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Comparative genomic analysis of ten Streptococcus pneumoniae temperate bacteriophages. J Bacteriol 2009; 191:4854-62. [PMID: 19502408 PMCID: PMC2715734 DOI: 10.1128/jb.01272-08] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptococcus pneumoniae is an important human pathogen that often carries temperate bacteriophages. As part of a program to characterize the genetic makeup of prophages associated with clinical strains and to assess the potential roles that they play in the biology and pathogenesis in their host, we performed comparative genomic analysis of 10 temperate pneumococcal phages. All of the genomes are organized into five major gene clusters: lysogeny, replication, packaging, morphogenesis, and lysis clusters. All of the phage particles observed showed a Siphoviridae morphology. The only genes that are well conserved in all the genomes studied are those involved in the integration and the lysis of the host in addition to two genes, of unknown function, within the replication module. We observed that a high percentage of the open reading frames contained no similarities to any sequences catalogued in public databases; however, genes that were homologous to known phage virulence genes, including the pblB gene of Streptococcus mitis and the vapE gene of Dichelobacter nodosus, were also identified. Interestingly, bioinformatic tools showed the presence of a toxin-antitoxin system in the phage phiSpn_6, and this represents the first time that an addition system in a pneumophage has been identified. Collectively, the temperate pneumophages contain a diverse set of genes with various levels of similarity among them.
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Desai BV, Morrison DA. An unstable competence-induced protein, CoiA, promotes processing of donor DNA after uptake during genetic transformation in Streptococcus pneumoniae. J Bacteriol 2006; 188:5177-86. [PMID: 16816189 PMCID: PMC1539964 DOI: 10.1128/jb.00103-06] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Natural genetic transformation in Streptococcus pneumoniae entails transcriptional activation of at least two sets of genes. One set of genes, activated by the competence-specific response regulator ComE, is involved in initiating competence, whereas a second set is activated by the competence-specific alternative sigma factor ComX and functions in DNA uptake and recombination. Here we report an initial characterization of CoiA, a ComX-dependent gene product that is induced during competence and is required for transformation. CoiA is widely conserved among gram-positive bacteria, and in streptococci, the entire coiA locus composed of four genes is conserved. By use of immunoblot assay, we show that, similar to its message, CoiA protein is transient, appearing at 10 min and largely disappearing by 30 min post-competence induction. Using complementation analysis, we establish that coiA is the only gene of this induced locus needed for transformability. We find no indication of CoiA having a role in regulating competence. Finally, using 32P- and 3H-labeled donor DNA, we demonstrate that a coiA mutant can internalize normal amounts of donor DNA compared to the wild-type strain but is unable to process it into viable transformants, suggesting a role for CoiA after DNA uptake, either in DNA processing or recombination.
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Affiliation(s)
- Bhushan V Desai
- Laboratory for Molecular Biology, Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
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3
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Yoo TH, Chang KH, Ryu DR, Kim JS, Choi HY, Park HC, Kang SW, Choi KH, Kim JM, Ha SK, Han DS, Lee HY. Usefulness of 23S rRNA amplification by PCR in the detection of bacteria in CAPD peritonitis. Am J Nephrol 2006; 26:115-20. [PMID: 16543715 DOI: 10.1159/000092040] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2005] [Accepted: 01/06/2006] [Indexed: 11/19/2022]
Abstract
BACKGROUND Peritonitis is the most common complication of continuous ambulatory peritoneal dialysis (CAPD), and the spectrum of organisms causing CAPD peritonitis is broad. Polymerase chain reaction (PCR) has recently broadened its diagnostic capabilities in infectious diseases. PCR can provide a sensitive method for identifying causative infectious organisms. METHODS To evaluate the usefulness of 23S bacterial ribosomal RNA amplification and direct sequencing for the detection of infectious organisms, we compared PCR with bacteriological culture for the analysis of dialysates from CAPD peritonitis patients. Thirty-two samples from CAPD peritonitis patients with current antibiotic use and control samples from 30 CAPD patients without peritonitis were examined by PCR with sequencing analysis and by conventional bacteriological culture. In addition, 95 culture-positive samples and 39 culture-negative samples from CAPD peritonitis patients before antibiotic treatment were analyzed by PCR assay. RESULTS In the control samples from patients without CAPD peritonitis, false-positive rates were relatively rare: 3 of 30 in the PCR study and 2 of 30 in the culture study. Of the 134 CAPD peritonitis samples collected before antibiotic therapy, positive cultures were obtained in 70.9% (95/134) of them. In 75 of the culture-positive samples, the same microorganisms were confirmed by PCR assay, and the others showed discrepant results as compared with culture study. In 30 of the 39 culture-negative samples, microbial organisms were detected by PCR assay. Of the 32 samples from patients who developed CAPD peritonitis during antibiotic treatment, 17 (53.1%) were positive by PCR assay, and 5 (15.6%) were positive by culture. CONCLUSION Our study suggests that broad-spectrum PCR with RNA sequencing can complement culture methods in the diagnosis of CAPD peritonitis, especially in patients with previous or current antibiotic use.
