes NP, Shi L, Yoon H, Smith RD, Heffron F. Use of high-throughput mass spectrometry to elucidate host-pathogen interactions in Salmonella. Future Microbiol 2009; 3:625-34. [PMID: 19072180 DOI: 10.2217/17460913.3.6.625] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Capabilities in mass spectrometry are evolving rapidly, with recent improvements in sensitivity, data analysis and, most important from the standpoint of this review, much higher throughput, allowing analysis of many samples in a single day. This short review describes how these improvements in mass spectrometry can be used to dissect host-pathogen interactions using Salmonella as a model system. This approach has enabled direct identification of the majority of annotated Salmonella proteins, quantitation of expression changes under various in vitro growth conditions and new insights into virulence and expression of Salmonella proteins within host cells. One of the most significant findings is that a relatively high percentage of all the annotated genes (>20%) in Salmonella are regulated post-transcriptionally. In addition, new and unexpected interactions have been identified for several Salmonella virulence regulators that involve protein-protein interactions, suggesting additional functions of these regulators in coordinating virulence expression. Overall high-throughput mass spectrometry provides a new view of host-pathogen interactions, emphasizing the protein products and defining how protein interactions determine the outcome of infection.
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Affiliation(s)
- Karin D Rodland
- Pacific Northwest National Laboratory, Richland, WA 99354, USA.
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8
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Lal S, Cheema S, Kalia VC. Phylogeny vs genome reshuffling: horizontal gene transfer. Indian J Microbiol 2008; 48:228-42. [PMID: 23100716 PMCID: PMC3450171 DOI: 10.1007/s12088-008-0034-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2008] [Accepted: 06/06/2008] [Indexed: 10/21/2022] Open
Abstract
The evolutionary events in organisms can be tracked to the transfer of genetic material. The inheritance of genetic material among closely related organisms is a slow evolutionary process. On the other hand, the movement of genes among distantly related species can account for rapid evolution. The later process has been quite evident in the appearance of antibiotic resistance genes among human and animal pathogens. Phylogenetic trees based on such genes and those involved in metabolic activities reflect the incongruencies in comparison to the 16S rDNA gene, generally used for taxonomic relationships. Such discrepancies in gene inheritance have been termed as horizontal gene transfer (HGT) events. In the post-genomic era, the explosion of known sequences through large-scale sequencing projects has unraveled the weakness of traditional 16S rDNA gene tree based evolutionary model. Various methods to scrutinize HGT events include atypical composition, abnormal sequence similarity, anomalous phylogenetic distribution, unusual phyletic patterns, etc. Since HGT generates greater genetic diversity, it is likely to increase resource use and ecosystem resilience.
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Affiliation(s)
- Sadhana Lal
- Microbial Biotechnology and Genomics; Institute of Genomics and Integrative Biology (CSIR), Delhi University Campus, Mall Road, Delhi, 110 007 India
| | - Simrita Cheema
- Microbial Biotechnology and Genomics; Institute of Genomics and Integrative Biology (CSIR), Delhi University Campus, Mall Road, Delhi, 110 007 India
| | - Vipin C. Kalia
- Microbial Biotechnology and Genomics; Institute of Genomics and Integrative Biology (CSIR), Delhi University Campus, Mall Road, Delhi, 110 007 India
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9
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Using the nucleotide substitution rate matrix to detect horizontal gene transfer. BMC Bioinformatics 2006; 7:476. [PMID: 17067382 PMCID: PMC1657035 DOI: 10.1186/1471-2105-7-476] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Accepted: 10/26/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Horizontal gene transfer (HGT) has allowed bacteria to evolve many new capabilities. Because transferred genes perform many medically important functions, such as conferring antibiotic resistance, improved detection of horizontally transferred genes from sequence data would be an important advance. Existing sequence-based methods for detecting HGT focus on changes in nucleotide composition or on differences between gene and genome phylogenies; these methods have high error rates. RESULTS First, we introduce a new class of methods for detecting HGT based on the changes in nucleotide substitution rates that occur when a gene is transferred to a new organism. Our new methods discriminate simulated HGT events with an error rate up to 10 times lower than does GC content. Use of models that are not time-reversible is crucial for detecting HGT. Second, we show that using combinations of multiple predictors of HGT offers substantial improvements over using any single predictor, yielding as much as a factor of 18 improvement in performance (a maximum reduction in error rate from 38% to about 3%). Multiple predictors were combined by using the random forests machine learning algorithm to identify optimal classifiers that separate HGT from non-HGT trees. CONCLUSION The new class of HGT-detection methods introduced here combines advantages of phylogenetic and compositional HGT-detection techniques. These new techniques offer order-of-magnitude improvements over compositional methods because they are better able to discriminate HGT from non-HGT trees under a wide range of simulated conditions. We also found that combining multiple measures of HGT is essential for detecting a wide range of HGT events. These novel indicators of horizontal transfer will be widely useful in detecting HGT events linked to the evolution of important bacterial traits, such as antibiotic resistance and pathogenicity.
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Joardar V, Lindeberg M, Jackson RW, Selengut J, Dodson R, Brinkac LM, Daugherty SC, Deboy R, Durkin AS, Giglio MG, Madupu R, Nelson WC, Rosovitz MJ, Sullivan S, Crabtree J, Creasy T, Davidsen T, Haft DH, Zafar N, Zhou L, Halpin R, Holley T, Khouri H, Feldblyum T, White O, Fraser CM, Chatterjee AK, Cartinhour S, Schneider DJ, Mansfield J, Collmer A, Buell CR. Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition. J Bacteriol 2005; 187:6488-98. [PMID: 16159782 PMCID: PMC1236638 DOI: 10.1128/jb.187.18.6488-6498.2005] [Citation(s) in RCA: 274] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight of bean. In this study, we report on the genome sequence of P. syringae pv. phaseolicola isolate 1448A, which encodes 5,353 open reading frames (ORFs) on one circular chromosome (5,928,787 bp) and two plasmids (131,950 bp and 51,711 bp). Comparative analyses with a phylogenetically divergent pathovar, P. syringae pv. tomato DC3000, revealed a strong degree of conservation at the gene and genome levels. In total, 4,133 ORFs were identified as putative orthologs in these two pathovars using a reciprocal best-hit method, with 3,941 ORFs present in conserved, syntenic blocks. Although these two pathovars are highly similar at the physiological level, they have distinct host ranges; 1448A causes disease in beans, and DC3000 is pathogenic on tomato and Arabidopsis. Examination of the complement of ORFs encoding virulence, fitness, and survival factors revealed a substantial, but not complete, overlap between these two pathovars. Another distinguishing feature between the two pathovars is their distinctive sets of transposable elements. With access to a fifth complete pseudomonad genome sequence, we were able to identify 3,567 ORFs that likely comprise the core Pseudomonas genome and 365 ORFs that are P. syringae specific.
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Affiliation(s)
- Vinita Joardar
- The Institute for Genomic Research, 9712 Medical Center Dr., Rockville, MD 20850, USA
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11
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Wang Q, Frye JG, McClelland M, Harshey RM. Gene expression patterns during swarming in Salmonella typhimurium: genes specific to surface growth and putative new motility and pathogenicity genes. Mol Microbiol 2004; 52:169-87. [PMID: 15049819 DOI: 10.1111/j.1365-2958.2003.03977.x] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Swarming is a specialized form of surface motility displayed by several flagellated bacterial genera, which shares features with other surface phenomenon such as biofilm formation and host invasion. Swarmer cells are generally more flagellated and longer than vegetative cells of the same species propagated in liquid media, and move within an encasement of polysaccharide 'slime'. Signals and signalling pathways controlling swarm cell differentiation are largely unknown. In order to test whether there is a genetic programme specific to swarming, we have determined global gene expression profiles of Salmonella typhimurium over an 8 h time course during swarming, and compared the microarray data with a similar time course of growth in liquid media as well as on harder agar where the bacteria do not swarm. Our data show that bacteria growing on the surface of agar have a markedly different physiology from those in broth, as judged by differential regulation of nearly one-third of the functional genome. The large number of genes showing surface-specific upregulation included those for lipopolysaccharide synthesis, iron metabolism and type III secretion. Although swarming-specific induction of flagellar gene expression was not generally apparent, genes for iron metabolism were strongly induced specifically on swarm agar. Surface-dependent regulation of many virulence genes suggests that growth on an agar surface could serve as a model for gene expression during the initial stages of host infection. Based on cluster analysis of distinctive expression patterns, we report here the identification of putative new genes involved in motility and virulence.
