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Wang X, Zhu S, Zhao JH, Bao HX, Liu H, Ding TM, Liu GR, Li YG, Johnston RN, Cao FL, Tang L, Liu SL. Genetic boundaries delineate the potential human pathogen Salmonella bongori into discrete lineages: divergence and speciation. BMC Genomics 2019; 20:930. [PMID: 31801462 PMCID: PMC6894293 DOI: 10.1186/s12864-019-6259-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 11/05/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Salmonella bongori infect mainly cold-blooded hosts, but infections by S. bongori in warm-blooded hosts have been reported. We hypothesized that S. bongori might have diverged into distinct phylogenetic lineages, with some being able to infect warm-blooded hosts. RESULTS To inspect the divergence status of S. bongori, we first completely sequenced the parakeet isolate RKS3044 and compared it with other sequenced S. bongori strains. We found that RKS3044 contained a novel T6SS encoded in a pathogenicity island-like structure, in addition to a T6SS encoded in SPI-22, which is common to all S. bongori strains so far reported. This novel T6SS resembled the SPI-19 T6SS of the warm-blooded host infecting Salmonella Subgroup I lineages. Genomic sequence comparisons revealed different genomic sequence amelioration events among the S. bongori strains, including a unique CTAG tetranucleotide degeneration pattern in RKS3044, suggesting non-overlapping gene pools between RKS3044 and other S. bongori lineages/strains leading to their independent accumulation of genomic variations. We further proved the existence of a clear-cut genetic boundary between RKS3044 and the other S. bongori lineages/strains analyzed in this study. CONCLUSIONS The warm-blooded host-infecting S. bongori strain RKS3044 has diverged with distinct genomic features from other S. bongori strains, including a novel T6SS encoded in a previously not reported pathogenicity island-like structure and a unique genomic sequence degeneration pattern. These findings alert cautions about the emergence of new pathogens originating from non-pathogenic ancestors by acquiring specific pathogenic traits.
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Affiliation(s)
- Xiaoyu Wang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081 China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Songling Zhu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081 China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Jian-Hua Zhao
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081 China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Hong-Xia Bao
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081 China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Huidi Liu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081 China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Tie-Min Ding
- Department of Medicine and Food Engineering, Harbin Labor Technician College, Harbin, China
| | - Gui-Rong Liu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081 China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Yong-Guo Li
- Department of Infectious Diseases, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Randal N. Johnston
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Feng-Lin Cao
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081 China
- Department of Hematology, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Le Tang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081 China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
- Department of Ecosystems and Public Health, University of Calgary, Calgary, Canada
| | - Shu-Lin Liu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081 China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
- Department of Infectious Diseases, The First Affiliated Hospital, Harbin Medical University, Harbin, China
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
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Conserved intergenic sequences revealed by CTAG-profiling in Salmonella: thermodynamic modeling for function prediction. Sci Rep 2017; 7:43565. [PMID: 28262684 PMCID: PMC5337935 DOI: 10.1038/srep43565] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/23/2017] [Indexed: 01/14/2023] Open
Abstract
Highly conserved short sequences help identify functional genomic regions and facilitate genomic annotation. We used Salmonella as the model to search the genome for evolutionarily conserved regions and focused on the tetranucleotide sequence CTAG for its potentially important functions. In Salmonella, CTAG is highly conserved across the lineages and large numbers of CTAG-containing short sequences fall in intergenic regions, strongly indicating their biological importance. Computer modeling demonstrated stable stem-loop structures in some of the CTAG-containing intergenic regions, and substitution of a nucleotide of the CTAG sequence would radically rearrange the free energy and disrupt the structure. The postulated degeneration of CTAG takes distinct patterns among Salmonella lineages and provides novel information about genomic divergence and evolution of these bacterial pathogens. Comparison of the vertically and horizontally transmitted genomic segments showed different CTAG distribution landscapes, with the genome amelioration process to remove CTAG taking place inward from both terminals of the horizontally acquired segment.
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Tang L, Liu WQ, Fang X, Sun Q, Zhu SL, Wang CX, Wang XY, Li YG, Zhu DL, Sanderson KE, Johnston RN, Liu GR, Liu SL. CTAG-containing cleavage site profiling to delineate Salmonella into natural clusters. PLoS One 2014; 9:e103388. [PMID: 25137186 PMCID: PMC4138082 DOI: 10.1371/journal.pone.0103388] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 06/30/2014] [Indexed: 11/24/2022] Open
Abstract
Background The bacterial genus Salmonella contains thousands of serotypes that infect humans or other hosts, causing mild gastroenteritis to potentially fatal systemic infections in humans. Pathogenically distinct Salmonella serotypes have been classified as individual species or as serological variants of merely one or two species, causing considerable confusion in both research and clinical settings. This situation reflects a long unanswered question regarding whether the Salmonella serotypes exist as discrete genetic clusters (natural species) of organisms or as phenotypic (e.g. pathogenic) variants of a single (or two) natural species with a continuous spectrum of genetic divergence among them. Our recent work, based on genomic sequence divergence analysis, has demonstrated that genetic boundaries exist among Salmonella serotypes, circumscribing them into clear-cut genetic clusters of bacteria. Methodologies/Principal Findings To further test the genetic boundary concept for delineating Salmonella into clearly defined natural lineages (e.g., species), we sampled a small subset of conserved genomic DNA sequences, i.e., the endonuclease cleavage sites that contain the highly conserved CTAG sequence such as TCTAGA for XbaI. We found that the CTAG-containing cleavage sequence profiles could be used to resolve the genetic boundaries as reliably and efficiently as whole genome sequence comparisons but with enormously reduced requirements for time and resources. Conclusions Profiling of CTAG sequence subsets reflects genetic boundaries among Salmonella lineages and can delineate these bacteria into discrete natural clusters.