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Affiliation(s)
- Tae-Hyun Yoo
- Division of Nephrology, Department of Internal Medicine, Yonsei University College of Medicine, Seodaemun-ku, Seoul, Korea
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4
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Abstract
The terminal 39 nucleotides on the 3' end of the 16S rRNA gene, along with the complete DNA sequences of the 5S rRNA, 23S rRNA, tRNA(Ile), and tRNA(Ala) genes were determined for Paenibacillus popilliae using strains NRRL B-2309 and Dutky 1. Southern hybridization analysis with a 16S rDNA hybridization probe and restriction-digested genomic DNA demonstrated 8 copies of the 16S rRNA gene in P. popilliae strains KLN 3 and Dutky 1. Additionally, the 23S rRNA gene in P. popilliae strains NRRL B-2309, KLN 3, and Dutky 1 was shown by I-CeuI digestion and pulsed-field gel electrophoresis of genomic DNA to occur as 8 copies. It was concluded that these 3 P. popilliae strains contained 8 rrn operons. The 8 operon copies were preferentially located on approximately one-half of the chromosome and were organized into 3 different patterns of genes, as follows: 16S-23S-5S, 16S-ala-23S-5S, and 16S-5S-ile-ala-23S-5S. This is the first report to identify a 5S rRNA gene between the 16S and 23S rRNA genes of a bacterial rrn operon. Comparative analysis of the nucleotides on the 3' end of the 16S rRNA gene suggests that translation of P. popilliae mRNA may occur in Bacillus subtilis and Escherichia coli.
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MESH Headings
- Bacillus subtilis
- Base Sequence
- Blotting, Southern
- Chromosomes, Bacterial
- DNA Fingerprinting
- DNA, Bacterial
- DNA, Ribosomal/chemistry
- Escherichia coli
- Gene Order/genetics
- Genes, rRNA
- Gram-Positive Endospore-Forming Bacteria/genetics
- Molecular Sequence Data
- Protein Biosynthesis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 5S/genetics
- rRNA Operon/genetics
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Affiliation(s)
- Douglas W Dingman
- Department of Biochemistry and Genetics, Connecticut Agricultural Experiment Station, 123 Huntington Street, PO Box 1106, New Haven, CT 06504, USA.
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5
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Romero P, López R, García E. Genomic organization and molecular analysis of the inducible prophage EJ-1, a mosaic myovirus from an atypical pneumococcus. Virology 2004; 322:239-52. [PMID: 15110522 DOI: 10.1016/j.virol.2004.01.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2003] [Revised: 01/09/2004] [Accepted: 01/31/2004] [Indexed: 10/26/2022]
Abstract
We report the complete genomic sequence of EJ-1, an inducible prophage isolated from an atypical Streptococcus pneumoniae strain that belongs to the Myoviridae morphology family. The phage and bacterial recombinational sites (attachment sites) have been also determined. The genome of the EJ-1 prophage (42935 bp) is organized in 73 open reading frames (ORFs) and in at least five major clusters. Bioinformatic and N-terminal amino acid sequence analyses enabled the assignment of possible functions to 52 ORFs. The predicted proteins coded for the EJ-1 genome revealed similarities in the lysogeny, DNA replication, regulation, packaging, and head morphogenesis protein clusters with those from several siphoviruses infecting lactic acid bacteria. However, the proteins encoded by genes orf53 to orf64, corresponding to putative tail proteins of the virion, were very similar to those of the defective Bacillus subtilis myovirus PBSX with the notable exception of the gene product of orf56 (the tape measure tail protein) that was similar to proteins from phages infecting Gram-negative bacteria. The first description of the genome of a myovirus infecting a low G + C content Gram-positive bacterium, a member of a group embracing important human pathogens and industrial relevant species, will contribute to expand our current knowledge on phage biology and evolution.