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Affiliation(s)
- Qingfeng Wang
- Section of Molecular Genetics and Microbiology and Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
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12
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Foulongne V, Michaux-Charachon S, Jumas-Bilak E, O'Callaghan D, Ramuz M. [Strategies for bacterial virulence genes identification]. ACTA ACUST UNITED AC 2004; 52:104-14. [PMID: 15065563 DOI: 10.1016/j.patbio.2003.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
One of the recent preoccupations of medical microbiology has been to characterise the mechanisms of virulence of bacterial pathogens at the molecular level. One hundred years after Koch, Stanley Falkow proposed a new, molecular version of Koch's postulates to define avirulence gene: (a) the gene confers a certain phenotype to the studied bacteria, (b) inactivation of the gene abolishes the phenotype, (c)reintroduction of the gene restores the wild type to the mutant. Although this strategy, based upon mutagenesis and the use of experimental models, allows the identification of many genes, it is not comprehensive. Other methods can be used to complete the identification of virulence factors such as differential expression, either at the level of transcription (transcriptome) or at the level of protein expression (proteome). All these techniques are now supported by the data from complete genome sequencing projects. The pool of information obtained from these approaches allows the definition of the 'virulome', which is the assembly of factors a pathogen requires for virulence. Understanding the virulome will open the way to the development of new strategies for vaccination or the development of new generation of antimicrobials.
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Affiliation(s)
- V Foulongne
- Inserm U431, faculté de médecine, avenue Kennedy, 30900, Nîmes, France.
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13
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van Berkum P, Terefework Z, Paulin L, Suomalainen S, Lindström K, Eardly BD. Discordant phylogenies within the rrn loci of Rhizobia. J Bacteriol 2003; 185:2988-98. [PMID: 12730157 PMCID: PMC154066 DOI: 10.1128/jb.185.10.2988-2998.2003] [Citation(s) in RCA: 150] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2002] [Accepted: 03/03/2003] [Indexed: 11/20/2022] Open
Abstract
It is evident from complete genome sequencing results that lateral gene transfer and recombination are essential components in the evolutionary process of bacterial genomes. Since this has important implications for bacterial systematics, the primary objective of this study was to compare estimated evolutionary relationships among a representative set of alpha-Proteobacteria by sequencing analysis of three loci within their rrn operons. Tree topologies generated with 16S rRNA gene sequences were significantly different from corresponding trees assembled with 23S rRNA gene and internally transcribed space region sequences. Besides the incongruence in tree topologies, evidence that distinct segments along the 16S rRNA gene sequences of bacteria currently classified within the genera Bradyrhizobium, Mesorhizobium and Sinorhizobium have a reticulate evolutionary history was also obtained. Our data have important implications for bacterial taxonomy, because currently most taxonomic decisions are based on comparative 16S rRNA gene sequence analysis. Since phylogenetic placement based on 16S rRNA gene sequence divergence perhaps is questionable, we suggest that the proposals of bacterial nomenclature or changes in their taxonomy that have been made may not necessarily be warranted. Accordingly, a more conservative approach should be taken in the future, in which taxonomic decisions are based on the analysis of a wider variety of loci and comparative analytical methods are used to estimate phylogenetic relationships among the genomes under consideration.
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Affiliation(s)
- Peter van Berkum
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, Maryland 20705, USA.
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14
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Folkesson A, Löfdahl S, Normark S. The Salmonella enterica subspecies I specific centisome 7 genomic island encodes novel protein families present in bacteria living in close contact with eukaryotic cells. Res Microbiol 2002; 153:537-45. [PMID: 12437215 DOI: 10.1016/s0923-2508(02)01348-7] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We have determined the genetic structure of the Salmonella enterica centisome 7 genomic island (SCI) located at the aspV loci in S. enterica subspecies I strains. The 47-kb long genomic island encodes 37 putative proteins, including the previously described saf fimbrial operon and the sinR transcriptional regulator. Other open reading frames (designated sci A to Z) in the island encode putative proteins with homologies to virulence-associated proteins in a number of gram-negative bacteria such as Pseudomonas aeruginosa, Yersinia pestis and enterohemorrhagic Escherichia coli, bacteria that have the ability to interact with and manipulate eukaryotic cells. The Sci proteins have putative cytoplasmic, periplasmic and outer membrane localizations pointing to a role in extracellular processes such as secretion or organelle biosynthesis. The genes encoding Sci-like proteins are clustered in all sequenced bacterial genomes available in the databases and a core set can be defined by the presence of genes encoding proteins with similarity to the SciB, C, G, H, I, O proteins. The SCI genomic island DNA sequences are restricted to Salmonella strains belonging to S. enterica subspecies I and deletion of the entire island affects the ability of the organisms to enter eukaryotic cells.
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Affiliation(s)
- Anders Folkesson
- Mikrobiologiskt och Tumörbiologiskt Centrum, Karolinska Institutet, Stockholm, Sweden.
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Hansen-Wester I, Hensel M. Genome-based identification of chromosomal regions specific for Salmonella spp. Infect Immun 2002; 70:2351-60. [PMID: 11953370 PMCID: PMC127916 DOI: 10.1128/iai.70.5.2351-2360.2002] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acquisition of genomic elements by horizontal gene transfer represents an important mechanism in the evolution of bacterial species. Pathogenicity islands are a subset of horizontally acquired elements present in various pathogens. These elements are frequently located adjacent to tRNA genes. We performed a comparative genome analysis of Salmonella enterica serovars Typhi and Typhimurium and Escherichia coli and scanned tRNA loci for the presence of species-specific, horizontally acquired genomic elements. A large number of species-specific elements were identified. Here, we describe the characteristics of four large chromosomal insertions at tRNA genes of Salmonella spp. The tRNA-associated elements harbor various genes previously identified as single virulence genes, indicating that these genes have been acquired with large chromosomal insertions. Southern blot analyses confirmed that the tRNA-associated elements are specific to Salmonella and also indicated a heterogeneous distribution within the salmonellae. Systematic scanning for insertions at tRNA genes thus represents a tool for the identification of novel pathogenicity islands.
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Affiliation(s)
- Imke Hansen-Wester
- Institut für Klinische Mikrobiologie, Immunologie und Hygiene, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
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16
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Liu GR, Rahn A, Liu WQ, Sanderson KE, Johnston RN, Liu SL. The evolving genome of Salmonella enterica serovar Pullorum. J Bacteriol 2002; 184:2626-33. [PMID: 11976291 PMCID: PMC135040 DOI: 10.1128/jb.184.10.2626-2633.2002] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Salmonella enterica serovar Pullorum is a fowl-adapted bacterial pathogen that causes dysentery (pullorum disease). Host adaptation and special pathogenesis make S. enterica serovar Pullorum an exceptionally good system for studies of bacterial evolution and speciation, especially regarding pathogen-host interactions and the acquisition of pathogenicity. We constructed a genome map of S. enterica serovar Pullorum RKS5078, using I-CeuI, XbaI, AvrII, and SpeI and Tn10 insertions. Pulsed-field gel electrophoresis was employed to separate the large DNA fragments generated by the endonucleases. The genome is 4,930 kb, which is similar to most salmonellas. However, the genome of S. enterica serovar Pullorum RKS5078 is organized very differently from the majority of salmonellas, with three major inversions and one translocation. This extraordinary genome structure was seen in most S. enterica serovar Pullorum strains examined, with different structures in a minority of S. enterica serovar Pullorum strains. We describe the coexistence of different genome structures among the same bacteria as genomic plasticity. Through comparisons with S. enterica serovar Typhimurium, we resolved seven putative insertions and eight deletions ranging in size from 12 to 157 kb. The genomic plasticity seen among S. enterica serovar Pullorum strains supported our hypothesis about its association with bacterial evolution: a large genomic insertion (157 kb in this case) disrupted the genomic balance, and rebalancing by independent recombination events in individual lineages resulted in diverse genome structures. As far as the structural plasticity exists, the S. enterica serovar Pullorum genome will continue evolving to reach a further streamlined and balanced structure.