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Affiliation(s)
- Le Tang
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
- Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Wei-Qiao Liu
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Canada
| | - Xin Fang
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
- Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Qiang Sun
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
- Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Song-Ling Zhu
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
- Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Chun-Xiao Wang
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
- Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Xiao-Yu Wang
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
- Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Yong-Guo Li
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Department of Infectious Diseases of First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Da-Ling Zhu
- Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China
- College of Pharmacy, Daqing Campus, Harbin Medical University, Daqing, China
| | - Kenneth E. Sanderson
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Canada
| | - Randal N. Johnston
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Gui-Rong Liu
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
- Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- * E-mail: grliu.natsumi@gmailcom (GRL); (SLL)
| | - Shu-Lin Liu
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
- Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Canada
- Department of Infectious Diseases of First Affiliated Hospital, Harbin Medical University, Harbin, China
- * E-mail: grliu.natsumi@gmailcom (GRL); (SLL)
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Tang L, Wang CX, Zhu SL, Li Y, Deng X, Johnston RN, Liu GR, Liu SL. Genetic boundaries to delineate the typhoid agent and other Salmonella serotypes into distinct natural lineages. Genomics 2013; 102:331-7. [PMID: 23933189 DOI: 10.1016/j.ygeno.2013.07.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 07/22/2013] [Accepted: 07/24/2013] [Indexed: 11/16/2022]
Abstract
The deadly human typhoid agent was initially classified as a species called Salmonella typhi but later reclassified as a serovar of Salmonella enterica together with other pathogenically diverse serovars. The dynamic changes of Salmonella taxonomy reflect the need to clarify the phylogenetic status of the Salmonella serovars: are they discrete lineages or variants of a genetic lineage? To answer this question, we compared S. typhi and other Salmonella serotypes. We found that the S. typhi and Salmonella typhimurium strains had over 90% and ca. 80%, respectively, of their genes identical; however, between S. typhi and S. typhimurium, this percentage dropped to 6%, suggesting the existence of genetic boundaries between them. We conclude that S. typhi and the other compared Salmonella serovars have developed into distinct lineages circumscribed by the genetic boundary. This concept and methods may be used to delineate other Salmonella serotypes, many of which are polyphyletic, needing differentiation.
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Affiliation(s)
- Le Tang
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
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Tang L, Li Y, Deng X, Johnston RN, Liu GR, Liu SL. Defining natural species of bacteria: clear-cut genomic boundaries revealed by a turning point in nucleotide sequence divergence. BMC Genomics 2013; 14:489. [PMID: 23865772 PMCID: PMC3751360 DOI: 10.1186/1471-2164-14-489] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 07/15/2013] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Bacteria are currently classified into arbitrary species, but whether they actually exist as discrete natural species was unclear. To reveal genomic features that may unambiguously group bacteria into discrete genetic clusters, we carried out systematic genomic comparisons among representative bacteria. RESULTS We found that bacteria of Salmonella formed tight phylogenetic clusters separated by various genetic distances: whereas over 90% of the approximately four thousand shared genes had completely identical sequences among strains of the same lineage, the percentages dropped sharply to below 50% across the lineages, demonstrating the existence of clear-cut genetic boundaries by a steep turning point in nucleotide sequence divergence. Recombination assays supported the genetic boundary hypothesis, suggesting that genetic barriers had been formed between bacteria of even very closely related lineages. We found similar situations in bacteria of Yersinia and Staphylococcus. CONCLUSIONS Bacteria are genetically isolated into discrete clusters equivalent to natural species.
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Affiliation(s)
- Le Tang
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin, China
- Department of Biopharmaceutics, Harbin Medical University, 157 Baojian Road, Harbin 150081, China
| | - Yang Li
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin, China
| | - Xia Deng
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin, China
| | | | - Gui-Rong Liu
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin, China
- Department of Biopharmaceutics, Harbin Medical University, 157 Baojian Road, Harbin 150081, China
| | - Shu-Lin Liu
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin, China
- Department of Biopharmaceutics, Harbin Medical University, 157 Baojian Road, Harbin 150081, China
- Microbiology and Infectious Diseases, University of Calgary, Calgary, Canada
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Zou QH, Li RQ, Wang YJ, Liu SL. Identification of genes to differentiate closely related Salmonella lineages. PLoS One 2013; 8:e55988. [PMID: 23441160 PMCID: PMC3575412 DOI: 10.1371/journal.pone.0055988] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 01/07/2013] [Indexed: 01/23/2023] Open
Abstract
Background Salmonella are important human and animal pathogens. Though highly related, the Salmonella lineages may be strictly adapted to different hosts or cause different diseases, from mild local illness like gastroenteritis to fatal systemic infections like typhoid. Therefore, rapid and accurate identification of Salmonella is essential for timely and correct diagnosis of Salmonella infections. The current identification methods such as 16S rRNA sequencing and multilocus sequence typing are expensive and time consuming. Additionally, these methods often do not have sufficient distinguishing resolution among the Salmonella lineages. Methodologies/Principal Findings We compared 27 completely sequenced Salmonella genomes to identify possible genomic features that could be used for differentiation of individual lineages. We concatenated 2372 core genes in each of the 27 genomes and constructed a neighbor-joining tree. On the tree, strains of each serotype were clustered tightly together and different serotypes were unambiguously separated with clear genetic distances, demonstrating systematic genomic divergence among the Salmonella lineages. We made detailed comparisons among the 27 genomes and identified distinct sets of genomic differences, including nucleotide variations and genomic islands (GIs), among the Salmonella lineages. Two core genes STM4261 and entF together could unambiguously distinguish all Salmonella lineages compared in this study. Additionally, strains of a lineage have a common set of GIs and closely related lineages have similar sets of GIs. Conclusions Salmonella lineages have accumulated distinct sets of mutations and laterally acquired DNA (e.g., GIs) in evolution. Two genes entF and STM4261 have diverged sufficiently among the Salmonella lineages to be used for their differentiation. Further investigation of the distinct sets of mutations and GIs will lead to novel insights into genomic evolution of Salmonella and greatly facilitate the elucidation of pathogeneses of Salmonella infections.