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Affiliation(s)
- Patricia Romero
- Departamento de Microbiología Molecular, Centro de Investigaciones Biológicas, CSIC, 28040 Madrid, Spain
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6
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Chapuy-Regaud S, Ogunniyi AD, Diallo N, Huet Y, Desnottes JF, Paton JC, Escaich S, Trombe MC. RegR, a global LacI/GalR family regulator, modulates virulence and competence in Streptococcus pneumoniae. Infect Immun 2003; 71:2615-25. [PMID: 12704136 PMCID: PMC153264 DOI: 10.1128/iai.71.5.2615-2625.2003] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The homolactic and catalase-deficient pathogen Streptococcus pneumoniae is not only tolerant to oxygen but requires the activity of its NADH oxidase, Nox, to develop optimal virulence and competence for genetic transformation. In this work, we show that the global regulator RegR is also involved in these traits. Genetic dissection revealed that RegR regulates competence and the expression of virulence factors, including hyaluronidase. In bacteria grown in vitro, RegR represses hyaluronidase. At neutral pH, it increases adherence to A549 epithelial cells, and at alkaline pH, it acts upstream of the CiaRH two-component signaling system to activate competence. These phenotypes are not associated with changes in antibiotic resistance, central metabolism, and carbohydrate utilization. Although the RegR(0) (where 0 indicates the loss of the protein) mutation is sufficient to attenuate experimental virulence of strain 23477 in mice, the introduction of an additional hyl(0) (where 0 indicates the loss of function) mutation in the RegR(0) strain 23302 dramatically reduces its virulence. This indicates that residual virulence of the RegR(0) Hyl(+) derivative is due to hyaluronidase and supports the dual role of RegR in virulence. This LacI/GalR regulator, not essential for in vitro growth in rich media, is indeed involved in the adaptive response of the pneumococcus via its control of competence, adherence, and virulence.
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Affiliation(s)
- Sabine Chapuy-Regaud
- Laboratoire Interactions et Signalisation Cellulaire: Relation Hôte Pathogène, Institut Louis Bugnard, Centre Hospitalo-Universitaire de Rangueil, Université Paul Sabatier, 31403 Toulouse Cedex, France
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7
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Blaiotta G, Pepe O, Mauriello G, Villani F, Andolfi R, Moschetti G. 16S-23S rDNA intergenic spacer region polymorphism of Lactococcus garvieae, Lactococcus raffinolactis and Lactococcus lactis as revealed by PCR and nucleotide sequence analysis. Syst Appl Microbiol 2002; 25:520-7. [PMID: 12583712 DOI: 10.1078/07232020260517652] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The intergenic spacer region (ISR) between the 16S and 23S rRNA genes was tested as a tool for differentiating lactococci commonly isolated in a dairy environment. 17 reference strains, representing 11 different species belonging to the genera Lactococcus, Streptococcus, Lactobacillus, Enterococcus and Leuconostoc, and 127 wild streptococcal strains isolated during the whole fermentation process of "Fior di Latte" cheese were analyzed. After 16S-23S rDNA ISR amplification by PCR, species or genus-specific patterns were obtained for most of the reference strains tested. Moreover, results obtained after nucleotide analysis show that the 16S-23S rDNA ISR sequences vary greatly, in size and sequence, among Lactococcus garvieae, Lactococcus raffinolactis, Lactococcus lactis as well as other streptococci from dairy environments. Because of the high degree of inter-specific polymorphism observed, 16S-23S rDNA ISR can be considered a good potential target for selecting species-specific molecular assays, such as PCR primer or probes, for a rapid and extremely reliable differentiation of dairy lactococcal isolates.
