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Caimi K, Repetto SA, Varni V, Ruybal P. Leptospira species molecular epidemiology in the genomic era. INFECTION GENETICS AND EVOLUTION 2017; 54:478-485. [PMID: 28818623 DOI: 10.1016/j.meegid.2017.08.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/26/2017] [Accepted: 08/13/2017] [Indexed: 10/19/2022]
Abstract
Leptospirosis is a zoonotic disease which global burden is increasing often related to climatic change. Hundreds of whole genome sequences from worldwide isolates of Leptospira spp. are available nowadays, together with online tools that permit to assign MLST sequence types (STs) directly from raw sequence data. In this work we have applied R7L-MLST to near 500 genomes and strains collection globally distributed. All 10 pathogenic species as well as intermediate were typed using this MLST scheme. The correlation observed between STs and serogroups in our previous work, is still satisfied with this higher dataset sustaining the implementation of MLST to assist serological classification as a complementary approach. Bayesian phylogenetic analysis of concatenated sequences from R7-MLST loci allowed us to resolve taxonomic inconsistencies but also showed that events such as recombination, gene conversion or lateral gene transfer played an important role in the evolution of Leptospira genus. Whole genome sequencing allows us to contribute with suitable epidemiologic information useful to apply in the design of control strategies and also in diagnostic methods for this illness.
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Affiliation(s)
- K Caimi
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - S A Repetto
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Facultad de Medicina, Buenos Aires, Argentina
| | - V Varni
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - P Ruybal
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Facultad de Medicina, Buenos Aires, Argentina.
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Warrier I, Walter MC, Frangoulidis D, Raghavan R, Hicks LD, Minnick MF. The Intervening Sequence of Coxiella burnetii: Characterization and Evolution. Front Cell Infect Microbiol 2016; 6:83. [PMID: 27595093 PMCID: PMC4990558 DOI: 10.3389/fcimb.2016.00083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 08/02/2016] [Indexed: 11/23/2022] Open
Abstract
The intervening sequence (IVS) of Coxiella burnetii, the agent of Q fever, is a 428-nt selfish genetic element located in helix 45 of the precursor 23S rRNA. The IVS element, in turn, contains an ORF that encodes a hypothetical ribosomal S23 protein (S23p). Although S23p can be synthesized in vitro in the presence of an engineered E. coli promoter and ribosome binding site, results suggest that the protein is not synthesized in vivo. In spite of a high degree of IVS conservation among different strains of C. burnetii, the region immediately upstream of the S23p start codon is prone to change, and the S23p-encoding ORF is evidently undergoing reductive evolution. We determined that IVS excision from 23S rRNA was mediated by RNase III, and IVS RNA was rapidly degraded, thereafter. Levels of the resulting 23S rRNA fragments that flank the IVS, F1 (~1.2 kb) and F2 (~1.7 kb), were quantified over C. burnetii's logarithmic growth phase (1–5 d). Results showed that 23S F1 quantities were consistently higher than those of F2 and 16S rRNA. The disparity between levels of the two 23S rRNA fragments following excision of IVS is an interesting phenomenon of unknown significance. Based upon phylogenetic analyses, IVS was acquired through horizontal transfer after C. burnetii's divergence from an ancestral bacterium and has been subsequently maintained by vertical transfer. The widespread occurrence, maintenance and conservation of the IVS in C. burnetii imply that it plays an adaptive role or has a neutral effect on fitness.
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Affiliation(s)
- Indu Warrier
- Program in Cellular, Molecular and Microbial Biology, Division of Biological Sciences, University of Montana Missoula, MT, USA
| | | | | | - Rahul Raghavan
- Department of Biology and Center for Life in Extreme Environments, Portland State University Portland, OR, USA
| | - Linda D Hicks
- Program in Cellular, Molecular and Microbial Biology, Division of Biological Sciences, University of Montana Missoula, MT, USA
| | - Michael F Minnick
- Program in Cellular, Molecular and Microbial Biology, Division of Biological Sciences, University of Montana Missoula, MT, USA
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Ricaldi JN, Fouts DE, Selengut JD, Harkins DM, Patra KP, Moreno A, Lehmann JS, Purushe J, Sanka R, Torres M, Webster NJ, Vinetz JM, Matthias MA. Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity. PLoS Negl Trop Dis 2012; 6:e1853. [PMID: 23145189 PMCID: PMC3493377 DOI: 10.1371/journal.pntd.0001853] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 08/25/2012] [Indexed: 12/25/2022] Open
Abstract
The whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced (Leptospira licerasiae strains VAR010 and MMD0835) provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution. Comparative analysis of eight leptospiral genomes shows the existence of a core leptospiral genome comprising 1547 genes and 452 conserved genes restricted to infectious species (including L. licerasiae) that are likely to be pathogenicity-related. Comparisons of the functional content of the genomes suggests that L. licerasiae retains several proteins related to nitrogen, amino acid and carbohydrate metabolism which might help to explain why these Leptospira grow well in artificial media compared with pathogenic species. L. licerasiae strains VAR010T and MMD0835 possess two prophage elements. While one element is circular and shares homology with LE1 of L. biflexa, the second is cryptic and homologous to a previously identified but unnamed region in L. interrogans serovars Copenhageni and Lai. We also report a unique O-antigen locus in L. licerasiae comprised of a 6-gene cluster that is unexpectedly short compared with L. interrogans in which analogous regions may include >90 such genes. Sequence homology searches suggest that these genes were acquired by lateral gene transfer (LGT). Furthermore, seven putative genomic islands ranging in size from 5 to 36 kb are present also suggestive of antecedent LGT. How Leptospira become naturally competent remains to be determined, but considering the phylogenetic origins of the genes comprising the O-antigen cluster and other putative laterally transferred genes, L. licerasiae must be able to exchange genetic material with non-invasive environmental bacteria. The data presented here demonstrate that L. licerasiae is genetically more closely related to pathogenic than to saprophytic Leptospira and provide insight into the genomic bases for its infectiousness and its unique antigenic characteristics. Leptospirosis is one of the most common diseases transmitted by animals worldwide and is important because it is a major cause of febrile illness in tropical areas and also occurs in epidemic form associated with natural disasters and flooding. The mechanisms through which Leptospira cause disease are not well understood. In this study we have sequenced the genomes of two strains of Leptospira licerasiae isolated from a person and a marsupial in the Peruvian Amazon. These strains were thought to be able to cause only mild disease in humans. We have compared these genomes with other leptospires that can cause severe illness and death and another leptospire that does not infect humans or animals. These comparisons have allowed us to demonstrate similarities among the disease-causing Leptospira. Studying genes that are common among infectious strains will allow us to identify genetic factors necessary for infecting, causing disease and determining the severity of disease. We have also found that L. licerasiae seems to be able to uptake and incorporate genetic information from other bacteria found in the environment. This information will allow us to begin to understand how Leptospira species have evolved.