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Affiliation(s)
- Qing-Hua Zou
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Ren-Qing Li
- Institute of Immunology, Beijing Center for Disease Control and Prevention, Beijing, China
| | - Ye-Jun Wang
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
| | - Shu-Lin Liu
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- * E-mail:
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Eisenstark A. Genetic diversity among offspring from archived Salmonella enterica ssp. enterica serovar typhimurium (Demerec Collection): in search of survival strategies. Annu Rev Microbiol 2010; 64:277-92. [PMID: 20825350 DOI: 10.1146/annurev.micro.091208.073614] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Extensive phenotypic and genomic diversity was detected among offspring of Salmonella enterica ssp. enterica serovar Typhimurium LT2 (nonmutator) and LT7 (mutator, mutL) strains after decades of storage in sealed nutrient agar stabs. In addition to numerous losses in carbon and nitrogen metabolism, the acquired new metabolites indicated that alternate pathways were established. Particularly striking was the array of phage types when this phenotype was expected to be a stable feature. Evidence is presented regarding the role of mutator gene mutL(-) in the establishment of diversity as well as the ability of cells to return to mutL(+) genetic stabilization. Mutations included deletions, duplications, frameshifts, inversions and transpositions. In competition tests, survivors were more fit than were wild type. Because survival strategies continue to intrigue microbiologists, observations are compared with those of others who have addressed related questions. A brief genealogy of the archived strains is also recorded.
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Affiliation(s)
- Abraham Eisenstark
- Cancer Research Center and Division of Biological Sciences, University of Missouri, Columbia, Missouri 65201, USA.
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Matthews TD, Edwards R, Maloy S. Chromosomal rearrangements formed by rrn recombination do not improve replichore balance in host-specific Salmonella enterica serovars. PLoS One 2010; 5:e13503. [PMID: 20976060 PMCID: PMC2957434 DOI: 10.1371/journal.pone.0013503] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 09/23/2010] [Indexed: 01/16/2023] Open
Abstract
Background Most of the ∼2,600 serovars of Salmonella enterica have a broad host range as well as a conserved gene order. In contrast, some Salmonella serovars are host-specific and frequently exhibit large chromosomal rearrangements from recombination between rrn operons. One hypothesis explaining these rearrangements suggests that replichore imbalance introduced from horizontal transfer of pathogenicity islands and prophages drives chromosomal rearrangements in an attempt to improve balance. Methodology/Principal Findings This hypothesis was directly tested by comparing the naturally-occurring chromosomal arrangement types to the theoretically possible arrangement types, and estimating their replichore balance using a calculator. In addition to previously characterized strains belonging to host-specific serovars, the arrangement types of 22 serovar Gallinarum strains was also determined. Only 48 out of 1,440 possible arrangement types were identified in 212 host-specific strains. While the replichores of most naturally-occurring arrangement types were well-balanced, most theoretical arrangement types had imbalanced replichores. Furthermore, the most common types of rearrangements did not change replichore balance. Conclusions/Significance The results did not support the hypothesis that replichore imbalance causes these rearrangements, and suggest that the rearrangements could be explained by aspects of a host-specific lifestyle.
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Affiliation(s)
- T. David Matthews
- Center for Microbial Sciences, Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Robert Edwards
- Center for Microbial Sciences, Department of Biology, San Diego State University, San Diego, California, United States of America
- Department of Computer Science, San Diego State University, San Diego, California, United States of America
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Stanley Maloy
- Center for Microbial Sciences, Department of Biology, San Diego State University, San Diego, California, United States of America
- * E-mail:
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Liu WQ, Feng Y, Wang Y, Zou QH, Chen F, Guo JT, Peng YH, Jin Y, Li YG, Hu SN, Johnston RN, Liu GR, Liu SL. Salmonella paratyphi C: genetic divergence from Salmonella choleraesuis and pathogenic convergence with Salmonella typhi. PLoS One 2009; 4:e4510. [PMID: 19229335 PMCID: PMC2640428 DOI: 10.1371/journal.pone.0004510] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2008] [Accepted: 12/15/2008] [Indexed: 01/13/2023] Open
Abstract
Background Although over 1400 Salmonella serovars cause usually self-limited gastroenteritis in humans, a few, e.g., Salmonella typhi and S. paratyphi C, cause typhoid, a potentially fatal systemic infection. It is not known whether the typhoid agents have evolved from a common ancestor (by divergent processes) or acquired similar pathogenic traits independently (by convergent processes). Comparison of different typhoid agents with non-typhoidal Salmonella lineages will provide excellent models for studies on how similar pathogens might have evolved. Methodologies/Principal Findings We sequenced a strain of S. paratyphi C, RKS4594, and compared it with previously sequenced Salmonella strains. RKS4594 contains a chromosome of 4,833,080 bp and a plasmid of 55,414 bp. We predicted 4,640 intact coding sequences (4,578 in the chromosome and 62 in the plasmid) and 152 pseudogenes (149 in the chromosome and 3 in the plasmid). RKS4594 shares as many as 4346 of the 4,640 genes with a strain of S. choleraesuis, which is primarily a swine pathogen, but only 4008 genes with another human-adapted typhoid agent, S. typhi. Comparison of 3691 genes shared by all six sequenced Salmonella strains placed S. paratyphi C and S. choleraesuis together at one end, and S. typhi at the opposite end, of the phylogenetic tree, demonstrating separate ancestries of the human-adapted typhoid agents. S. paratyphi C seemed to have suffered enormous selection pressures during its adaptation to man as suggested by the differential nucleotide substitutions and different sets of pseudogenes, between S. paratyphi C and S. choleraesuis. Conclusions S. paratyphi C does not share a common ancestor with other human-adapted typhoid agents, supporting the convergent evolution model of the typhoid agents. S. paratyphi C has diverged from a common ancestor with S. choleraesuis by accumulating genomic novelty during adaptation to man.