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MESH Headings
- Base Sequence
- DNA, Intergenic/genetics
- DNA, Ribosomal/analysis
- Genes, Bacterial
- Lactococcus/classification
- Lactococcus/genetics
- Lactococcus lactis/genetics
- Molecular Sequence Data
- Polymerase Chain Reaction
- Polymorphism, Genetic
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Giuseppe Blaiotta
- Dipartimento di Scienza degli Alimenti, Sezione di Microbiologia Agraria, Alimentare ed Ambientale e di Igiene, Università degli Studi di Napoli Federico II, Portici, Italy
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8
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Agbo EC, Majiwa PA, Claassen EJ, Roos MH. Measure of molecular diversity within the Trypanosoma brucei subspecies Trypanosoma brucei brucei and Trypanosoma brucei gambiense as revealed by genotypic characterization. Exp Parasitol 2001; 99:123-31. [PMID: 11846522 DOI: 10.1006/expr.2001.4666] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have evaluated whether sequence polymorphisms in the rRNA intergenic spacer region can be used to study the relatedness of two subspecies of Trypanosoma brucei. Thirteen T. brucei isolates made up of 6 T. b. brucei and 7 T. b. gambiense were analyzed using restriction fragment length polymorphism (RFLP). By PCR-based restriction mapping of the ITS1-5.8S-ITS2 ribosomal repeat unit, we found a fingerprint pattern that separately identifies each of the two subspecies analyzed, with unique restriction fragments observed in all but 1 of the T. b. gambiense "human" isolates. Interestingly, the restriction profile for a virulent group 2 T. b. gambiense human isolate revealed an unusual RFLP pattern different from the profile of other human isolates. Sequencing data from four representatives of each of the two subspecies indicated that the intergenic spacer region had a conserved ITS-1 and a variable 5.8S with unique transversions, insertions, or deletions. The ITS-2 regions contained a single repeated element at similar positions in all isolates examined, but not in 2 of the human isolates. A unique 4-bp [C(3)A] sequence was found within the 5.8S region of human T. b. gambiense isolates. Phylogenetic analysis of the data suggests that their common ancestor was a nonhuman animal pathogen and that human pathogenicity might have evolved secondarily. Our data show that cryptic species within the T. brucei group can be distinguished by differences in the PCR-RFLP profile of the rDNA repeat.
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Affiliation(s)
- E C Agbo
- Division of Animal Sciences, Section for Animal Genomics, Institute for Animal Science and Health, ID-Lelystad, The Netherlands.
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9
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Beukes M, Hastings JW. Self-protection against cell wall hydrolysis in Streptococcus milleri NMSCC 061 and analysis of the millericin B operon. Appl Environ Microbiol 2001; 67:3888-96. [PMID: 11525982 PMCID: PMC93106 DOI: 10.1128/aem.67.9.3888-3896.2001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptococcus milleri NMSCC 061 produces an endopeptidase, millericin B, which hydrolyzes the peptide moiety of susceptible cell wall peptidoglycan. The nucleotide sequence of a 4.9-kb chromosomal region showed three open reading frames (ORFs) and a putative tRNA(Leu) sequence. The three ORFs encode a millericin B preprotein (MilB), a putative immunity protein (MilF), and a putative transporter protein (MilT). The milB gene encodes a 277-amino-acid preprotein with an 18-amino-acid signal peptide with a consensus IIGG cleavage motif. The predicted protein encoded by milT is homologous to ABC (ATP-binding cassette) transporters of several bacteriocin systems and to proteins implicated in the signal-sequence-independent export of Escherichia coli hemolysin A. These similarities strongly suggest that the milT gene product is involved in the translocation of millericin B. The gene milF encodes a protein of 302 amino acids that shows similarities to the FemA and FemB proteins of Staphylococcus aureus, which are involved in the addition of glycine to a pentapeptide peptidoglycan precursor. Comparisons of the cell wall mucopeptide of S. milleri NMSCC 061(resistant to lysis by millericin B) and S. milleri NMSCC 051(sensitive) showed a single amino acid difference. Serial growth of S. milleri NMSCC 051 in a cell wall minimal medium containing an increased concentration of leucine resulted in the in vivo substitution of leucine for threonine in the mucopeptide of the cell wall. A cell wall variant of S. milleri NMSCC 051 (sensitive) that contained an amino acid substitution (leucine for threonine) within its peptidoglycan cross bridge showed partial susceptibility to millericin B. The putative tRNA(Leu) sequence located upstream of milB may be a cell wall-specific tRNA and could together with the milF protein, play a potential role in the addition of leucine to the pentapeptide peptidoglycan precursor and thereby, contributing to self-protection to millericin B in the producer strain.