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Affiliation(s)
- Jessica N. Ricaldi
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Derrick E. Fouts
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Jeremy D. Selengut
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Derek M. Harkins
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Kailash P. Patra
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Angelo Moreno
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Jason S. Lehmann
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Janaki Purushe
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Ravi Sanka
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Michael Torres
- Departamento de Ciencias Celulares y Moleculares, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Nicholas J. Webster
- Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Joseph M. Vinetz
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
- Departamento de Ciencias Celulares y Moleculares, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias, Universidad Peruana Cayetano Heredia, Lima, Peru
- * E-mail: (JMV); (MAM)
| | - Michael A. Matthias
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
- * E-mail: (JMV); (MAM)
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A century of Leptospira strain typing. INFECTION GENETICS AND EVOLUTION 2009; 9:760-8. [DOI: 10.1016/j.meegid.2009.06.009] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Revised: 06/09/2009] [Accepted: 06/10/2009] [Indexed: 10/20/2022]
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Meinersmann RJ, Phillips RW, Ladely SR. Inter- and intra-genomic heterogeneity of the intervening sequence in the 23S ribosomal RNA gene of Campylobacter jejuni and Campylobacter coli. Syst Appl Microbiol 2009; 32:91-100. [PMID: 19201124 DOI: 10.1016/j.syapm.2008.12.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Revised: 12/15/2008] [Accepted: 12/22/2008] [Indexed: 11/30/2022]
Abstract
An intervening sequence (IVS) can be present or absent in the 23S rRNA of Campylobacter jejuni and Campylobacter coli. As part of a survey, we used a polymerase chain reaction (PCR) assay to detect the presence of the IVS in 43 isolates of C. coli and 82 isolates of C. jejuni. An IVS was present in 40 (93.0%) of the C. coli and only 34 (41.5%) of the C. jejuni isolates. Twelve (27.9%) of the C. coli isolates and seven (8.5%) of the C. jejuni isolates resulted in two polymerase chain reaction products, indicating heterogeneity in the presence of the 23S rRNA IVS. Fourteen of the isolates with two products were evaluated by pulse-field gel electrophoresis; 13 different patterns were observed. The total band size of one isolate was substantially greater than the expected 1.7 Mb, possibly indicating a mixed culture. Southern blot analyses demonstrated the expected three rRNA operons in all tested isolates. Nested PCR reactions with operon-specific primers followed by primers for the IVS confirmed that the strains of interest contained either one or two operons carrying the IVS and the remaining operon(s) did not. Sequence analysis of the IVS and flanking regions of the 23S rRNA genes did not discriminate C. jejuni and C. coli as distinct populations. These results indicate horizontal transfer of 23S rRNA genes or portions of the genes between C. jejuni and C. coli. Also, data showing sequence polymorphisms between the three 23S rRNA loci outside of the IVS region suggest that the isolates with intra-genomic heterogeneity appear to be members of clones that have an ancient defect in gene conversion mechanisms needed for concerted evolution of the ribosomal operons.
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Affiliation(s)
- R J Meinersmann
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA Agricultural Research Service, Athens, Richard J. Russell Research Center, P.O. Box 5677, Athens, GA 30604, USA.
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Affiliation(s)
- Paul N Levett
- Saskatchewan Disease Control Laboratory, Saskatchewan Health, Regina, Canada.