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Affiliation(s)
- Gui-Rong Liu
- Department of Microbiology and Infectious Diseases, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada
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17
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Koski LB, Morton RA, Golding GB. Codon bias and base composition are poor indicators of horizontally transferred genes. Mol Biol Evol 2001; 18:404-12. [PMID: 11230541 DOI: 10.1093/oxfordjournals.molbev.a003816] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Horizontal gene transfer is now recognized as an important mechanism of evolution. Several methods to detect horizontally transferred genes have been suggested. These methods are based on either nucleotide composition or the failure to find a similar gene in closely related species. Genes that evolve vertically between closely related species can be divided into those that retain homologous chromosomal positions (positional orthologs) and those that do not. By comparing open reading frames in the Escherichia coli and Salmonella typhi genomes, we identified 2,728 positional orthologs since these species split 100 MYA. A group of 1,144 novel E. coli genes were unusually diverged from their S. typhi counterparts. These novel genes included those that had been horizontally transferred into E. coli, as well as members of gene pairs that had been rearranged or deleted. Positional orthologs were used to investigate compositional methods of identifying horizontally transferred genes. A large number of E. coli genes with normal nucleotide composition have no apparent ortholog in S. typhi, and many genes of atypical composition do, in fact, have positional orthologs. A phylogenetic approach was employed to confirm selected examples of horizontal transmission among the novel groups of genes. Our analysis of 80 E. coli genes determined that a number of genes previously classified as horizontally transferred based on base composition and codon bias were native, and genes previously classified as native appeared to be horizontally transferred. Hence, atypical nucleotide composition alone is not a reliable indicator of horizontal transmission.
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Affiliation(s)
- L B Koski
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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18
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Parke JL, Gurian-Sherman D. Diversity of the Burkholderia cepacia complex and implications for risk assessment of biological control strains. ANNUAL REVIEW OF PHYTOPATHOLOGY 2001; 39:225-258. [PMID: 11701865 DOI: 10.1146/annurev.phyto.39.1.225] [Citation(s) in RCA: 221] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The Burkholderia cepacia complex (Bcc) consists of several species of closely related and extremely versatile gram-negative bacteria found naturally in soil, water, and the rhizosphere of plants. Strains of Bcc have been used in biological control of plant diseases and bioremediation, while some strains are plant pathogens or opportunistic pathogens of humans with cystic fibrosis. The ecological versatility of these bacteria is likely due to their unusually large genomes, which are often comprised of several (typically two or three) large replicons, as well as their ability to use a large array of compounds as sole carbon sources. The original species B. cepacia has been split into eight genetic species (genomovars), including five named species, but taxonomic distinctions have not enabled biological control strains to be clearly distinguished from human pathogenic strains. This has led to a reassessment of the risk of several strains registered by the U.S. Environmental Protection Agency for biological control. We review the biology of Bcc bacteria, especially how our growing knowledge of Bcc ecology and pathogenicity might be used in risk assessment. The capability of this bacterial complex to cause disease in plants and humans, as well as to control plant diseases, affords a rare opportunity to explore traits that may function in all three environments.
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Affiliation(s)
- J L Parke
- Department of Botany and Plant Pathology, Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon 97331-7306, USA.
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19
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Wösten MM, Kox LF, Chamnongpol S, Soncini FC, Groisman EA. A signal transduction system that responds to extracellular iron. Cell 2000; 103:113-25. [PMID: 11051552 DOI: 10.1016/s0092-8674(00)00092-1] [Citation(s) in RCA: 273] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Iron is essential for all organisms but can be toxic in excess. Iron homeostasis is typically regulated by cytoplasmic iron binding proteins, but here we describe a signal transduction system (PmrA/PmrB) that responds to extracytoplasmic ferric iron. Iron promoted transcription of PmrA-activated genes and resistance to the antibiotic polymyxin in Salmonella. The PmrB protein bound iron via its periplasmic domain which harbors two copies of the sequence ExxE, a motif present in the Saccharomyces FTR1 iron transporter and in mammalian ferritin light chain. A pmrA mutant was hypersensitive to killing by iron but displayed wild-type resistance to a variety of oxidants, suggesting PmrA/PmrB controls a novel pathway mediating the avoidance of iron toxicity.
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Affiliation(s)
- M M Wösten
- Department of Molecular Microbiology, Howard Hughes Medical Institute, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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20
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Chamnongpol S, Groisman EA. Acetyl phosphate-dependent activation of a mutant PhoP response regulator that functions independently of its cognate sensor kinase. J Mol Biol 2000; 300:291-305. [PMID: 10873466 DOI: 10.1006/jmbi.2000.3848] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The two-component system is a signal communication network generally consisting of a sensor kinase that receives inputs from the environment and modifies the phosphorylated state of a response regulator that executes an adaptive behavior. PhoP is a response regulator that controls virulence gene expression in Salmonella enterica. Transcription of PhoP-regulated genes is modulated by the Mg(2+) levels detected by the sensor PhoQ. Here, we describe a PhoP mutant protein, PhoP*, that functions in the absence of its cognate sensor, thereby allowing transcription of PhoP-activated genes independently of the Mg(2+ )concentration in the environment. The PhoP* protein harbors a S93N substitution in the response regulator receiver domain. PhoP*-mediated transcription is abolished by either mutation of the aspartate residue that is conserved among response regulators as the site of phosphorylation or inactivation of the pta-encoded phosphotransacetylase. This enzyme mediates the production of acetyl phosphate, which has been shown to serve as a low molecular mass phosphate donor for certain response regulators. The purified PhoP* protein autophosphorylated from acetyl phosphate more efficiently than the wild-type PhoP protein in vitro. The PhoP* protein retained the capacity to interact with the PhoQ protein, which promoted phosphorylation of the PhoP* protein in vitro and abolished PhoP*-mediated transcription under high Mg(2+ )concentrations in vivo. Cumulatively, our results uncover a role of PhoQ in transcriptional repression during growth in millimolar Mg(2+ )and define a mutant response regulator form with an increased capacity to be phosphorylated by acetyl phosphate.
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Affiliation(s)
- S Chamnongpol
- Howard Hughes Medical Institute, Department of Molecular Microbiology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
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21
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Abstract
Systemic infections by Salmonella enterica, such as typhoid fever, are a significant threat to human health. Recent studies indicate that the function of a type III secretion system encoded by Salmonella Pathogenicity Island 2 (SPI2) is central for the ability of S. enterica to cause systemic infections and for intracellular pathogenesis. This review summarizes approaches leading to the identification of SPI2, the molecular genetics and evolution of SPI2, and the current understanding of the regulation of gene expression. Recent studies have indicated that SPI2 is used by intracellular Salmonella to actively modify functions of the host cells. The role of SPI2 during pathogenesis of salmonellosis and current models regarding function will be discussed.
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Affiliation(s)
- M Hensel
- Lehrstuhl Bakteriologie, Max von Pettenkofer-Institut, Ludwig-Maximilians-Universität München, Germany.
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22
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Kox LF, Wösten MM, Groisman EA. A small protein that mediates the activation of a two-component system by another two-component system. EMBO J 2000; 19:1861-72. [PMID: 10775270 PMCID: PMC302009 DOI: 10.1093/emboj/19.8.1861] [Citation(s) in RCA: 209] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The PmrA-PmrB two-component system of Salmonella enterica controls resistance to the peptide antibiotic polymyxin B and to several antimicrobial proteins from human neutrophils. Transcription of PmrA-activated genes is induced by high iron, but can also be promoted by growth in low magnesium in a process that requires another two-component system, PhoP-PhoQ. Here, we define the genetic basis for the interaction between the PhoP-PhoQ and PmrA-PmrB systems. We have identified pmrD as a PhoP-activated gene that mediates the transcriptional activation of PmrA-regulated genes during growth in low magnesium. When transcription of pmrD is driven from a heterologous promoter, expression of PmrA-activated genes occurs even at repressing magnesium concentrations and becomes independent of the phoP and phoQ genes. The PmrD effect is specific for PmrA-regulated genes and requires functional PmrA and PmrB proteins. A pmrD mutant is sensitive to polymyxin if grown in low magnesium, but resistant if grown in high iron. The PmrD protein controls the activity of the PmrA-PmrB system at a post-transcriptional level.