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Affiliation(s)
- M Beukes
- School of Molecular and Cellular Biosciences, University of Natal, Pietermaritzburg, Scottsville 3209, South Africa
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10
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Boyer SL, Flechtner VR, Johansen JR. Is the 16S-23S rRNA internal transcribed spacer region a good tool for use in molecular systematics and population genetics? A case study in cyanobacteria. Mol Biol Evol 2001; 18:1057-69. [PMID: 11371594 DOI: 10.1093/oxfordjournals.molbev.a003877] [Citation(s) in RCA: 148] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We amplified, TA-cloned, and sequenced the 16S-23S internal transcribed spacer (ITS) regions from single isolates of several cyanobacterial species, Calothrix parietina, Scytonema hyalinum, Coelodesmium wrangelii, Tolypothrix distorta, and a putative new genus (isolates SRS6 and SRS70), to investigate the potential of this DNA sequence for phylogenetic and population genetic studies. All isolates carried ITS regions containing the sequences coding for two tRNA molecules (tRNA and tRNA). We retrieved additional sequences without tRNA features from both C. parietina and S. hyalinum. Furthermore, in S. hyalinum, we found two of these non-tRNA-encoding regions to be identical in length but different in sequence. This is the first report of ITS regions from a single cyanobacterial isolate not only different in configuration, but also, within one configuration, different in sequence. The potential of the ITS region as a tool for studying molecular systematics and population genetics is significant, but the presence of multiple nonidentical rRNA operons poses problems. Multiple nonidentical rRNA operons may impact both studies that depend on comparisons of phylogenetically homologous sequences and those that employ restriction enzyme digests of PCR products. We review current knowledge of the numbers and kinds of 16S-23S ITS regions present across bacterial groups and plastids, and we discuss broad patterns congruent with higher-level systematics of prokaryotes.
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Affiliation(s)
- S L Boyer
- Department of Biology, John Carroll University, 20700 North Park Boulevard, University Heights, OH 44118, USA
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11
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Vester B, Douthwaite S. Macrolide resistance conferred by base substitutions in 23S rRNA. Antimicrob Agents Chemother 2001; 45:1-12. [PMID: 11120937 PMCID: PMC90232 DOI: 10.1128/aac.45.1.1-12.2001] [Citation(s) in RCA: 380] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- B Vester
- Department of Molecular Biology, University of Copenhagen, DK-1307 Copenhagen K, Denmark.
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12
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Adrian PV, Mendrick C, Loebenberg D, McNicholas P, Shaw KJ, Klugman KP, Hare RS, Black TA. Evernimicin (SCH27899) inhibits a novel ribosome target site: analysis of 23S ribosomal DNA mutants. Antimicrob Agents Chemother 2000; 44:3101-6. [PMID: 11036030 PMCID: PMC101610 DOI: 10.1128/aac.44.11.3101-3106.2000] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2000] [Accepted: 08/21/2000] [Indexed: 11/20/2022] Open
Abstract
Spontaneous mutants of susceptible clinical and laboratory isolates of Streptococcus pneumoniae exhibiting reduced susceptibility to evernimicin (SCH27899; MIC, 0.5 to 4.0 mg/liter) were selected on plates containing evernimicin. Four isolates that did not harbor mutations in rplP (which encodes ribosomal protein L16) were further analyzed. Whole chromosomal DNA or PCR products of the 23S ribosomal DNA (rDNA) operons from these mutants could be used to transform the susceptible S. pneumoniae strain R6 to resistance at frequencies of 10(-5) and 10(-4), respectively, rates 10- to 100-fold lower than that for a single-allele chromosomal marker. The transformants appeared slowly (48 to 72 h) on selective medium, and primary transformants passaged on nonselective medium produced single colonies that displayed heterogeneous susceptibilities to evernimicin. A single passage on selective medium of colonies derived from a single primary transformant homogenized the resistance phenotype. Sequence analysis of the 23S rDNA and rRNA from the resistant mutants revealed single, unique mutations in each isolate at the equivalent Escherichia coli positions 2469 (A --> C), 2480 (C --> T), 2535 (G --> A), and 2536 (G --> C). The mutations map within two different stems of the peptidyltransferase region of domain V. Because multiple copies of rDNA are present in the chromosome, gene conversion between mutant and wild-type 23S rDNA alleles may be necessary for stable resistance. Additionally, none of the characterized mutants showed cross-resistance to any of a spectrum of protein synthesis inhibitors, suggesting that the target site of evernimicin may be unique.