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He P, Sheng YY, Shi YZ, Jiang XG, Qin JH, Zhang ZM, Zhao GP, Guo XK. Genetic diversity among major endemic strains of Leptospira interrogans in China. BMC Genomics 2007; 8:204. [PMID: 17603913 PMCID: PMC1936430 DOI: 10.1186/1471-2164-8-204] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2007] [Accepted: 07/01/2007] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Leptospirosis is a world-widely distributed zoonosis. Humans become infected via exposure to pathogenic Leptospira spp. from contaminated water or soil. The availability of genomic sequences of Leptospira interrogans serovar Lai and serovar Copenhageni opened up opportunities to identify genetic diversity among different pathogenic strains of L. interrogans representing various kinds of serotypes (serogroups and serovars). RESULTS Comparative genomic hybridization (CGH) analysis was used to compare the gene content of L. interrogans serovar Lai strain Lai with that of other 10 L. interrogans strains prevailed in China and one identified from Brazil using a microarray spotted with 3,528 protein coding sequences (CDSs) of strain Lai. The cutoff ratio of sample/reference (S/R) hybridization for detecting the absence of genes from one tested strain was set by comparing the ratio of S/R hybridization and the in silico sequence similarities of strain Lai and serovar Copenhageni strain Fiocruz L1-130. Among the 11 strains tested, 275 CDSs were found absent from at least one strain. The common backbone of the L. interrogans genome was estimated to contain about 2,917 CDSs. The genes encoding fundamental cellular functions such as translation, energy production and conversion were conserved. While strain-specific genes include those that encode proteins related to either cell surface structures or carbohydrate transport and metabolism. We also found two genomic islands (GIs) in strain Lai containing genes divergently absent in other strains. Because genes encoding proteins with potential pathogenic functions are located within GIs, these elements might contribute to the variations in disease manifestation. Differences in genes involved in O-antigen biosynthesis were also identified for strains belonging to different serogroups, which offers an opportunity for future development of genomic typing tools for serological classification. CONCLUSION CGH analyses for pathogenic leptospiral strains prevailed in China against the L. interrogans serovar Lai strain Lai CDS-spotted microarrays revealed 2,917 common backbone CDSs and strain specific genes encoding proteins mainly related to cell surface structures and carbohydrated transport/metabolism. Of the 275 CDSs considered absent from at least one of the L. interrogans strains tested, most of them were clustered in the rfb gene cluster and two putative genomic islands (GI A and B) in strain Lai. The strain-specific genes detected via this work will provide a knowledge base for further investigating the pathogenesis of L interrogans and/or for the development of effective vaccines and/or diagnostic tools.
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Affiliation(s)
- Ping He
- Department of Microbiology and Parasitology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yue-Ying Sheng
- Department of Microbiology and Parasitology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yao-Zhou Shi
- National Engineering Center for Biochip at Shanghai, Zhangjiang High Tech Park, Shanghai 201203, China
| | - Xiu-Gao Jiang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (ICDC, CCDC), Beijing 102206, China
| | - Jin-Hong Qin
- Department of Microbiology and Parasitology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zhi-Ming Zhang
- National Engineering Center for Biochip at Shanghai, Zhangjiang High Tech Park, Shanghai 201203, China
| | - Guo-Ping Zhao
- National Engineering Center for Biochip at Shanghai, Zhangjiang High Tech Park, Shanghai 201203, China
- State Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Zhangjiang High Tech Park, Shanghai 201203, China
| | - Xiao-Kui Guo
- Department of Microbiology and Parasitology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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Chan K, Miller WG, Mandrell RE, Kathariou S. The absence of intervening sequences in 23S rRNA genes of Campylobacter coli isolates from Turkeys is a unique attribute of a cluster of related strains which also lack resistance to erythromycin. Appl Environ Microbiol 2006; 73:1208-14. [PMID: 17189444 PMCID: PMC1828655 DOI: 10.1128/aem.01995-06] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Certain Campylobacter strains harbor a transcribed intervening sequence (IVS) in their 23S rRNA genes. Following transcription, the IVS is excised, leading to fragmentation of the 23S rRNA. The origin and possible functions of the IVS are unknown. Furthermore, the distribution of IVS-harboring strains within Campylobacter populations is poorly understood. In this study, 104 strains of Campylobacter coli from turkeys, representing 27 different multilocus sequence typing-based sequence types (STs), were characterized in terms of IVS content and erythromycin susceptibility. Sixty-nine strains harbored IVSs in all three 23S rRNA genes, whereas the other 35 strains lacked IVSs from at least one of the genes. The STs of the latter strains belonged to an unusual cluster of C. coli STs (cluster II), earlier found primarily in turkey strains and characterized by the presence of the C. jejuni aspA103 allele. The majority (66/69) of strains harboring IVSs in all three 23S rRNA genes were resistant to erythromycin, whereas none of the 35 strains with at least one IVS-free 23S rRNA gene were resistant. Cluster II strains could be transformed to erythromycin resistance with genomic DNA from C. coli that harbored IVS and the A2075G transition in the 23S rRNA gene, associated with resistance to erythromycin in Campylobacter. Erythromycin-resistant transformants harbored both the A2075 transition and IVS. The findings suggest that the absence of IVS in C. coli from turkeys is characteristic of a unique clonal group of erythromycin-susceptible strains and that IVS can be acquired by these strains via natural transformation to erythromycin resistance.
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Affiliation(s)
- Kamfai Chan
- Department of Food Science, North Carolina State University, Raleigh, NC 27695-7624, USA
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Morey RE, Galloway RL, Bragg SL, Steigerwalt AG, Mayer LW, Levett PN. Species-specific identification of Leptospiraceae by 16S rRNA gene sequencing. J Clin Microbiol 2006; 44:3510-6. [PMID: 17021075 PMCID: PMC1594759 DOI: 10.1128/jcm.00670-06] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genus Leptospira is classified into 13 named species and 4 genomospecies based upon DNA-DNA reassociation studies. Phenotypic tests are unable to distinguish between species of Leptospira, and there is a need for a simplified molecular approach to the identification of leptospires. 16S rRNA gene sequences are potentially useful for species identification of Leptospira, but there are a large number of sequences of various lengths and quality in the public databases. 16S rRNA gene sequences of near full length and bidirectional high redundancy were determined for all type strains of the species of the Leptospiraceae. Three clades were identified within the genus Leptospira, composed of pathogenic species, nonpathogenic species, and another clade of undetermined pathogenicity with intermediate 16S rRNA gene sequence relatedness. All type strains could be identified by 16S rRNA gene sequences, but within both pathogenic and nonpathogenic clades as few as two or three base pairs separated some species. Sequences within the nonpathogenic clade were more similar, and in most cases < or =10 bp distinguished these species. These sequences provide a reference standard for identification of Leptospira species and confirm previously established relationships within the genus. 16S rRNA gene sequencing is a powerful method for identification in the clinical laboratory and offers a simplified approach to the identification of Leptospira species.