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Affiliation(s)
- Wei-Qiao Liu
- Genomics Research Center, Harbin Medical University, Harbin, China
- Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Ye Feng
- JD Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yan Wang
- Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Qing-Hua Zou
- Department of Microbiology, Peking University Health Science Center, Beijing, China
| | - Fang Chen
- Department of Microbiology, Peking University Health Science Center, Beijing, China
| | - Ji-Tao Guo
- Department of Microbiology, Peking University Health Science Center, Beijing, China
| | - Yi-Hong Peng
- Department of Microbiology, Peking University Health Science Center, Beijing, China
| | - Yan Jin
- Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Yong-Guo Li
- Depatment of Infectious Diseases, First Hospital, Harbin Medical University, Harbin, China
| | - Song-Nian Hu
- JD Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Randal N. Johnston
- Departments of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Gui-Rong Liu
- Genomics Research Center, Harbin Medical University, Harbin, China
- Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Peking University Health Science Center, Beijing, China
- * E-mail: (G-RL); (S-LL)
| | - Shu-Lin Liu
- Genomics Research Center, Harbin Medical University, Harbin, China
- Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Peking University Health Science Center, Beijing, China
- Depatment of Infectious Diseases, First Hospital, Harbin Medical University, Harbin, China
- * E-mail: (G-RL); (S-LL)
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Abstract
Physical mapping is a key methodology for determining the genome structure of Salmonella and revealing genomic differences among different strains, especially regarding phylogenetic relationships and evolution of these bacteria. In fact, physical mapping is the only practical approach to genomic comparisons among Salmonella involving large numbers of strains to document their insertions, deletions, and rearrangements that may be related to pathogenesis and host specificity. The core technique in physical mapping is pulsed field gel electrophoresis (PFGE), which can separate DNA fragments ranging from less than one kilobase to several thousand kilobases. After genomic DNA has been cleaved by an endonuclease and the DNA fragments have been separated on PFGE, a number of techniques will be employed to arrange the separated DNA fragments back to the original order as in the genome. These techniques include Southern hybridization with known DNA as the probe to identify the DNA fragments, Tn10 insertion inactivation to locate genes and identify the fragments that contain these genes, double cleavage to determine the physical distances of cleavage sites between different endonucleases for further refining the physical map, and I-CeuI partial cleavage to lay out the overall genome structure of the bacteria. The combination of these mapping techniques makes it possible to construct a Salmonella genome map of high resolution, sufficient for comparisons among different Salmonella lineages or among strains of the same lineage.
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11
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Evguenieva-Hackenberg E, Selenska-Pobell S. Genome analysis of five soil bacterial isolates named formerlyEnterobacter agglomerans. ACTA ACUST UNITED AC 2008. [DOI: 10.1111/j.1365-2672.1995.tb03123.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Liu WQ, Liu GR, Li JQ, Xu GM, Qi D, He XY, Deng J, Zhang FM, Johnston RN, Liu SL. Diverse genome structures of Salmonella paratyphi C. BMC Genomics 2007; 8:290. [PMID: 17718928 PMCID: PMC2000905 DOI: 10.1186/1471-2164-8-290] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Accepted: 08/27/2007] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Salmonella paratyphi C, like S. typhi, is adapted to humans and causes typhoid fever. Previously we reported different genome structures between two strains of S. paratyphi C, which suggests that S. paratyphi C might have a plastic genome (large DNA segments being organized in different orders or orientations on the genome). As many but not all host-adapted Salmonella pathogens have large genomic insertions as well as the supposedly resultant genomic rearrangements, bacterial genome plasticity presents an extraordinary evolutionary phenomenon. Events contributing to genomic plasticity, especially large insertions, may be associated with the formation of particular Salmonella pathogens. RESULTS We constructed a high resolution genome map in S. paratyphi C strain RKS4594 and located four insertions totaling 176 kb (including the 90 kb SPI7) and seven deletions totaling 165 kb relative to S. typhimurium LT2. Two rearrangements were revealed, including an inversion of 1602 kb covering the ter region and the translocation of the 43 kb I-CeuI F fragment. The 23 wild type strains analyzed in this study exhibited diverse genome structures, mostly as a result of recombination between rrn genes. In at least two cases, the rearrangements involved recombination between genomic sites other than the rrn genes, possibly homologous genes in prophages. Two strains had a 20 kb deletion between rrlA and rrlB, which is a highly conservative region and no deletion has been reported in this region in any other Salmonella lineages. CONCLUSION S. paratyphi C has diverse genome structures among different isolates, possibly as a result of large genomic insertions, e.g., SPI7. Although the Salmonella typhoid agents may not be more closely related among them than each of them to other Salmonella lineages, they may have evolved in similar ways, i.e., acquiring typhoid-associated genes followed by genome structure rearrangements. Comparison of multiple Salmonella typhoid agents at both single sequenced genome and population levels will facilitate the studies on the evolutionary process of typhoid pathogenesis, especially the identification of typhoid-associated genes.