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MESH Headings
- Alleles
- Aminoglycosides
- Anti-Bacterial Agents/pharmacology
- Bacterial Proteins/genetics
- Base Sequence
- DNA, Bacterial/genetics
- Drug Resistance, Microbial
- Humans
- Microbial Sensitivity Tests
- Molecular Sequence Data
- Mutation
- Nucleic Acid Conformation
- RNA, Bacterial/analysis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/drug effects
- RNA, Ribosomal, 23S/genetics
- Streptococcus pneumoniae/drug effects
- Streptococcus pneumoniae/genetics
- Transformation, Bacterial
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Affiliation(s)
- P V Adrian
- Pneumococcal Diseases Research Unit, South African Institute for Medical Research, University of the Witwatersrand, and the Medical Research Council, Johannesburg, South Africa.
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13
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Tait-Kamradt A, Davies T, Cronan M, Jacobs MR, Appelbaum PC, Sutcliffe J. Mutations in 23S rRNA and ribosomal protein L4 account for resistance in pneumococcal strains selected in vitro by macrolide passage. Antimicrob Agents Chemother 2000; 44:2118-25. [PMID: 10898684 PMCID: PMC90022 DOI: 10.1128/aac.44.8.2118-2125.2000] [Citation(s) in RCA: 222] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The mechanisms responsible for macrolide resistance in Streptococcus pneumoniae mutants, selected from susceptible strains by serial passage in azithromycin, were investigated. These mutants were resistant to 14- and 15-membered macrolides, but resistance could not be explained by any clinically relevant resistance determinant [mef(A), erm(A), erm(B), erm(C), erm(TR), msr(A), mph(A), mph(B), mph(C), ere(A), ere(B)]. An investigation into the sequences of 23S rRNAs in the mutant and parental strains revealed individual changes of C2611A, C2611G, A2058G, and A2059G (Escherichia coli numbering) in four mutants. Mutations at these residues in domain V of 23S rRNA have been noted to confer erythromycin resistance in other species. Not all four 23S rRNA alleles have to contain the mutation to confer resistance. Some of the mutations also confer coresistance to streptogramin B (C2611A, C2611G, and A2058G), 16-membered macrolides (all changes), and clindamycin (A2058G and A2059G). Interestingly, none of these mutations confer high-level resistance to telithromycin (HMR-3647). Further, two of the mutants which had no changes in their 23S rRNA sequences had changes in a highly conserved stretch of amino acids ((63)KPWRQKGTGRAR(74)) in ribosomal protein L4. One mutant contained a single amino acid change (G69C), while the other mutant had a 6-base insert, resulting in two amino acids (S and Q) being inserted between amino acids Q67 and K68. To our knowledge, this is the first description of mutations in 23S rRNA genes or ribosomal proteins in macrolide-resistant S. pneumoniae strains.