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Affiliation(s)
- L F Kox
- Department of Molecular Microbiology, Howard Hughes Medical Institute, Washington University School of Medicine, St Louis, MO 63110-1093, USA
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23
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Morrow BJ, Graham JE, Curtiss R. Genomic subtractive hybridization and selective capture of transcribed sequences identify a novel Salmonella typhimurium fimbrial operon and putative transcriptional regulator that are absent from the Salmonella typhi genome. Infect Immun 1999; 67:5106-16. [PMID: 10496884 PMCID: PMC96859 DOI: 10.1128/iai.67.10.5106-5116.1999] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/1999] [Accepted: 07/29/1999] [Indexed: 11/20/2022] Open
Abstract
Salmonella typhi, the etiologic agent of typhoid fever, is adapted to the human host and unable to infect nonprimate species. The genetic basis for host specificity in S. typhi is unknown. The avirulence of S. typhi in animal hosts may result from a lack of genes present in the broad-host-range pathogen Salmonella typhimurium. Genomic subtractive hybridization was successfully employed to isolate S. typhimurium genomic sequences which are absent from the S. typhi genome. These genomic subtracted sequences mapped to 17 regions distributed throughout the S. typhimurium chromosome. A positive cDNA selection method was then used to identify subtracted sequences which were transcribed by S. typhimurium following macrophage phagocytosis. A novel putative transcriptional regulator of the LysR family was identified as transcribed by intramacrophage S. typhimurium. This putative transcriptional regulator was absent from the genomes of the human-adapted serovars S. typhi and Salmonella paratyphi A. Mutations within this gene did not alter the level of S. typhimurium survival within macrophages or virulence within mice. A subtracted genomic fragment derived from the ferrichrome operon also hybridized to the intramacrophage cDNA. Nucleotide sequence analysis of S. typhimurium and S. typhi chromosomal sequences flanking the ferrichrome operon identified a novel S. typhimurium fimbrial operon with a high level of similarity to sequences encoding Proteus mirabilis mannose-resistant fimbriae. The novel fimbrial operon was absent from the S. typhi genome. The absence of specific genes may have allowed S. typhi to evolve as a highly invasive, systemic human pathogen.
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Affiliation(s)
- B J Morrow
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA
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24
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Yap WH, Zhang Z, Wang Y. Distinct types of rRNA operons exist in the genome of the actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon. J Bacteriol 1999; 181:5201-9. [PMID: 10464188 PMCID: PMC94023 DOI: 10.1128/jb.181.17.5201-5209.1999] [Citation(s) in RCA: 209] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe here the presence of two distinct types of rRNA operons in the genome of a thermophilic actinomycete Thermomonospora chromogena. The genome of T. chromogena contains six rRNA operons (rrn), of which four complete and two incomplete ones were cloned and sequenced. Comparative analysis revealed that the operon rrnB exhibits high levels of sequence variations to the other five nearly identical ones throughout the entire length of the operon. The coding sequences for the 16S and 23S rRNA genes differ by approximately 6 and 10%, respectively, between the two types of operons. Normal functionality of rrnB is concluded on the basis of the nonrandom distribution of nucleotide substitutions, the presence of compensating nucleotide covariations, the preservation of secondary and tertiary rRNA structures, and the detection of correctly processed rRNAs in the cell. Comparative sequence analysis also revealed a close evolutionary relationship between rrnB operon of T. chromogena and rrnA operon of another thermophilic actinomycete Thermobispora bispora. We propose that T. chromogena acquired rrnB operon from T. bispora or a related organism via horizontal gene transfer.
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MESH Headings
- Actinomycetales/classification
- Actinomycetales/genetics
- Base Sequence
- Blotting, Southern
- Cloning, Molecular
- DNA, Bacterial
- DNA, Ribosomal/analysis
- Evolution, Molecular
- Gene Amplification
- Gene Expression
- Genetic Variation
- Genome, Bacterial
- Molecular Sequence Data
- Nucleic Acid Conformation
- Polymerase Chain Reaction
- RNA, Bacterial
- RNA, Ribosomal, 16S
- Sequence Analysis, DNA
- rRNA Operon
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Affiliation(s)
- W H Yap
- Microbial Collection and Screening Laboratory, Institute of Molecular and Cell Biology, National University of Singapore, Singapore 117609
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25
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Folkesson A, Advani A, Sukupolvi S, Pfeifer JD, Normark S, Löfdahl S. Multiple insertions of fimbrial operons correlate with the evolution of Salmonella serovars responsible for human disease. Mol Microbiol 1999; 33:612-22. [PMID: 10417651 DOI: 10.1046/j.1365-2958.1999.01508.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
On centisome 7, Salmonella spp. contain a large region not present in the corresponding region of Escherichia coli. This region is flanked by sequences with significant homology to the E. coli tRNA gene aspV and the hypothetical E. coli open reading frame yafV. The locus consists of a mosaic of differentially acquired inserts forming a dynamic cs7 region of horizontally transferred inserts. Salmonella enterica subspecies I, responsible for most Salmonella infections in warm-blooded animals, carries a fimbrial gene cluster (saf) in this region as well as a regulatory gene (sinR). These genes are flanked by inverted repeats and are inserted in another laterally transferred region present in most members of Salmonella spp. encoding a putative invasin (pagN ). S. enterica subspecies I serovar Typhi, the Salmonella serovar that causes the most severe form of human salmonellosis, contains an additional insert of at least 8 kb in the sinR-pagN intergenic region harbouring a novel fimbrial operon (tcf ) similar to the coo operon encoding the CS1 fimbrial adhesin expressed by human-specific enterotoxigenic E. coli. It is suggested that the multiple insertions of fimbrial genes that have occurred in the cs7 region have contributed to phylogenetic diversity and host adaptation of Salmonella spp.
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Affiliation(s)
- A Folkesson
- Mikrobiologiskt och Tumörbiologiskt Centrum, Karolinska Institutet, Box 280, Tomtebodavagen 34, S-17177 Stockholm, Sweden.
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26
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Borg S, Björkman J, Eriksson S, Syk A, Andersson DI, Schesser K, Rhen M, Pettersson S, French NS. Novel Salmonella typhimurium properties in host--parasite interactions. Immunol Lett 1999; 68:247-9. [PMID: 10424427 DOI: 10.1016/s0165-2478(99)00073-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Inflammatory bowel disease (IBD) comprises different diseases in the gastrointestinal tract in human, of which Crohn's disease (CD) and ulcerative colitis (UC) are the most prominent. A key factor in the etiology of IBD is the chronic inflammatory process, and a large body of evidence suggests that the transcription factor nuclear factor-kappa B (NF-kappaB) is the key regulator of responses determining the clinical inflammatory condition. Recent findings using antisense oligonucleotides provide direct evidence that the p65 subunit of NF-kappaB plays a central role in chronic intestinal inflammation. It has previously been shown that the Gram negative bacteria Yersinia pseudotubercolosis targets the eukaryotic signal transduction pathway(s) that lead to NF-kappaB activation (and thus avoid an anti-bacterial inflammatory response). In this paper, growth-based selected Salmonella typhimurium clones have been used to generate a clearer picture of the molecular mechanisms involved in host-parasite interactions. From the results presented here, S. typhimurium and Y. pseudotubercolosis may use the same mechanism to block NF-kappaB activation, following host cell infection. A new adaptational feature could also be shown, where a growth-based selected bacteria avoided the normally induced translocation of NF-kappaB in host cells.
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Affiliation(s)
- S Borg
- Center for Genomics Research, Karolinska Institute, Stockholm, Sweden.