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Affiliation(s)
- Wei-Qiao Liu
- Microbiology, Peking University Health Science Center, Beijing, China
- Microbiology and Infectious Diseases, University of Calgary, Calgary, Canada
| | - Gui-Rong Liu
- Microbiology, Peking University Health Science Center, Beijing, China
- Microbiology and Infectious Diseases, University of Calgary, Calgary, Canada
- Microbiology, Harbin Medical University, Harbin, China
| | - Jun-Qian Li
- Microbiology, Peking University Health Science Center, Beijing, China
| | - Guo-Min Xu
- Microbiology, Peking University Health Science Center, Beijing, China
| | - Danni Qi
- Microbiology, Harbin Medical University, Harbin, China
| | - Xiao-Yan He
- Microbiology, Peking University Health Science Center, Beijing, China
| | - Juan Deng
- Microbiology, Peking University Health Science Center, Beijing, China
| | | | - Randal N Johnston
- Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Shu-Lin Liu
- Microbiology, Peking University Health Science Center, Beijing, China
- Microbiology and Infectious Diseases, University of Calgary, Calgary, Canada
- Microbiology, Harbin Medical University, Harbin, China
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13
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Wu KY, Liu GR, Liu WQ, Wang AQ, Zhan S, Sanderson KE, Johnston RN, Liu SL. The genome of Salmonella enterica serovar gallinarum: distinct insertions/deletions and rare rearrangements. J Bacteriol 2005; 187:4720-7. [PMID: 15995186 PMCID: PMC1169526 DOI: 10.1128/jb.187.14.4720-4727.2005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Salmonella enterica serovar Gallinarum is a fowl-adapted pathogen, causing typhoid fever in chickens. It has the same antigenic formula (1,9,12:--:--) as S. enterica serovar Pullorum, which is also adapted to fowl but causes pullorum disease (diarrhea). The close relatedness but distinct pathogeneses make this pair of fowl pathogens good models for studies of bacterial genomic evolution and the way these organisms acquired pathogenicity. To locate and characterize the genomic differences between serovar Gallinarum and other salmonellae, we constructed a physical map of serovar Gallinarum strain SARB21 by using I-CeuI, XbaI, and AvrII with pulsed-field gel electrophoresis techniques. In the 4,740-kb genome, we located two insertions and six deletions relative to the genome of S. enterica serovar Typhimurium LT2, which we used as a reference Salmonella genome. Four of the genomic regions with reduced lengths corresponded to the four prophages in the genome of serovar Typhimurium LT2, and the others contained several smaller deletions relative to serovar Typhimurium LT2, including regions containing srfJ, std, and stj and gene clusters encoding a type I restriction system in serovar Typhimurium LT2. The map also revealed some rare rearrangements, including two inversions and several translocations. Further characterization of these insertions, deletions, and rearrangements will provide new insights into the molecular basis for the specific host-pathogen interactions and mechanisms of genomic evolution to create a new pathogen.
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Affiliation(s)
- Kai-Yu Wu
- Department of Microbiology and Infectious Diseases, University of Calgary, Alberta, Canada
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14
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Kothapalli S, Nair S, Alokam S, Pang T, Khakhria R, Woodward D, Johnson W, Stocker BAD, Sanderson KE, Liu SL. Diversity of genome structure in Salmonella enterica serovar Typhi populations. J Bacteriol 2005; 187:2638-50. [PMID: 15805510 PMCID: PMC1070368 DOI: 10.1128/jb.187.8.2638-2650.2005] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The genomes of most strains of Salmonella and Escherichia coli are highly conserved. In contrast, all 136 wild-type strains of Salmonella enterica serovar Typhi analyzed by partial digestion with I-CeuI (an endonuclease which cuts within the rrn operons) and pulsed-field gel electrophoresis and by PCR have rearrangements due to homologous recombination between the rrn operons leading to inversions and translocations. Recombination between rrn operons in culture is known to be equally frequent in S. enterica serovar Typhi and S. enterica serovar Typhimurium; thus, the recombinants in S. enterica serovar Typhi, but not those in S. enterica serovar Typhimurium, are able to survive in nature. However, even in S. enterica serovar Typhi the need for genome balance and the need for gene dosage impose limits on rearrangements. Of 100 strains of genome types 1 to 6, 72 were only 25.5 kb off genome balance (the relative lengths of the replichores during bidirectional replication from oriC to the termination of replication [Ter]), while 28 strains were less balanced (41 kb off balance), indicating that the survival of the best-balanced strains was greater. In addition, the need for appropriate gene dosage apparently selected against rearrangements which moved genes from their accustomed distance from oriC. Although rearrangements involving the seven rrn operons are very common in S. enterica serovar Typhi, other duplicated regions, such as the 25 IS200 elements, are very rarely involved in rearrangements. Large deletions and insertions in the genome are uncommon, except for deletions of Salmonella pathogenicity island 7 (usually 134 kb) from fragment I-CeuI-G and 40-kb insertions, possibly a prophage, in fragment I-CeuI-E. The phage types were determined, and the origins of the phage types appeared to be independent of the origins of the genome types.
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Affiliation(s)
- Sushma Kothapalli
- Department of Biological Sciences, University of Calgary, Calgary T2N 1N4, Canada
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15
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Liu GR, Edwards K, Eisenstark A, Fu YM, Liu WQ, Sanderson KE, Johnston RN, Liu SL. Genomic diversification among archival strains of Salmonella enterica serovar typhimurium LT7. J Bacteriol 2003; 185:2131-42. [PMID: 12644482 PMCID: PMC151480 DOI: 10.1128/jb.185.7.2131-2142.2003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2002] [Accepted: 01/07/2003] [Indexed: 11/20/2022] Open
Abstract
To document genomic changes during long periods of storage, we analyzed Salmonella enterica serovar Typhimurium LT7, a mutator strain that was previously reported to have higher rates of mutations compared to other serovar Typhimurium strains such as LT2. Upon plating directly from sealed agar stabs that had been stocked at room temperature for up to four decades, many auxotrophic mutants derived from LT7 gave rise to colonies of different sizes. Restreaking from single colonies consistently yielded colonies of diverse sizes even when we repeated single-colony isolation nine times. Colonies from the first plating had diverse genomic changes among and even within individual vials, including translocations, inversions, duplications, and point mutations, which were detected by rare-cutting endonuclease analysis with pulsed-field gel electrophoresis. Interestingly, even though the colony size kept diversifying, all descendents of the same single colonies from the first plating had the same sets of detected genomic changes. We did not detect any colony size or genome structure diversification in serovar Typhimurium LT7 stocked at -70 degrees C or in serovar Typhimurium LT2 stocked either at -70 degrees C or at room temperature. These results suggest that, although colony size diversification occurred during rapid growth, all detected genomic changes took place during the storage at room temperature and were carried over to their descendents without further changes during rapid growth in rich medium. We constructed a genomic cleavage map on the LT7 strain that had been stocked at -70 degrees C and located all of the detected genomic changes on the map. We speculated on the significance of mutators for survival and evolution under environmentally stressed conditions.