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Affiliation(s)
- A Tait-Kamradt
- Department of Infectious Diseases, Pfizer, Inc., Groton, Connecticut 06340, USA
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14
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Abstract
An overview of gene cloning in Streptococcus pneumoniae is presented. The advantages of such cloning, especially for pneumococcal genes, are enumerated. The molecular fate of DNA in transformation of S. pneumoniae, in particular, the conversion of DNA to single-strand segments on entry, determines the mechanisms for plasmid establishment and interaction with the chromosome. One of these mechanisms, the chromosomal facilitation of plasmid establishment, is useful for obtaining recombinant plasmids and for introducing an allele from the chromosome into a plasmid. The difference between linear and circular synapsis of donor DNA strands with the chromosome is illustrated. Circular synapsis can give rise to circular integration, which is useful for insertional mutagenesis of chromosomal genes, for coupled cloning in Escherichia coli, and for sequential cloning of DNA along the pneumococcal chromosome. Cloning in S. pneumoniae is not notably affected by DNA mismatch repair or restriction systems in the host cell. Unusual features of gene expression in S. pneumoniae are discussed. Transcription begins most often at promoters with extended -10 sequences, and in a small but significant number of cases, translation does not require a ribosome-binding site with a Shine-Dalgarno sequence.
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Affiliation(s)
- S A Lacks
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
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15
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Lacks SA, Ayalew S, de la Campa AG, Greenberg B. Regulation of competence for genetic transformation in Streptococcus pneumoniae: expression of dpnA, a late competence gene encoding a DNA methyltransferase of the DpnII restriction system. Mol Microbiol 2000; 35:1089-98. [PMID: 10712690 DOI: 10.1046/j.1365-2958.2000.01777.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The chromosomal DpnII gene cassette of Streptococcus pneumoniae encodes two methyltransferases and an endonuclease. One methyltransferase acts on double-stranded and the other on single-stranded DNA. Two mRNAs are transcribed from the cassette. One, a SigA promoter transcript, includes all three genes; the other includes a truncated form of the second methyltransferase gene (dpnA) and the endonuclease gene. The truncated dpnA, which is translated from the second start codon in the full gene, was shown to produce active enzyme. A promoter reporter plasmid for S. pneumoniae was devised to characterize the promoter for the second mRNA. This transcript was found to depend on a promoter that responded to the induction of competence for genetic transformation. The promoter contains the combox sequence recognized by a SigH-containing RNA polymerase. As part of the competence regulon, the dpnA gene makes a product able to methylate incoming plasmid strands to protect them from the endonuclease and allow plasmid establishment. Its function differs from most genes in the regulon, which are involved in DNA uptake. Comparison of R6 and Rx strains of S. pneumoniae showed the temperature dependence of transformation in R6 to result from temperature sensitivity of the uptake apparatus and not the development of competence.
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Affiliation(s)
- S A Lacks
- Department of Biology, Brookhaven National Laboratory, Upton, NY 11973, USA.
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16
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Anthony RM, Brown TJ, French GL. Rapid diagnosis of bacteremia by universal amplification of 23S ribosomal DNA followed by hybridization to an oligonucleotide array. J Clin Microbiol 2000; 38:781-8. [PMID: 10655385 PMCID: PMC86203 DOI: 10.1128/jcm.38.2.781-788.2000] [Citation(s) in RCA: 145] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/1999] [Accepted: 10/29/1999] [Indexed: 11/20/2022] Open
Abstract
The rapid identification of bacteria in blood cultures and other clinical specimens is important for patient management and antimicrobial therapy. We describe a rapid (<4 h) detection and identification system that uses universal PCR primers to amplify a variable region of bacterial 23S ribosomal DNA, followed by reverse hybridization of the products to a panel of oligonucleotides. This procedure was successful in discriminating a range of bacteria in pure cultures. When this procedure was applied directly to 158 unselected positive blood culture broths on the day when growth was detected, 125 (79.7%) were correctly identified, including 4 with mixed cultures. Nine (7.2%) yielded bacteria for which no oligonucleotide targets were present in the oligonucleotide panel, and 16 culture-positive broths (10.3%) produced no PCR product. In seven of the remaining eight broths, streptococci were identified but not subsequently grown, and one isolate of Staphylococcus aureus was misidentified as a coagulase-negative staphylococcus. The accuracy, range, and discriminatory power of the assay can be continually extended by adding further oligonucleotides to the panel without significantly increasing complexity or cost.