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Affiliation(s)
- Roger E Morey
- Saskatchewan Health, Provincial Laboratory, 3211 Albert Street, Regina, Saskatchewan S4S 5W6, Canada
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Abstract
The exact knowledge on the ribosomal RNA (rRNA) structure is an important prerequisite for work with rRNA sequences in bioinformatic analyses and in experimental research. Most available rRNA sequences of bacteria are based on gene sequences and on similarity analyses using Escherichia coli rRNA as a standard. Therefore, it is often overlooked that many bacteria harbour mature rRNA 'in pieces'. In some cases, the processing steps during the fragmentation lead to the removal of rRNA segments that are usually found in the ribosome. In this review, the current knowledge on the mechanisms of rRNA fragmentation and on the occurrence of fragmented rRNA in bacteria is summarized, and the physiological implications of this phenomenon are discussed.
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Affiliation(s)
- Elena Evguenieva-Hackenberg
- Institut für Mikrobiologie und Molekularbiologie der Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.
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11
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Majed Z, Bellenger E, Postic D, Pourcel C, Baranton G, Picardeau M. Identification of variable-number tandem-repeat loci in Leptospira interrogans sensu stricto. J Clin Microbiol 2005; 43:539-45. [PMID: 15695642 PMCID: PMC548069 DOI: 10.1128/jcm.43.2.539-545.2005] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Leptospira interrogans sensu stricto is responsible for the most frequent and severe cases of human leptospirosis. The epidemiology and clinical features of leptospirosis are usually associated with the serovars and serogroups of Leptospira. Because of the difficulties associated with serological identification of Leptospira strains, we evaluated a novel PCR-based method for typing L. interrogans serovars. Based upon the genome sequence of L. interrogans serovar Lai type strain 5660, 44 loci were analyzed by PCR for their variability in size due to the presence of variable-number tandem repeats (VNTR). Seven VNTR loci were found to be powerful markers for serovar identification, epidemiology, and phylogenetic studies of L. interrogans. This rapid and easy method should greatly contribute to a better knowledge of the epidemiology of Leptospira.
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Affiliation(s)
- Z Majed
- Laboratoire des Spirochètes, Institut Pasteur, 28 rue du docteur Roux, 75724 Paris Cedex 15, France
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Haake DA, Suchard MA, Kelley MM, Dundoo M, Alt DP, Zuerner RL. Molecular evolution and mosaicism of leptospiral outer membrane proteins involves horizontal DNA transfer. J Bacteriol 2004; 186:2818-28. [PMID: 15090524 PMCID: PMC387810 DOI: 10.1128/jb.186.9.2818-2828.2004] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Leptospires belong to a genus of parasitic bacterial spirochetes that have adapted to a broad range of mammalian hosts. Mechanisms of leptospiral molecular evolution were explored by sequence analysis of four genes shared by 38 strains belonging to the core group of pathogenic Leptospira species: L. interrogans, L. kirschneri, L. noguchii, L. borgpetersenii, L. santarosai, and L. weilii. The 16S rRNA and lipL32 genes were highly conserved, and the lipL41 and ompL1 genes were significantly more variable. Synonymous substitutions are distributed throughout the ompL1 gene, whereas nonsynonymous substitutions are clustered in four variable regions encoding surface loops. While phylogenetic trees for the 16S, lipL32, and lipL41 genes were relatively stable, 8 of 38 (20%) ompL1 sequences had mosaic compositions consistent with horizontal transfer of DNA between related bacterial species. A novel Bayesian multiple change point model was used to identify the most likely sites of recombination and to determine the phylogenetic relatedness of the segments of the mosaic ompL1 genes. Segments of the mosaic ompL1 genes encoding two of the surface-exposed loops were likely acquired by horizontal transfer from a peregrine allele of unknown ancestry. Identification of the most likely sites of recombination with the Bayesian multiple change point model, an approach which has not previously been applied to prokaryotic gene sequence analysis, serves as a model for future studies of recombination in molecular evolution of genes.
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Affiliation(s)
- David A Haake
- Division of Infectious Diseases, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA.