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Affiliation(s)
- Gui-Rong Liu
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, T2N 4N1 Alberta, Canada
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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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Ng I, Liu SL, Sanderson KE. Role of genomic rearrangements in producing new ribotypes of Salmonella typhi. J Bacteriol 1999; 181:3536-41. [PMID: 10348867 PMCID: PMC93822 DOI: 10.1128/jb.181.11.3536-3541.1999] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Salmonella typhi is the only species of Salmonella which grows exclusively in humans, in whom it causes enteric typhoid fever. Strains of S. typhi show very little variation in electrophoretic types, restriction fragment length polymorphisms, cell envelope proteins, and intervening sequences, but the same strains are very heterogeneous for ribotypes which are detected with the restriction endonuclease PstI. In addition, the genome of S. typhi has been proven to undergo genomic rearrangement due to homologous recombination between the seven copies of rrn genes. The relationship between ribotype heterogeneity and genomic rearrangement was investigated. Strains of S. typhi which belong to 23 different genome types were analyzed by ribotyping. A limited number of ribotypes were found within the same genome type group; e. g., most strains of genome type 3 belonged to only two different ribotypes, which result from recombination between rrnH and rrnG operons. Different genome type groups normally have different ribotypes. The size and identity of the PstI fragment containing each of the seven different rrn operons from S. typhi Ty2 were determined, and from these data, one can infer how genomic rearrangement forms new ribotypes. It is postulated that genomic rearrangement, rather than mutation, is largely responsible for producing the ribotype heterogeneity in S. typhi.
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Affiliation(s)
- I Ng
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
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18
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Liu SL, Sanderson KE. Homologous recombination between rrn operons rearranges the chromosome in host-specialized species of Salmonella. FEMS Microbiol Lett 1998; 164:275-81. [PMID: 9682477 DOI: 10.1111/j.1574-6968.1998.tb13098.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Partial digestion with I-CeuI, which digests bacterial DNA at the gene coding for the large subunit rRNA, established the rrn genomic skeleton (the distance in kb between rRNA operons) in 56 strains of Salmonella, from Salmonella Reference B (SARB) set. All had seven I-CeuI sites, indicating seven rrn operons. The order of I-CeuI fragments was ABCDEFG in S. typhimurium LT2 and in 31 other species, mostly host-generalists; in S. typhi, S. paratyphi C, S. gallinarum, and S. pullorum (host-specialized species), these fragments are rearranged, due to homologous recombination between the rrn operons. Rearrangements, such as inversions and translocations not involving the rrn operons, are rare. I-CeuI fragments of some species are larger than the norm, suggesting the insertion of unique blocks of DNA by lateral transfer from other species.
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Affiliation(s)
- S L Liu
- Department of Biological Sciences, University of Calgary, Alberta, Canada
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19
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Abstract
Early genetic studies showed conservation of gene order in the enteric bacteria. Two recent methods using pulsed field gel electrophoresis (PFGE) to determine the physical map of the genome are: (i) partial digestion with the endonuclease I-CeuI, which digests the DNA of bacteria in the rrn operon for rRNA (ribosomal RNA), thus establishing the "rrn genomic skeleton" (the size in kbp of the intervals between rRNA operons); (ii) analysis of XbaI and B1nI sites within Tn10 insertions in the chromosome. The order of I-CeuI fragments, which is ABCDEFG in S. typhimurium LT2 and E. coli K-12, was found to be conserved in most Salmonella species, most of which grow in many hosts (host-generalists). However, in S. typhi, S. paratyphi C, S. gallinarum, and S. pullorum, species which are host-specialized, these fragments are rearranged, due to homologous recombination between the rrn operons, resulting in translocations and inversions. Inversions and translocations not involving the rrn operons are seldom detected except for inversions over the TER (termination of replication) region. Additive genetic changes (due to lateral transfer resulting in insertion of nonhomologous DNA) have resulted in "loops" containing blocks of DNA which provide new genes to specific strains, thus driving rapid evolution of new traits.
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Affiliation(s)
- K E Sanderson
- Salmonella Genetic Stock Centre, Department of Biological Sciences, University of Calgary, Alberta, Canada.
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20
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Jumas-Bilak E, Michaux-Charachon S, Bourg G, O'Callaghan D, Ramuz M. Differences in chromosome number and genome rearrangements in the genus Brucella. Mol Microbiol 1998; 27:99-106. [PMID: 9466259 DOI: 10.1046/j.1365-2958.1998.00661.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We have studied the genomic structure and constructed the SpeI, PacI and I-CeuI restriction maps of the four biovars of the pathogenic bacterium Brucella suis. B. suis biovar 1 has two chromosomes of 2.1 Mb and 1.15 Mb, similar to those of the other Brucella species: B. melitensis, B. abortus, B. ovis and B. neotomae. Two chromosomes were also observed in the genome of B. suis biovars 2 and 4, but with sizes of 1.85 Mb and 1.35 Mb, whereas only one chromosome with a size of 3.1 Mb was found in B. suis biovar 3. We show that the differences in chromosome size and number can be explained by rearrangements at chromosomal regions containing the three rrn genes. The location and orientation of these genes confirmed that these rearrangements are due to homologous recombination at the rrn loci. This observation allows us to propose a scheme for the evolution of the genus Brucella in which the two chromosome-containing strains can emerge from an hypothetical ancestor with a single chromosome, which is probably similar to that of B. suis biovar 3. As the genus Brucella is certainly monospecific, this is the first time that differences in chromosome number have been observed in strains of the same bacterial species.