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27
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Guard-Petter J, Parker CT, Asokan K, Carlson RW. Clinical and veterinary isolates of Salmonella enterica serovar enteritidis defective in lipopolysaccharide O-chain polymerization. Appl Environ Microbiol 1999; 65:2195-201. [PMID: 10224019 PMCID: PMC91316 DOI: 10.1128/aem.65.5.2195-2201.1999] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/1998] [Accepted: 02/25/1999] [Indexed: 11/20/2022] Open
Abstract
Twelve human and chicken isolates of Salmonella enterica serovar Enteritidis belonging to phage types 4, 8, 13a, and 23 were characterized for variability in lipopolysaccharide (LPS) composition. Isolates were differentiated into two groups, i.e., those that lacked immunoreactive O-chain, termed rough isolates, and those that had immunoreactive O-chain, termed smooth isolates. Isolates within these groups could be further differentiated by LPS compositional differences as detected by gel electrophoresis and gas liquid chromatography of samples extracted with water, which yielded significantly more LPS in comparison to phenol-chloroform extraction. The rough isolates were of two types, the O-antigen synthesis mutants and the O-antigen polymerization (wzy) mutants. Smooth isolates were also of two types, one producing low-molecular-weight (LMW) LPS and the other producing high-molecular-weight (HMW) LPS. To determine the genetic basis for the O-chain variability of the smooth isolates, we analyzed the effects of a null mutation in the O-chain length determinant gene, wzz (cld) of serovar Typhimurium. This mutation results in a loss of HMW LPS; however, the LMW LPS of this mutant was longer and more glucosylated than that from clinical isolates of serovar Enteritidis. Cluster analysis of these data and of those from two previously characterized isogenic strains of serovar Enteritidis that had different virulence attributes indicated that glucosylation of HMW LPS (via oafR function) is variable and results in two types of HMW structures, one that is highly glucosylated and one that is minimally glucosylated. These results strongly indicate that naturally occurring variability in wzy, wzz, and oafR function can be used to subtype isolates of serovar Enteritidis during epidemiological investigations.
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Affiliation(s)
- J Guard-Petter
- Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Athens, Georgia 30605, USA.
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28
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Lee VT, Schneewind O. Type III secretion machines and the pathogenesis of enteric infections caused by Yersinia and Salmonella spp. Immunol Rev 1999; 168:241-55. [PMID: 10399078 DOI: 10.1111/j.1600-065x.1999.tb01296.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Salmonella and Yersinia spp. infect the intestinal tract of humans. Although these organisms cause fundamentally different diseases, each pathogen relies on type III secretion machines to either inject virulence factors into the cytosol of eukaryotic cells or release toxins into the extracellular milieu. Type III secretion machines are composed of many different subunits and export several polypeptides with unique substrate requirements. During Salmonella pathogenesis, the type III machine encoded by the Salmonella pathogenicity island (SPI)-1 genetic element functions to cause invasion of the intestinal epithelium, whereas another type III machine (SPI-2) is required for survival in macrophages. Yersinia enterocolitica and Yersinia pseudotuberculosis employ type III machines to resist macrophage phagocytosis and to manipulate the host's immune response, thereby colonizing intestinal lymphoid tissues. We describe what is known about the pathogenic functions of virulence factors secreted by type III machines. Furthermore, type III secretion machines may be exploited for the injection of recombinant proteins, a strategy that has already been successfully employed to elicit a cell-mediated immune response.
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Affiliation(s)
- V T Lee
- Department of Microbiology & Immunology, UCLA School of Medicine, USA
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29
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Hilbert F, García-del Portillo F, Groisman EA. A periplasmic D-alanyl-D-alanine dipeptidase in the gram-negative bacterium Salmonella enterica. J Bacteriol 1999; 181:2158-65. [PMID: 10094694 PMCID: PMC93629 DOI: 10.1128/jb.181.7.2158-2165.1999] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The VanX protein is a D-alanyl-D-alanine (D-Ala-D-Ala) dipeptidase essential for resistance to the glycopeptide antibiotic vancomycin. While this enzymatic activity has been typically associated with vancomycin- and teicoplainin-resistant enterococci, we now report the identification of a D-Ala-D-Ala dipeptidase in the gram-negative species Salmonella enterica. The Salmonella enzyme is only 36% identical to VanX but exhibits a similar substrate specificity: it hydrolyzes D-Ala-D-Ala, DL-Ala-DL-Phe, and D-Ala-Gly but not the tripeptides D-Ala-D-Ala-D-Ala and DL-Ala-DL-Lys-Gly or the dipeptides L-Ala-L-Ala, N-acetyl-D-Ala-D-Ala, and L-Leu-Pro. The Salmonella dipeptidase gene, designated pcgL, appears to have been acquired by horizontal gene transfer because pcgL-hybridizing sequences were not detected in related bacterial species and the G+C content of the pcgL-containing region (41%) is much lower than the overall G+C content of the Salmonella chromosome (52%). In contrast to wild-type Salmonella, a pcgL mutant was unable to use D-Ala-D-Ala as a sole carbon source. The pcgL gene conferred D-Ala-D-Ala dipeptidase activity upon Escherichia coli K-12 but did not allow growth on D-Ala-D-Ala. The PcgL protein localizes to the periplasmic space of Salmonella, suggesting that this dipeptidase participates in peptidoglycan metabolism.
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Affiliation(s)
- F Hilbert
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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30
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Blanc-Potard AB, Solomon F, Kayser J, Groisman EA. The SPI-3 pathogenicity island of Salmonella enterica. J Bacteriol 1999; 181:998-1004. [PMID: 9922266 PMCID: PMC93469 DOI: 10.1128/jb.181.3.998-1004.1999] [Citation(s) in RCA: 133] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pathogenicity islands are chromosomal clusters of pathogen-specific virulence genes often found at tRNA loci. We have determined the molecular genetic structure of SPI-3, a 17-kb pathogenicity island located at the selC tRNA locus of Salmonella enterica serovar Typhimurium. The G+C content of SPI-3 (47.5%) differs from that of the Salmonella genome (52%), consistent with the notion that these sequences have been horizontally acquired. SPI-3 harbors 10 open reading frames organized in six transcriptional units, which include the previously described mgtCB operon encoding the macrophage survival protein MgtC and the Mg2+ transporter MgtB. Among the newly identified open reading frames, one exhibits sequence similarity to the ToxR regulatory protein of Vibrio cholerae and one is similar to the AIDA-I adhesin of enteropathogenic Escherichia coli. The distribution of SPI-3 sequences varies among the salmonellae: the right end of the island, which harbors the virulence gene mgtC, is present in all eight subspecies of Salmonella; however, a four-gene cluster at the center of SPI-3 is found in only some of the subspecies and is bracketed by remnants of insertion sequences, suggesting a multistep process in the evolution of SPI-3 sequences.
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Affiliation(s)
- A B Blanc-Potard
- Department of Molecular Microbiology, Howard Hughes Medical Institute, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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31
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Gunn JS, Belden WJ, Miller SI. Identification of PhoP-PhoQ activated genes within a duplicated region of the Salmonella typhimurium chromosome. Microb Pathog 1998; 25:77-90. [PMID: 9712687 DOI: 10.1006/mpat.1998.0217] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Salmonellae virulence requires the PhoP-PhoQ two-component regulatory system. PhoP-PhoQ activate the transcription of genes following phagocytosis by macrophages which are necessary for survival within the phagosome environment. Thirteen previously undefined PhoP-activated gene fusions generated by MudJ and TnphoA (pag A, and E-P, respectively) were cloned and sequenced. Most pag products show no similarity to proteins in the database, while others are predicted to encode: a UDP-glucose dehydrogenase (pagA); a protein with similarity to the product of an E. coli aluminium-induced gene (pagH); a protein encoded within a Salmonella-unique region adjacent to the sinR gene (pagN); a protein similar to a product of the Yersinia virulence plasmid (pagO); and a protein with similarity to CrcA which is necessary for resistance of E. coli to camphor (pagP). Of the pag characterized, only pagK, M and O were closely linked. pagJ and pagK were shown to be unlinked but nearly identical in DNA sequence, as each was located within a 1.6 kb DNA duplication. The translations of sequences surrounding pagJ and pagK show similarity to proteins from extrachromosomal elements as well as those involved in DNA transposition and rearrangement, suggesting that this region may have been or is a mobile element. The transcriptional start sites of pagK, M, and J were determined; however, comparison to other known pag gene promoters failed to reveal a consensus sequence for PhoP-regulated activation. DNA sequences hybridizing to a Salmonella typhimurium pagK specific probe were found in S. enteritidis but absent in other Salmonella serotypes and Enterobacteriaceae tested, suggesting that these genes are specific for broad host range Salmonellae that cause diarrhoea in humans. Cumulatively, these data further demonstrate: (1) that PhoP-PhoQ is a global regulator of the production of diverse envelope or secreted proteins; (2) that PhoP-PhoQ regulate the production of proteins of redundant function; and (3) that pag are often located in regions of horizontally acquired DNA that are absent in other Enterobacteriaceae.