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Baker BJ, Hugenholtz P, Dawson SC, Banfield JF. Extremely acidophilic protists from acid mine drainage host Rickettsiales-lineage endosymbionts that have intervening sequences in their 16S rRNA genes. Appl Environ Microbiol 2003; 69:5512-8. [PMID: 12957940 PMCID: PMC194945 DOI: 10.1128/aem.69.9.5512-5518.2003] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2003] [Accepted: 06/11/2003] [Indexed: 11/20/2022] Open
Abstract
During a molecular phylogenetic survey of extremely acidic (pH < 1), metal-rich acid mine drainage habitats in the Richmond Mine at Iron Mountain, Calif., we detected 16S rRNA gene sequences of a novel bacterial group belonging to the order Rickettsiales in the Alphaproteobacteria. The closest known relatives of this group (92% 16S rRNA gene sequence identity) are endosymbionts of the protist Acanthamoeba. Oligonucleotide 16S rRNA probes were designed and used to observe members of this group within acidophilic protists. To improve visualization of eukaryotic populations in the acid mine drainage samples, broad-specificity probes for eukaryotes were redesigned and combined to highlight this component of the acid mine drainage community. Approximately 4% of protists in the acid mine drainage samples contained endosymbionts. Measurements of internal pH of the protists showed that their cytosol is close to neutral, indicating that the endosymbionts may be neutrophilic. The endosymbionts had a conserved 273-nucleotide intervening sequence (IVS) in variable region V1 of their 16S rRNA genes. The IVS does not match any sequence in current databases, but the predicted secondary structure forms well-defined stem loops. IVSs are uncommon in rRNA genes and appear to be confined to bacteria living in close association with eukaryotes. Based on the phylogenetic novelty of the endosymbiont sequences and initial culture-independent characterization, we propose the name "Candidatus Captivus acidiprotistae." To our knowledge, this is the first report of an endosymbiotic relationship in an extremely acidic habitat.
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Affiliation(s)
- Brett J Baker
- Department of Earth and Planetary Sciences, University of California at Berkeley, Berkeley, California 94720, USA.
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Pronk LM, Sanderson KE. Intervening sequences in rrl genes and fragmentation of 23S rRNA in genera of the family Enterobacteriaceae. J Bacteriol 2001; 183:5782-7. [PMID: 11544246 PMCID: PMC95475 DOI: 10.1128/jb.183.19.5782-5787.2001] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intervening sequences (IVSs) in the rrl genes for 23S rRNA are transcribed but later removed by RNase III without religation during RNA processing, leading to fragmented rRNA. We examined about 240 strains of the family Enterobacteriaceae for presence of IVSs using PCR. No IVSs were detected in strains belonging to Escherichia, Shigella, Enterobacter, Erwinia, Ewingella, Hafnia, Kluyvera, Morganella, Pantoea, or Serratia. Previously unreported IVSs were detected in Klebsiella oxytoca, Citrobacter amalonaticus, and Providencia stuartii; previously reported IVSs are in species of Salmonella, Proteus, Providencia, and Yersinia. The sporadic distribution of IVSs indicates lateral genetic transfer of IVSs.
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Affiliation(s)
- L M Pronk
- Salmonella Genetic Stock Centre, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
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Abstract
Leptospirosis is a worldwide zoonotic infection with a much greater incidence in tropical regions and has now been identified as one of the emerging infectious diseases. The epidemiology of leptospirosis has been modified by changes in animal husbandry, climate, and human behavior. Resurgent interest in leptospirosis has resulted from large outbreaks that have received significant publicity. The development of simpler, rapid assays for diagnosis has been based largely on the recognition that early initiation of antibiotic therapy is important in acute disease but also on the need for assays which can be used more widely. In this review, the complex taxonomy of leptospires, previously based on serology and recently modified by a genotypic classification, is discussed, and the clinical and epidemiological value of molecular diagnosis and typing is also evaluated.
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Affiliation(s)
- P N Levett
- University of the West Indies, School of Clinical Medicine & Research, and Leptospira Laboratory, Ministry of Health, Barbados.
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16
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Barocchi MA, Ko AI, Ferrer SR, Faria MT, Reis MG, Riley LW. Identification of new repetitive element in Leptospira interrogans serovar copenhageni and its application to PCR-based differentiation of Leptospira serogroups. J Clin Microbiol 2001; 39:191-5. [PMID: 11136769 PMCID: PMC87700 DOI: 10.1128/jcm.39.1.191-195.2001] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A new repetitive DNA element was identified in an isolate of Leptospira interrogans serovar copenhageni from a patient in Salvador, Brazil. A Sau3A genomic library from this strain was constructed and screened for repetitive DNA elements. An insert of 438 bp (Rep1) from one library clone hybridized to multiple chromosomal DNA fragments resolved electrophoretically after digestion with BamHI, HindIII, and MfeI. A single oligonucleotide primer, designated iRepl, was designed to generate multiple PCR amplicons of various electrophoretic mobilities in a PCR typing method. The method distinguished strains belonging to the eight pathogenic and three saprophytic species of the genus Leptospira. Clinical isolates obtained during urban epidemics between 1996 and 1998 in Salvador, Brazil, were analyzed by this PCR method. Although the iRep1 primer was unable to discriminate strains among L. interrogans serovar copenhageni isolates, it was able to differentiate strains belonging to different species and serogroups of Leptospira identified in Salvador. This PCR-based method may provide a faster and less expensive alternative to serologic tests used in reference laboratories.