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Affiliation(s)
- E Jumas-Bilak
- Institut National de la Santé et de la Recherche Médicale, Unité 431, Faculté de Médecine, Nîmes, France
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21
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7.4 Physical Analysis of the Salmonella Typhimurium Genome. METHODS IN MICROBIOLOGY 1998. [DOI: 10.1016/s0580-9517(08)70298-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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22
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Liu SL, Sanderson KE. Highly plastic chromosomal organization in Salmonella typhi. Proc Natl Acad Sci U S A 1996; 93:10303-8. [PMID: 8816795 PMCID: PMC38379 DOI: 10.1073/pnas.93.19.10303] [Citation(s) in RCA: 133] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Gene order in the chromosomes of Escherichia coli K-12 and Salmonella typhimurium LT2, and in many other species of Salmonella, is strongly conserved, even though the genera diverged about 160 million years ago. However, partial digestion of chromosomal DNA of Salmonella typhi, the causal organism of typhoid fever, with the endonuclease I-CeuI followed by separation of the DNA fragments by pulsed-field gel electrophoresis showed that the chromosomes of independent wild-type isolates of S. typhi are rearranged due to homologous recombination between the seven rrn genes that code for ribosomal RNA. The order of genes within the I-CeuI fragments is largely conserved, but the order of the fragments on the chromosome is rearranged. Twenty-one different orders of the I-CeuI fragments were detected among the 127 wild-type strains we examined. Duplications and deletions were not found, but transpositions and inversions were common. Transpositions of I-CeuI fragments into sites that do not change their distance from the origin of replication (oriC) are frequently detected among the wild-type strains, but transpositions that move the fragments much further from oriC were rare. This supports the gene dosage hypothesis that genes at different distances from oriC have different gene dosages and, hence, different gene expression, and that during evolution genes become adapted to their specific location; thus, cells with changes in gene location due to transpositions may be less fit. Therefore, gene dosage may be one of the forces that conserves gene order, although its effects seem less strong in S. typhi than in other enteric bacteria. However, both the gene dosage and the genomic balance hypotheses, the latter of which states that the origin (oriC) and terminus (TER) of replication must be separated by 180 degrees C, need further investigation.
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Affiliation(s)
- S L Liu
- Department of Biological Sciences, University of Calgary, AB, Canada
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23
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Liu SL, Sanderson KE. The chromosome of Salmonella paratyphi A is inverted by recombination between rrnH and rrnG. J Bacteriol 1995; 177:6585-92. [PMID: 7592437 PMCID: PMC177512 DOI: 10.1128/jb.177.22.6585-6592.1995] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Salmonella paratyphi A, a human-adapted bacterial pathogen, causes paratyphoid enteric fever. We established the genome map of strain ATCC 9150 by the use of four endonucleases, XbaI, I-CeuI, AvrII (= BlnI), and SpeI, which generated 27, 7, 19, and 38 fragments, respectively; the sum of the fragments in each case indicates a genome size of ca. 4,600 kb. With phage P22, we transduced Tn10 insertions in known genes from Salmonella typhimurium LT2 to S. paratyphi A ATCC 9150 and located these insertions on the S. paratyphi A chromosome through the XbaI and AvrII sites in Tn10 and through the increased size of the SpeI fragment bearing a Tn10. Compared with the maps of other Salmonella species, the S. paratyphi A genomic map showed two major differences: (i) an insertion of about 100 kb of DNA between rrnH/G and proB and (ii) an inversion of half the genome between rrnH and rrnG, postulated to be due to homologous recombination between the rrn genes. We propose that during the evolution of S. paratyphi A, the first rearrangement event was the 100-kb insertion, which disrupted the chromosomal balance between oriC and the termination of replication, forcing the rrnH/G inversion to restore the balance. The insertion and the inversion are both present in all 10 independent wild-type S. paratyphi A strains tested.
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Affiliation(s)
- S L Liu
- Department of Biological Sciences, University of Calgary, Alberta, Canada
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24
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Abstract
Comparisons of the genetic maps of Escherichia coli K-12 and Salmonella typhimurium LT2 suggest that the size and organization of bacterial chromosomes are highly conserved. Employing pulsed-field gel electrophoresis, we have estimated the extent of variation in genome size among 14 natural isolates of E. coli. The BlnI and NotI restriction fragment patterns were highly variable among isolates, and genome sizes ranged from 4,660 to 5,300 kb, which is several hundred kilobases larger than the variation detected between enteric species. Genome size differences increase with the evolutionary genetic distance between lineages of E. coli, and there are differences in genome size among the major subgroups of E. coli. In general, the genomes of natural isolates are larger than those of laboratory strains, largely because of the fact that laboratory strains were derived from the subgroup of E. coli with the smallest genomes.
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Affiliation(s)
- U Bergthorsson
- Department of Biology, University of Rochester, New York 14627, USA
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25
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Abstract
The genomic cleavage map of Salmonella typhi Ty2, 4,780 kb in size, was determined through digestion of the genomic DNA with endonucleases and separation of the fragments by pulsed-field gel electrophoresis. The chromosome has 33, 26, 7, and 35 sites for the enzymes XbaI, BlnI, I-CeuI, and SpeI, respectively. The fragments were arranged around the chromosome through excision of fragments from the gel, redigestion with a second enzyme, and labelling with 32P, and reelectrophoresis and named in alphabetical order. Tn10 transposons inserted in 82 different genes of Salmonella typhimurium were transduced by phage P22 into S. typhi, and the location of Tn10, and thus of the gene, was mapped through the XbaI and BlnI sites of Tn10. All seven I-CeuI sites (in rrl genes for 23S rRNA) were conserved, and the gene order within the I-CeuI fragments resembles that of S. typhimurium LT2, but the order of I-CeuI fragments is rearranged from ABCDEFG in S. typhimurium LT2 to AGCEFDB in S. typhi. In addition, there is a 500-kb inversion which covers the terminus region. Comparisons of lengths of segments between genes showed that S. typhi has segments which differ in size from those in S. typhimurium. The viaB locus, for synthesis of the Vi antigen of S. typhi, was shown to be within a 118-kb loop (a segment of DNA with no homolog in most other Salmonella species) between mel and poxA on the chromosome.