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Affiliation(s)
- J S Gunn
- Department of Medicine, University of Washington, HSB K-140, Box 357710, Seattle, WA 98195, USA
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32
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Boerlin P, Chen S, Colbourne JK, Johnson R, De Grandis S, Gyles C. Evolution of enterohemorrhagic Escherichia coli hemolysin plasmids and the locus for enterocyte effacement in shiga toxin-producing E. coli. Infect Immun 1998; 66:2553-61. [PMID: 9596716 PMCID: PMC108238 DOI: 10.1128/iai.66.6.2553-2561.1998] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
This study assessed the diversity of the enterohemorrhagic Escherichia coli (EHEC) hemolysin gene (ehxA) in a variety of Shiga toxin-producing E. coli (STEC) serotypes and the relationship between ehxA types and virulence markers on the locus for enterocyte effacement (LEE). Restriction fragment length polymorphism of the ehxA gene and flanking sequences and of the E. coli attaching and effacing (eae) gene was determined for 79 EHEC hemolysin-positive STEC isolates of 37 serotypes. Two main groups of EHEC hemolysin sequences and associated plasmids, which corresponded to the eae-positive and the eae-negative isolates, were delineated. Comparisons of the ehxA gene sequences of representative isolates of each group showed that this gene and the rest of the EHEC hemolysin operon are highly conserved. Digestion of an ehxA PCR product with the restriction endonuclease TaqI showed a unique restriction pattern for eae-negative isolates and another one for isolates of serotypes O157:H7 and O157:NM. A conserved fragment of 5.6 kb with four potential open reading frames was identified on the EHEC hemolysin plasmid of eae-positive STEC. Phylogenetic analysis of a subset of 27 STEC isolates, one enteropathogenic E. coli isolate, and a K-12 reference isolate showed that eae-positive STEC isolates all belong to a single evolutionary lineage and that the EHEC hemolysin plasmid and the ehxA gene evolved within this lineage without recent horizontal transfer. However, the eae gene and the LEE appear to have been transferred horizontally within this STEC lineage on several occasions. The reasons for the lack of transfer or maintenance of the LEE in other STEC lineages are not clear and require further study.
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Affiliation(s)
- P Boerlin
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
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Conner CP, Heithoff DM, Julio SM, Sinsheimer RL, Mahan MJ. Differential patterns of acquired virulence genes distinguish Salmonella strains. Proc Natl Acad Sci U S A 1998; 95:4641-5. [PMID: 9539791 PMCID: PMC22543 DOI: 10.1073/pnas.95.8.4641] [Citation(s) in RCA: 116] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Analysis of several Salmonella typhimurium in vivo-induced genes located in regions of atypical base composition has uncovered acquired genetic elements that cumulatively engender pathogenicity. Many of these regions are associated with mobile elements, encode predicted adhesin and invasin-like functions, and are required for full virulence. Some of these regions distinguish broad host range from host-adapted Salmonella serovars and may contribute to inherent differences in host specificity, tissue tropism, and disease manifestation. Maintenance of this archipelago of acquired sequence by selection in specific hosts reveals a fossil record of the evolution of pathogenic species.
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Affiliation(s)
- C P Conner
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
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34
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Abstract
The year 1997 saw the publication of the complete nucleotide sequence of Helicobacter pylori and Escherichia coli. It is conceivable that the complete nucleotide sequence for all the major human bacterial pathogens will be available by the end of the century. Database alignments have been used to ascribe the putative functions of open reading frames in the sequenced isolates and to define the differences between bacterial species at the nucleotide level. The most striking finding from all genome projects has been the high proportion of open reading frames that have no known function. Experimental data demonstrating the utility of the genome sequencing projects are only just beginning to emerge.
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Affiliation(s)
- C M Tang
- Molecular Infectious Diseases Group, University Department of Paediatrics, Oxford University, John Radcliffe Hospital, Oxford OX3 9DU, UK.
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35
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Conner CP, Heithoff DM, Mahan MJ. In vivo gene expression: contributions to infection, virulence, and pathogenesis. Curr Top Microbiol Immunol 1997; 225:1-12. [PMID: 9386325 DOI: 10.1007/978-3-642-80451-9_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- C P Conner
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara 93106, USA
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36
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Blanc-Potard AB, Groisman EA. The Salmonella selC locus contains a pathogenicity island mediating intramacrophage survival. EMBO J 1997; 16:5376-85. [PMID: 9311997 PMCID: PMC1170169 DOI: 10.1093/emboj/16.17.5376] [Citation(s) in RCA: 253] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Pathogenicity islands are chromosomal clusters of horizontally acquired virulence genes that are often found at tRNA loci. The selC tRNA locus of Escherichia coli has served as the site of integration of two distinct pathogenicity islands which are responsible for converting benign strains into uro- and enteropathogens. Because virulence genes are targeted to the selC locus of E.coli, we investigated the homologous region of the Salmonella typhimurium chromosome for the presence of horizontally acquired sequences. At this site, we identified a 17 kb DNA segment that is both unique to Salmonella and necessary for virulence. This segment harbors a gene, mgtC, that is required for intramacrophage survival and growth in low Mg2+ media. The mgtC locus is regulated by the PhoP/PhoQ two-component system, a major regulator of virulence functions present in both pathogenic and non-pathogenic bacterial species. Cumulatively, our experiments indicate that the ability to replicate in low Mg2+ environments is necessary for Salmonella virulence, and suggest that a similar mechanism is responsible for the dissemination and acquisition of pathogenicity islands in enteric bacteria.
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Affiliation(s)
- A B Blanc-Potard
- Department of Molecular Microbiology, Washington University School of Medicine, 660 S.Euclid Ave, Campus Box 8230, St Louis, MO 63110, USA
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37
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Wang Y, Zhang Z, Ramanan N. The actinomycete Thermobispora bispora contains two distinct types of transcriptionally active 16S rRNA genes. J Bacteriol 1997; 179:3270-6. [PMID: 9150223 PMCID: PMC179106 DOI: 10.1128/jb.179.10.3270-3276.1997] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Here we present the first description of the presence of two distinct types of 16S rRNA genes in the genome of a (eu)bacterium, Thermobispora bispora. We cloned and determined the nucleotide sequences of all four rRNA operons of T. bispora. Sequence comparisons revealed that the genome of T. bispora contains two distinct types of 16S rRNA genes, each type consisting of two identical or nearly identical copies, and three identical copies of the 23S RNA gene. The nucleotide sequences of the two types of 16S rRNA genes differ at 98 nucleotide positions (6.4% of total nucleotides) together with six regions of deletion-insertions. None of the base substitutions or insertion-deletions corresponds to any of the approximately 600 evolutionarily invariable or rarely variable nucleotides, indicating that both genes are functional. Both types of 16S rRNA genes are transcribed and processed as determined by Northern (RNA) hybridization and reverse transcriptase-mediated PCR.
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MESH Headings
- Actinomycetales/genetics
- Base Sequence
- Blotting, Northern
- Blotting, Southern
- Cloning, Molecular
- Codon
- DNA, Ribosomal/genetics
- Molecular Sequence Data
- Polymerase Chain Reaction
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/isolation & purification
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/isolation & purification
- Sequence Homology, Nucleic Acid
- Transcription, Genetic
- rRNA Operon
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Affiliation(s)
- Y Wang
- Microbial Collection and Screening Laboratory, Institute of Molecular and Cell Biology, National University of Singapore.