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Affiliation(s)
- M A Barocchi
- Division of Infectious Diseases and Immunity, School of Public Health, University of California, Berkeley, California 94720, USA
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17
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Bricker BJ. Characterization of the three ribosomal RNA operons rrnA, rrnB, and rrnC, from Brucella melitensis. Gene 2000; 255:117-26. [PMID: 10974571 DOI: 10.1016/s0378-1119(00)00273-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The three Brucella melitensis ribosomal RNA operons rrnA, rrnB, and rrnC were characterized individually. Each locus consisted of the 16S rRNA gene (rrs), followed by an intergenic spacer containing the tRNA-Ile and tRNA-Ala genes, the 23S rRNA gene (rrl), an intergenic spacer devoid of tRNA genes, the 5S rRNA gene (rrf), and an f-Met tRNA gene. The DNA sequences were identical over a 6271bp region, diverging 594bp upstream of rrs and immediately downstream of the f-Met tRNA gene. The previously uncharacterized 23S rRNA genes each contained a 178bp insertion 130bp from the 5' end. The location of the insertion matched intervening sequences (IVSs) found in other Rhizobiaceae. However, the size and sequence of the Brucella IVS differed from all previously reported IVS sequences from bacteria. The IVS region was PCR-amplified from 20 Brucella isolates representing all known Brucella species and biovars. All isolates contained only the complete IVS fragment. We compared the IVS DNA sequences of rrlC from representative strains of each of the six known Brucella species. The data revealed that the sequences were identical and differed from the B. melitensis IVS sequences by a single base pair. In other bacterial species, the IVSs are associated with post-transcriptional processing of the 23S rRNA by RNase III. We found that the Brucella 23S rRNA was slightly smaller than the 23S rRNA of Escherichia coli, known to be devoid of IVS sequences.
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MESH Headings
- Base Sequence
- Brucella melitensis/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal Spacer/genetics
- Electrophoresis, Gel, Pulsed-Field
- Molecular Sequence Data
- Mutagenesis, Insertional
- Operon
- Physical Chromosome Mapping
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 5S/genetics
- RNA, Transfer, Ala/genetics
- RNA, Transfer, Ile/genetics
- RNA, Transfer, Met/genetics
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Species Specificity
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Affiliation(s)
- B J Bricker
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA.
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18
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Pabbaraju K, Sanderson KE. Sequence diversity of intervening sequences (IVSs) in the 23S ribosomal RNA in Salmonella spp. Gene 2000; 253:55-66. [PMID: 10925202 DOI: 10.1016/s0378-1119(00)00239-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Intervening sequences (IVSs) occur sporadically in the rrl (ribosomal RNA large) genes for 23S ribosomal RNA (rRNA) at helix-25 (base pair 550) and helix 45 (base pair 1170) in several bacterial genera, including Salmonella, Yersinia, Proteus, and Providencia, representing the Enterobacteriaceae, but are missing from other genera such as Escherichia. These sequences are transcribed, but later excised without re-ligation during RNaseIII processing of the rRNA, resulting in fragmented 23S rRNA. The IVSs from 22 strains of the SARB (Salmonella Reference Collection B) set were amplified by PCR and sequenced.IVSs with 90% or more sequence identity were placed in the same family; Salmonella has three families of IVSs in helix-25 (A, B, and C) and two in helix-45 (M and O). The rRNA secondary structure for the IVSs predicted from the mfold program reveals a primary stem of about 14bp, which is the postulated RNaseIII cleavage site, and a secondary region of stems and loops. The primary stem is considerably well conserved, with a high rate of compensatory mutations (positional covariants), confirming the reality of the secondary structure and indicating that removal of the IVSs exerts a positive selective pressure to retain the secondary structure. The pattern of possession and presence of families of IVSs was diverse and could not be related to the proposed ancestry of the strains as revealed by the multi-locus enzyme electrophoresis pattern of the strains, suggesting that the IVSs are transferred between strains by lateral transfer. Helix-25 IVSs from families A, B, and C of Salmonella and D of Proteus, which share almost identical primary stems, are placed in superfamily I, while the primary stems of other IVSs from Proteus and Providencia are unrelated to superfamily I and are thus placed into superfamily II; this indicates lateral transfer of members of superfamily I between Proteus and Salmonella, but an independent origin of IVSs of superfamily II in Proteus and Providencia.
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Affiliation(s)
- K Pabbaraju
- Salmonella Genetic Stock Centre, Department of Biological Sciences, University of Calgary, Alberta, T2N 1N4, Calgary, Canada
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19
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Postic D, Riquelme-Sertour N, Merien F, Perolat P, Baranton G. Interest of partial 16S rDNA gene sequences to resolve heterogeneities between Leptospira collections: application to L. meyeri. Res Microbiol 2000; 151:333-41. [PMID: 10919513 DOI: 10.1016/s0923-2508(00)00156-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
This paper describes the advantage of using the first 330 bp (positions 46 to 375, Escherichia coli numbering) of the 16S rDNA gene for comparison of Leptospira isolates. Phylogenetic analysis conducted from the whole 16S rDNA sequences available in databanks as well as that conducted from the partial sequences yielded quite similar results, in accordance with data inferred from previous DNA-DNA relatedness studies. This tool was used for the comparison of Leptospira strains from different reference collections. Consistent results were obtained from the analysis of the polymorphism generated by pulsed-field gel electrophoresis. The study focused on different serovars of L. meyeri species, the classification of which has been controversial. The results revealed large collection heterogeneities, and suggest that the classification of the L. meyeri species should be revised.
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Affiliation(s)
- D Postic
- Unité de bactériologie moléculaire et médicale, Institut Pasteur, Paris, France.