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Affiliation(s)
- S L Liu
- Department of Biological Sciences, University of Calgary, Alberta, Canada
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26
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Abstract
A major goal of comparative genomics is an understanding of the forces which control gene order. This assumes that gene order is important, a supposition backed by the existence of genomic colinearity between many related species. In the bacterial chromosome, a polarity in the order of genes has been suggested, influenced by distance and orientation relative to the origin of DNA replication. We propose a model of the bacterial chromosome in which gene order is maintained by the adaptation of gene expression to local superhelical context. This force acts not directly at the genomic level but rather at the local gene level. A full understanding of gene-order conservation must therefore come from the bottom up.
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Affiliation(s)
- R L Charlebois
- Department of Biology, University of Ottawa, Ontario, Canada
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27
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Affiliation(s)
- M Fonstein
- Department of Molecular Genetics and Cell Biology, University of Chicago, Illinois 60637, USA
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28
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Liu SL, Sanderson KE. Rearrangements in the genome of the bacterium Salmonella typhi. Proc Natl Acad Sci U S A 1995; 92:1018-22. [PMID: 7862625 PMCID: PMC42628 DOI: 10.1073/pnas.92.4.1018] [Citation(s) in RCA: 124] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
We have determined the genomic map of the bacterium Salmonella typhi Ty2, the causal organism of typhoid fever, by using pulsed-field gel electrophoresis. Digestion of the Ty2 genome with endonucleases Xba I, Bln I, and Ceu I yielded 33, 26, and 7 fragments, respectively, that were placed in order on a circular chromosome of 4780 kb. Transposon Tn10 was inserted in specific genes of Salmonella typhimurium and transduced into S. typhi, and thus, the positions of 37 S. typhi genes were located through the Xba I and Bln I sites of the Tn10. Gene order on chromosomes of Escherichia coli K-12 and S. typhimurium LT2 is remarkably conserved; however, the gene order in S. typhi Ty2 is different, suggesting it has undergone major genomic rearrangements during its evolution. These rearrangements include inversions and transpositions in the 7 DNA fragments between the seven rrn operons for rRNA (postulated to be due to homologous recombination in these rrn genes), another inversion that covers the replication terminus region (resembling inversions found in other enteric bacteria), and at least three insertions, one as large as 118 kb. Partial digestion of genomic DNA with the intron-encoded endonuclease I-Ceu I, which cuts only in rrn genes, shows chromosomal rearrangements, apparently due to homologous recombination in the rrn genes, that were detected in all wild-type strains of S. typhi tested. These rearrangements may have been selected to compensate for the insertions that otherwise would have altered the locations of genes with respect to the origin and terminus of replication. These observations are relevant to our view of the evolution of the bacterial genome and may be significant in the virulence of S. typhi.
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Affiliation(s)
- S L Liu
- Department of Biological Sciences, University of Calgary, AB, Canada
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Selenska-Pobell S, Evguenieva-Hackenberg E, Schwickerath O. Random and Repetitive Primer Amplified Polymorphic DNA Analysis of Five Soil and Two Clinical Isolates of Rahnella aquatilis. Syst Appl Microbiol 1995. [DOI: 10.1016/s0723-2020(11)80435-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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30
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Gorton TS, Goh MS, Geary SJ. Physical mapping of the Mycoplasma gallisepticum S6 genome with localization of selected genes. J Bacteriol 1995; 177:259-63. [PMID: 7798142 PMCID: PMC176583 DOI: 10.1128/jb.177.1.259-263.1995] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
We report the construction of a physical map of the Mycoplasma gallisepticum S6 genome by field-inversion gel electrophoresis of DNA fragments generated by digestion of genomic DNA with rare-cutting restriction endonucleases. The size of the M. gallisepticum S6 genome was calculated to be approximately 1,054 kb. The loci of several genes have been assigned to the map by Southern hybridization utilizing specific gene probes.
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Affiliation(s)
- T S Gorton
- Department of Pathobiology, University of Connecticut, Storrs 06269-3089
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31
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Schwarz S, Liebisch B. Pulsed-field gel electrophoretic identification of Salmonella enterica serovar Typhimurium live vaccine strain Zoosaloral H. Lett Appl Microbiol 1994; 19:469-72. [PMID: 7765707 DOI: 10.1111/j.1472-765x.1994.tb00984.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Salmonella enterica subsp. enterica serovar Typhimurium (Salm. Typhimurium) live vaccine strain Zoosaloral H was characterized by pulsed-field gel electrophoresis (PFGE). Each of the two suitable restriction enzymes, XbaI and SpeI, produced a unique restriction fragment pattern for this live vaccine strain which was not shared by field isolates of the same serovar. The characteristic fragment pattern proved to be stable during a 22 month observation period and was also not altered after animal passage of the vaccine strains. Thus PFGE analysis proved to be a helpful tool in the identification of Salm. Typhimurium live vaccine strain Zoosaloral H and its differentiation from wild-type isolates of the same serovar.
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Affiliation(s)
- S Schwarz
- Institut für Kleintierforschung Celle/Merbitz der Bundesforschungsanstalt für Landwirtschaft, Celle, Germany
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32
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Bloch CA, Rode CK, Obreque V, Russell KY. Comparative genome mapping with mobile physical map landmarks. J Bacteriol 1994; 176:7121-5. [PMID: 7961483 PMCID: PMC197093 DOI: 10.1128/jb.176.22.7121-7125.1994] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We describe a method for comparative macrorestriction mapping of the chromosomes of Escherichia coli strains. In this method, a series of physically tagged E. coli K-12 alleles serve as mobile landmarks for mapping DNAs from other strains. This technique revealed evidence of strain-specific chromosomal additions or deletions in a pathogenic isolate and can be applied to most strains, yielding information on genealogy as well as virulence. In theory, the same strategy can be used to map and compare genomic DNAs from a wide variety of species.
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Affiliation(s)
- C A Bloch
- Department of Pediatrics, School of Medicine, University of Michigan, Ann Arbor 48109
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