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38
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Bäumler AJ, Heffron F, Reissbrodt R. Rapid detection of Salmonella enterica with primers specific for iroB. J Clin Microbiol 1997; 35:1224-30. [PMID: 9114411 PMCID: PMC232733 DOI: 10.1128/jcm.35.5.1224-1230.1997] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The iroB gene of Salmonella enterica is absent from the chromosome of the related organism Escherichia coli. We determined the distribution of this gene among 150 bacterial isolates, representing 51 serotypes of different Salmonella species and subspecies and 8 other bacterial species which are frequent contaminants during routine enrichment procedures by Southern hybridization. An iroB-specific DNA probe detected homologous sequences in all strains of S. enterica, including serotypes of S. enterica subsp. enterica (I), salamae (II), diarizonae (IIIb), and houtenae (IV). No hybridization signal was obtained with strains of Salmonella bongori or other bacterial species. In contrast, hybridization with a DNA probe specific for purD, a purine biosynthesis gene, detected homologs in all bacterial species tested. Primers specific for iroB were used to amplify this gene from 197 bacterial isolates by PCR. The iroB gene could be PCR amplified from S. enterica subsp. enterica (I), salamae (II), diarizonae (IIIb), houtenae (IV), arizonae (IIIa), and indica (VI), but not from S. bongori or other bacterial species. Thus, PCR amplification of iroB can be used to distinguish between S. enterica and other bacterial species, including S. bongori. A combination of preenrichment in buffered peptone water supplemented with ferrioxamine E and amplification of iroB by magnetic immuno-PCR allowed detection of S. enterica in albumen within 24 h. In conclusion, PCR amplification of iroB is a new sensitive and selective method which has the potential to rapidly detect S. enterica serotypes.
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Affiliation(s)
- A J Bäumler
- Department of Molecular Microbiology and Immunology, Oregon Health Sciences University, Portland 97201-3098, USA
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39
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Boyd EF, Li J, Ochman H, Selander RK. Comparative genetics of the inv-spa invasion gene complex of Salmonella enterica. J Bacteriol 1997; 179:1985-91. [PMID: 9068645 PMCID: PMC178923 DOI: 10.1128/jb.179.6.1985-1991.1997] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The chromosomal region containing the Salmonella enterica pathogenic island inv-spa was present in the last common ancestor of all the contemporary lineages of salmonellae. For multiple strains of S. enterica, representing all eight subspecies, nucleotide sequences were obtained for five genes of the inv-spa invasion complex, invH, invE, invA, spaM, and spaN, al of which encode proteins that are required for entry of the bacteria into cultured epithelial cells. The invE, invA, spaM, and spaN genes were present in all eight subspecies of S. enterica, and for invE and invA and their products, levels of sequence variation among strains were within the ranges reported for housekeeping genes. In contrast, the InvH, SpaM, and SpaN proteins were unusually variable in amino acid sequence. Furthermore, invH was absent from the subspecies V isolates examined. The SpaM and SpaN proteins provide further evidence of a relationship (first detected by Li et al. [J. Li, H. Ochman, E. A. Groisman, E. F. Boyd, F. Solomon, K. Nelson, and R. K. Selander, Proc. Natl. Acad. Sci. USA 92:7252-7256, 1995]) between the cellular location of the products of the inv-spa genes and evolutionary rate, as reflected in the level of polymorphism within S. enterica. Invasion proteins that are membrane bound or membrane associated are relatively conserved in amino acid sequence, whereas those that are exported to the extracellular environment are hypervariable, possibly reflecting the action of diversifying selection.
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Affiliation(s)
- E F Boyd
- Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802, USA
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40
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Heithoff DM, Conner CP, Hanna PC, Julio SM, Hentschel U, Mahan MJ. Bacterial infection as assessed by in vivo gene expression. Proc Natl Acad Sci U S A 1997; 94:934-9. [PMID: 9023360 PMCID: PMC19617 DOI: 10.1073/pnas.94.3.934] [Citation(s) in RCA: 185] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
In vivo expression technology (IVET) has been used to identify > 100 Salmonella typhimurium genes that are specifically expressed during infection of BALB/c mice and/or murine cultured macrophages. Induction of these genes is shown to be required for survival in the animal under conditions of the IVET selection. One class of in vivo induced (ivi) genes, iviVI-A and iviVI-B, constitute an operon that resides in a region of the Salmonella genome with low G+C content and presumably has been acquired by horizontal transfer. These ivi genes encode predicted proteins that are similar to adhesins and invasins from prokaryotic and eukaryotic pathogens (Escherichia coli [tia], Plasmodium falciparum [PfEMP1]) and have coopted the PhoPQ regulatory circuitry of Salmonella virulence genes. Examination of the in vivo induction profile indicates (i) many ivi genes encode regulatory functions (e.g., phoPQ and pmrAB) that serve to enhance the sensitivity and amplitude of virulence gene expression (e.g., spvB); (ii) the biochemical function of many metabolic genes may not represent their sole contribution to virulence; (iii) the host ecology can be inferred from the biochemical functions of ivi genes; and (iv) nutrient limitation plays a dual signaling role in pathogenesis: to induce metabolic functions that complement host nutritional deficiencies and to induce virulence functions required for immediate survival and spread to subsequent host sites.
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Affiliation(s)
- D M Heithoff
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara 93106, USA
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41
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Censini S, Lange C, Xiang Z, Crabtree JE, Ghiara P, Borodovsky M, Rappuoli R, Covacci A. cag, a pathogenicity island of Helicobacter pylori, encodes type I-specific and disease-associated virulence factors. Proc Natl Acad Sci U S A 1996; 93:14648-53. [PMID: 8962108 PMCID: PMC26189 DOI: 10.1073/pnas.93.25.14648] [Citation(s) in RCA: 1359] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/1996] [Accepted: 10/09/1996] [Indexed: 02/07/2023] Open
Abstract
cagA, a gene that codes for an immunodominant antigen, is present only in Helicobacter pylori strains that are associated with severe forms of gastroduodenal disease (type I strains). We found that the genetic locus that contains cagA (cag) is part of a 40-kb DNA insertion that likely was acquired horizontally and integrated into the chromosomal glutamate racemase gene. This pathogenicity island is flanked by direct repeats of 31 bp. In some strains, cag is split into a right segment (cagI) and a left segment (cagII) by a novel insertion sequence (IS605). In a minority of H. pylori strains, cagI and cagII are separated by an intervening chromosomal sequence. Nucleotide sequencing of the 23,508 base pairs that form the cagI region and the extreme 3' end of the cagII region reveals the presence of 19 ORFs that code for proteins predicted to be mostly membrane associated with one gene (cagE), which is similar to the toxin-secretion gene of Bordetella pertussis, ptlC, and the transport systems required for plasmid transfer, including the virB4 gene of Agrobacterium tumefaciens. Transposon inactivation of several of the cagI genes abolishes induction of IL-8 expression in gastric epithelial cell lines. Thus, we believe the cag region may encode a novel H. pylori secretion system for the export of virulence determinants.
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Affiliation(s)
- S Censini
- Immunobiological Research Institute of Siena, Chiron Vaccines, Italy
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42
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Soncini FC, Groisman EA. Two-component regulatory systems can interact to process multiple environmental signals. J Bacteriol 1996; 178:6796-801. [PMID: 8955299 PMCID: PMC178578 DOI: 10.1128/jb.178.23.6796-6801.1996] [Citation(s) in RCA: 174] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The PhoP/PhoQ two-component system of Salmonella typhimurium governs transcription of some 25 loci in response to the extracellular concentration of Mg2+. We have now identified one of these loci as pmrCAB, which codes for a two-component system that mediates resistance to the antibiotic polymyxin B. Transcription of seven of 25 PhoP-activated loci was dependent on a functional PmrA protein, the response regulator of the PmrA/PmrB system. Expression of the PmrA-dependent loci was induced by either Mg2+ limitation or mild acidification, whereas transcription of a PmrA-independent gene was activated by Mg2+ limitation but not acid pH. Induction of PmrA-activated genes by Mg2 limitation required the PhoP and PhoQ proteins. In contrast, the acid-mediated activation of PmrA-regulated genes occurred in strains that were missing either one of these proteins. Transcriptional regulation by a cascade of two-component systems allows pathogenic bacteria to express their virulence determinants in response to a broader spectrum of environmental cues.