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20
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Pabbaraju K, Miller WL, Sanderson KE. Distribution of intervening sequences in the genes for 23S rRNA and rRNA fragmentation among strains of the Salmonella reference collection B (SARB) and SARC sets. J Bacteriol 2000; 182:1923-9. [PMID: 10714998 PMCID: PMC101879 DOI: 10.1128/jb.182.7.1923-1929.2000] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intervening sequences (IVSs) occur sporadically in several bacterial genera in the genes for 23S rRNA at relatively conserved locations. They are cleaved after transcription and lead to the presence of fragmented rRNA, which is incorporated into the ribosomes without religation but is nevertheless functional. The fragmentation of rRNA and the number of IVSs in all 72 strains of the Salmonella Reference Collection B set and 16 strains of the Salmonella Reference Collection C set, which have been established on the basis of multilocus enzyme electrophoresis (MLEE), were analyzed in the present study. Fragmentation of 23S rRNA was restricted to conserved cleavage sites located at bp 550 (helix 25) and bp 1170 (helix 45), locations where IVSs have been reported. Random cleavage at sites where IVSs could not be detected was not seen. Uncleaved IVSs were not detected in any case; thus, the IVSs invariably led to rRNA fragmentation, indicating a strong selection for maintenance of RNase III cleavage sites. The distribution of the number of IVSs carried by the different strains in the seven rrl genes is diverse, and the pattern of IVS possession could not be related to the MLEE pattern among the various Salmonella strains tested; this indicates that the IVSs are frequently exchanged between strains by lateral transfer. All eight subspecies of the genus Salmonella, including subspecies V represented by Salmonella bongori, have IVSs in both helix 25 and helix 45; this indicates that IVSs entered the genus after its divergence from Escherichia coli (more than 100 million years ago) but before separation of the genus Salmonella into many forms or that they were in the ancestor but have been lost from Escherichia.
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MESH Headings
- Base Pairing/genetics
- Biological Specimen Banks
- Conserved Sequence/genetics
- Endoribonucleases/metabolism
- Escherichia coli/genetics
- Escherichia coli Proteins
- Genes, Bacterial/genetics
- Genetic Variation/genetics
- Models, Genetic
- Molecular Weight
- Phylogeny
- Polymerase Chain Reaction
- RNA Processing, Post-Transcriptional/genetics
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- Recombination, Genetic/genetics
- Regulatory Sequences, Nucleic Acid/genetics
- Regulatory Sequences, Nucleic Acid/physiology
- Ribonuclease III
- Salmonella/classification
- Salmonella/genetics
- rRNA Operon/genetics
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Affiliation(s)
- K Pabbaraju
- Salmonella Genetic Stock Centre, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4.
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21
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22
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Miller WL, Pabbaraju K, Sanderson KE. Fragmentation of 23S rRNA in strains of Proteus and Providencia results from intervening sequences in the rrn (rRNA) genes. J Bacteriol 2000; 182:1109-17. [PMID: 10648538 PMCID: PMC94388 DOI: 10.1128/jb.182.4.1109-1117.2000] [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
Intervening sequences (IVSs) were originally identified in the rrl genes for 23S rRNA (rrl genes, for large ribosomal subunit, part of rrn operon encoding rRNA) of Salmonella enterica serovars Typhimurium LT2 and Arizonae. These sequences are transcribed but later removed during RNase III processing of the rRNA, resulting in fragmentation of the 23S species; IVSs are uncommon, but have been reported in at least 10 bacterial genera. Through PCR amplification of IVS-containing regions of the rrl genes we showed that most Proteus and Providencia strains contain IVSs similar to those of serovar Typhimurium in distribution and location in rrl genes. By extraction and Northern blotting of rRNA, we also found that these IVSs result in rRNA fragmentation. We report the first finding of two very different sizes of IVS (113 bp and 183 to 187 bp) in different rrl genes in the same strain, in helix 25 of Proteus and Providencia spp.; IVSs from helix 45 are 113 to 123 bp in size. Analysis of IVS sequence and postulated secondary structure reveals striking similarities of Proteus and Providencia IVSs to those of serovar Typhimurium, with the stems of the smaller IVSs from helix 25 being similar to those of Salmonella helix 25 IVSs and with both the stem and the central loop domain of helix 45 IVSs being similar. Thus, IVSs of related sequences are widely distributed throughout the Enterobacteriaceae, in Salmonella, Yersinia, Proteus, and Providencia spp., but we did not find them in Escherichia coli, Citrobacter, Enterobacter, Klebsiella, or Morganella spp.; the sporadic distribution of IVSs of related sequence indicates that lateral genetic transfer has occurred.
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Affiliation(s)
- W L Miller
- Salmonella Genetic Stock Centre, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
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23
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Sasaki F, Kano R, Nakamura Y, Tsujimoto H, Yamamoto S, Hasegawa A. Phylogenetic analysis of Leptospira strains of pathogenic serovars using 23S rDNA gene sequences. Microbiol Res 1999; 154:167-72. [PMID: 10522384 DOI: 10.1016/s0944-5013(99)80010-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The 23S ribosomal DNAs were amplified from 11 strains of Leptospira interrogans sensu lato by polymerase chain reaction (PCR) and sequenced. The PCR products of about 290-bp DNA fragments indicated more than 97% sequence similarity to each other. The phylogenetic tree based on the 23S ribosomal DNAs obtained in this study revealed that 11 strains of L. interrogans examined composed a cluster distinct to that of L. weilii and L. borgpetersenii, confirming that these strains were similar to strain Moulton of L. interrogans serovar canicola in 23S rDNA sequence.
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Affiliation(s)
- F Sasaki
- Department of Pathobiology, Nihon University School of Veterinary Medicine
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24
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Rosa P, Stevenson B, Tilly K. 7 Genetic Methods in Borrelia and Other Spirochaetes. METHODS IN MICROBIOLOGY 1999. [DOI: 10.1016/s0580-9517(08)70118-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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25
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von Wintzingerode F, Göbel UB, Stackebrandt E. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 1997; 21:213-29. [PMID: 9451814 DOI: 10.1111/j.1574-6976.1997.tb00351.x] [Citation(s) in RCA: 1054] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
After nearly 10 years of PCR-based analysis of prokaryotic small-subunit ribosomal RNAs for ecological studies it seems necessary to summarize reported pitfalls of this approach which will most likely lead to an erroneous description on the microbial diversity of a given habitat. The following article will cover specific aspects of sample collection, cell lysis, nucleic acid extraction, PCR amplification, separation of amplified DNA, application of nucleic probes and data analysis.
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MESH Headings
- Artifacts
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- DNA, Bacterial/analysis
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/analysis
- DNA, Ribosomal/genetics
- DNA, Ribosomal/isolation & purification
- Environmental Microbiology
- Equipment Contamination
- False Negative Reactions
- False Positive Reactions
- Mutagenesis
- Polymerase Chain Reaction/instrumentation
- Polymerase Chain Reaction/methods
- RNA, Bacterial/genetics
- RNA, Bacterial/isolation & purification
- RNA, Ribosomal/genetics
- RNA, Ribosomal/isolation & purification
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/isolation & purification
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Affiliation(s)
- F von Wintzingerode
- Institut für Mikrobiologie und Hygiene, Universitätsklinikum Charité, Berlin, Germany
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26
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Gregory ST, O'Connor M, Dahlberg AE. Functional Escherichia coli 23S rRNAs containing processed and unprocessed intervening sequences from Salmonella typhimurium. Nucleic Acids Res 1996; 24:4918-23. [PMID: 9016661 PMCID: PMC146334 DOI: 10.1093/nar/24.24.4918] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We have introduced the intervening sequence (IVS) from 23S rRNA of the rrnD operon of Salmonella typhimurium into the equivalent position of Escherichia coli 23S rRNA. Salmonella typhimurium 23S rRNA is fragmented due to the RNase III-dependent removal of the approximately 100 nt stem-loop structure that comprises the IVS. In this study, we have found that insertion of the S. typhimurium IVS into E. coli 23S rRNA causes fragmentation of the RNA but does not affect ribosome function. Cells expressing the fragmented 23S rRNA exhibited wild-type growth rates. Fragmented RNA was found in the actively translating polysome pool and did not alter the sedimentation profile of ribosomal subunits, 70S ribosomes or polysomes. Finally, hybrid 23S rRNA carrying the A2058G mutation conferred high level erythromycin resistance indistinguishable from that of intact 23S rRNA carrying this mutation. These observations indicate that the presence of this IVS and its removal are phenotypically silent. As observed in an RNase III-deficient strain, processing of the IVS was not required for the production of functional ribosomes.
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Affiliation(s)
- S T Gregory
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.
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27
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Mattatall NR, Sanderson KE. Salmonella typhimurium LT2 possesses three distinct 23S rRNA intervening sequences. J Bacteriol 1996; 178:2272-8. [PMID: 8636028 PMCID: PMC177935 DOI: 10.1128/jb.178.8.2272-2278.1996] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The rrl genes for 23S rRNA of Salmonella typhimurium LT2 are known to carry intervening sequences (IVSs) at two sites, helix-25 and helix-45, which are excised by RNase III during rRNA maturation, resulting in rRNA which is fragmented but nevertheless functional. We isolated DNA fragments containing the seven rrl genes from BlnI, I-CeuI, and SpeI genomic digests following pulsed-field gel electrophoresis and used these DNA fragments as templates for PCRs utilizing primers upstream and downstream of helix-25 and helix-45. Variance in amplicon length and cycle sequencing indicated that rrlG and rrlH have IVSs in helix-25 of approximately 110 bp which are only 56% identical. rrnA, rrnB, rrnC, rrnD, rrnE, and rrnH have IVSs of approximately 90 bp in helix-45, and all have the same nucleotide sequence. Twenty-one independent wild-type strains of S. typhimurium from Salmonella Reference Collection A were analyzed for IVSs by using PCRs with genomic DNAs and by denaturing agarose electrophoresis of RNAs. Many strains resemble LT2, but some have no IVSs in helix-25 and others have IVSs in helix-45 in all seven rrl genes. However, the IVSs in individual wild-type lines are relatively stable, for several LT2 isolates separated over many years by many single-colony isolations are indistinguishable from one another, with the exception of line LB5010, which differs by one helix-25 IVS. We postulate that IVSs have entered strain LT2 by three independent lateral-transfer events and that the IVS in helix-45 was dispersed to and maintained in the same sequence in six of the seven rrl genes by the mechanism of gene conversion.
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Affiliation(s)
- N R Mattatall
- Salmonella Genetic Stock Centre, Uniersity of Calgary, Alberta, Canada.
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28
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Afseth G, Mo YY, Mallavia LP. Characterization of the 23S and 5S rRNA genes of Coxiella burnetii and identification of an intervening sequence within the 23S rRNA gene. J Bacteriol 1995; 177:2946-9. [PMID: 7751314 PMCID: PMC176976 DOI: 10.1128/jb.177.10.2946-2949.1995] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Characterization of the rRNA operon from the obligate intracellular bacterium Coxiella burnetii has determined the order of the rRNA genes to be 16S-23S-5S. A 444-bp intervening sequence (IVS) was identified to interrupt the 23S rRNA gene beginning at position 1176. The IVS is predicted to form a stem-loop structure formed by flanking inverted repeats, and the absence of intact 23S rRNA molecules suggests that the loop is removed. An open reading frame in the IVS has been identified that shows 70% similarity at the amino acid level to IVS open reading frames characterized from four species of Leptospira.
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Affiliation(s)
- G Afseth
- Department of Microbiology, Washington State University, Pullman 99164-4233, USA
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