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Affiliation(s)
- F C Soncini
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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43
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Leveau JH, van der Meer JR. The tfdR gene product can successfully take over the role of the insertion element-inactivated TfdT protein as a transcriptional activator of the tfdCDEF gene cluster, which encodes chlorocatechol degradation in Ralstonia eutropha JMP134(pJP4). J Bacteriol 1996; 178:6824-32. [PMID: 8955303 PMCID: PMC178582 DOI: 10.1128/jb.178.23.6824-6832.1996] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The tfdT gene is located upstream of and transcribed divergently from the tfdCDEF chlorocatechol-degradative operon on plasmid pJP4 of Ralstonia eutropha (formerly Alcaligenes eutrophus) JMP134. It is 684 bp long and encodes a 25-kDa protein. On the basis of its predicted amino acid sequence, the TfdT protein could be classified as a LysR-type transcriptional regulator. It has the highest degree of similarity with the proteins TcbR, ClcR, and TfdR, which are involved in the regulation of chloroaromatic breakdown. Despite this homology, the TfdT protein failed to activate the expression of its presumed target operon, tfdCDEF. This failure could be attributed to the inability of TfdT to bind the tfdC promoter region, an absolute requirement for transcriptional activation. Sequence analysis downstream of the tfdT gene revealed the presence of an insertion element-like element. We postulate that this element disrupted the tfdT open reading frame, leading to a premature termination and the production of a truncated, disfunctional TfdT protein. As an alternative to the inactivated TfdT protein, we propose that the product of the tfdR gene (or its identical twin, tfdS), located elsewhere on plasmid pJP4, can successfully take over the regulation of tfdCDEF expression. The TfdR protein was capable of binding to the tfdC promoter region and activated tfdCDEF gene expression by a factor of 80 to 100 when provided in cis as a tfdR-tfdCDEF hybrid regulon. Although to a lesser extent, induction of tfdCDEF expression was also observed when no functional TfdR protein was provided, implying cross-activation by chromosomally encoded regulatory elements in R. eutropha JMP134(pJP4).
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Affiliation(s)
- J H Leveau
- Swiss Federal Institute for Environmental Science and Technology (EAWAG), Duebendorf.
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44
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Abstract
We investigated the phylogenetic distribution of the SPI-1 and SPI-2 pathogenicity islands in Salmonella spp. SPI-1 was present in representatives of all eight subspecific groups, but no SPI-2-hybridizing sequences were detected in group V (S. bongori). Our data suggest that SPI-2 was acquired by S. enterica after its split from S. bongori.
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Affiliation(s)
- H Ochman
- Department of Biology, University of Rochester, New York 14627, USA
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45
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Affiliation(s)
- E A Groisman
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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46
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Ochman H, Soncini FC, Solomon F, Groisman EA. Identification of a pathogenicity island required for Salmonella survival in host cells. Proc Natl Acad Sci U S A 1996; 93:7800-4. [PMID: 8755556 PMCID: PMC38828 DOI: 10.1073/pnas.93.15.7800] [Citation(s) in RCA: 505] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
We have identified a region unique to the Salmonella typhimurium chromosome that is essential for virulence in mice. This region harbors at least three genes: two (spiA and spiB) encode products that are similar to proteins found in type III secretion systems, and a third (spiR) encodes a putative regulator. A strain with a mutation in spiA was unable to survive within macrophages but displayed wild-type levels of epithelial cell invasion. The culture supernatants of the spi mutants lacked a modified form of flagellin, which was present in the supernatant of the wild-type strain. This suggests that the Spi secretory apparatus exports a protease, or a protein that can alter the activity of a secreted protease. The "pathogenicity island" harboring the spi genes may encode the virulence determinants that set Salmonella apart from other enteric pathogens.
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Affiliation(s)
- H Ochman
- Department of Biology, University of Rochester, NY 14627, USA
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47
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Hensel M, Holden DW. Molecular genetic approaches for the study of virulence in both pathogenic bacteria and fungi. MICROBIOLOGY (READING, ENGLAND) 1996; 142 ( Pt 5):1049-1058. [PMID: 8704948 DOI: 10.1099/13500872-142-5-1049] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Michael Hensel
- Department of Infectious Diseases and Bacteriology, Royal Postgraduate Medical School, Du Cane Road, London W12 ONN, UK
| | - David W Holden
- Department of Infectious Diseases and Bacteriology, Royal Postgraduate Medical School, Du Cane Road, London W12 ONN, UK
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48
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Stein MA, Leung KY, Zwick M, Garcia-del Portillo F, Finlay BB. Identification of a Salmonella virulence gene required for formation of filamentous structures containing lysosomal membrane glycoproteins within epithelial cells. Mol Microbiol 1996; 20:151-64. [PMID: 8861213 DOI: 10.1111/j.1365-2958.1996.tb02497.x] [Citation(s) in RCA: 223] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Salmonella species are facultative intracellular pathogens that invade epithelial cells and reside within lysosomal membrane glycoprotein (lgp)-containing vacuoles. Coincident with the onset of bacterial replication inside these vacuoles, Salmonella induce the formation of stable lgp-containing filamentous structures that connect with the Salmonella-containing vacuoles. Salmonella typhimurium SL1344::Tn l0dCm mutant strains unable to induce these structures were isolated. All contained insertions within a novel Salmonella induced filament gene A (sifA). sifA is present only in Salmonella species and encodes a protein with a predicted molecular mass of 38 kDa and an apparent molecular mass of 35 kDa. sifA is flanked by 300 base pairs, and sifA and its flanking DNA show no homology to sequences in DNA databases. sifA is located within the potABCD operon, a housekeeping locus involved in periplasmic transport of polyamines. Fourteen-base-pair direct repeats mark the probable site of integration of sifA and its flanking DNA have a significantly reduced G+C content (41%) when compared with the potABCD operon (51%) and the Salmonella genome (52-54%). Deletion mutant strains in sifA or in the downstream potC were constructed. Delta sifA does not produce Salmonella-induced filaments in epithelial cells, and is attenuated in mice. Delta potC produces Salmonella-induced filaments in epithelial cells, and was fully virulent. Collectively, these results suggest that sifA arose by horizontal gene transfer into Salmonella and its product is involved in a virulence-associated intracellular phenotype related to Salmonella-induced filament formation.
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Affiliation(s)
- M A Stein
- Biotechnology Laboratory, University of British Columbia, Vancouver, Canada
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49
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Shea JE, Hensel M, Gleeson C, Holden DW. Identification of a virulence locus encoding a second type III secretion system in Salmonella typhimurium. Proc Natl Acad Sci U S A 1996; 93:2593-7. [PMID: 8637919 PMCID: PMC39842 DOI: 10.1073/pnas.93.6.2593] [Citation(s) in RCA: 579] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Mapping the insertion points of 16 signature-tagged transposon mutants on the Salmonella typhimurium chromosome led to the identification of a 40-kb virulence gene cluster at minute 30.7. This locus is conserved among all other Salmonella species examined but is not present in a variety of other pathogenic bacteria or in Escherichia coli K-12. Nucleotide sequencing of a portion of this locus revealed 11 open reading frames whose predicted proteins encode components of a type III secretion system. To distinguish between this and the type III secretion system encoded by the inv/spa invasion locus known to reside on a pathogenicity island, we refer to the inv/spa locus as Salmonella pathogenicity island (SPI) 1 and the new locus as SPI2. SPI2 has a lower G+C content than that of the remainder of the Salmonella genome and is flanked by genes whose products share greater than 90% identity with those of the E. coli ydhE and pykF genes. Thus SPI2 was probably acquired horizontally by insertion into a region corresponding to that between the ydhE and pykF genes of E. coli. Virulence studies of SPI2 mutants have shown them to be attenuated by at least five orders of magnitude compared with the wild-type strain after oral or intraperitoneal inoculation of mice.
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Affiliation(s)
- J E Shea
- Department of Infectious Diseases and Bacteriology, Royal Postgraduate Medical School, London, United Kingdom
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Affiliation(s)
- J E Galán
- Department of Molecular Genetics and Microbiology, State University of New York at Stony Brook 11794-5222, USA
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