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Affiliation(s)
- R M Anthony
- Department of Microbiology, King's College St. Thomas' Campus, St. Thomas' Hospital, London SE1 7EH, United Kingdom
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17
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Palmen R, Ogunniyi AD, Berroy P, Larpin S, Paton JC, Trombe MC. Insertional mutation of orfD of the DCW cluster of Streptococcus pneumoniae attenuates virulence. Microb Pathog 1999; 27:337-48. [PMID: 10588907 DOI: 10.1006/mpat.1999.0310] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mutational analysis of a 5.5 kb fragment of the genome Streptococcus pneumoniae led to the identification of a putative new virulence gene, designated orfD. Insertion mutagenesis of flanking genes on the fragment suggested that the corresponding gene products were required for in vitro growth. In contrast, insertion mutation of orfD did not alter in vitro growth or the transformability pattern of the mutated strain. However, it did reduce bacterial growth in mice and attenuated virulence in an intraperitoneal model of infection. orfD is flanked by orfC (63 codons) and ftsL (105 codons) and all three genes are upstream of pbpx. orfC showed no similarity with other known proteins. ftsL of S. pneumoniae exhibits minimal sequence similarity with ftsL of E. coli, but shares 16% identical residues with the ftsL homologue encoded by ylld of B. subtilis. Also, ftsL of S. pneumoniae has a predicted topology similar to that described for ftsL of E. coli. Putative promoters with an extended -10 box could be identified upstream of both orfC or orfD. The four open reading frames (including pbpx) are orientated in the same direction, and polycistronic transcription could theoretically start at either promoter. Interestingly, this region shows organizational and sequence homologies with genes controlling division and cell wall biosynthesis (DCW) in other bacteria. The attenuation of virulence in the orfD insertion mutant might be due to the loss of function of the orfD gene product or to an altered level of expression of downstream genes.
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Affiliation(s)
- R Palmen
- Laboratoire de Microbiologie, Centre Hospitalo Universitaire de Rangueil, Toulouse, 31403, Cedex 4, France
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18
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Cappiello MG, Hantman MJ, Zuccon FM, Peruzzi F, Amjad M, Piggot PJ, Daneo-Moore L. Physical and genetic map of Streptococcus mutans GS-5 and localization of five rRNA operons. ORAL MICROBIOLOGY AND IMMUNOLOGY 1999; 14:225-32. [PMID: 10551166 DOI: 10.1034/j.1399-302x.1999.140405.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The physical map of the 2.1 megabase chromosome of Streptococcus mutans GS-5 has been refined by including all ApaI and SmaI fragments of 5 kbp or greater, and by positioning the fragments generated by the endonuclease I-CeuI. Sixty-three new genetic loci have been added to the map, so that it now contains 90 loci. The new loci include those for 35 cloned streptococcal genes of established function and for 23 S. mutans genes of putative function. In addition, five rrn operons were identified and placed on the map of the chromosome. The presence of a SmaI site in each of the rrn operons allowed the direction of transcription of each operon to be deduced. The orientation of the rrn loci indicates that their transcription is directed away from a small region of the chromosome, identifying a possible region for the initiation of chromosome replication.
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Affiliation(s)
- M G Cappiello
- Department of Microbiology and Immunology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140, USA
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19
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Naimi A, Beck G, Monique M, Lefèbvre G, Branlanti C. Determination of the nucleotide sequence of the 23S ribosomal RNA and flanking spacers of an Enterococcus faecium strain, reveals insertion-deletion events in the ribosomal spacer 1 of enterococci. Syst Appl Microbiol 1999; 22:9-21. [PMID: 10188274 DOI: 10.1016/s0723-2020(99)80023-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The usefulness of 16S-23S (ITS1) and 23S-5S (ITS2) ribosomal spacer nucleotide sequence determination, as a complementary approach to the biochemical tests traditionally used for enterococcal species identification, is shown by its application to the identification of a strain, E27, isolated from a natural bacteria mixture used for cheese production. Using combined approaches we showed, unambiguously, that strain E27 belongs to the Enterococcus faecium species. However, its ITS1 region has an interesting peculiarity. In our previous study of ITS1s from various enterococcal species (NAIMI et al., 1997, Microbiology 143, 823-834), the ITS1s of the two E. faecium strains studied, were found to contain an additional 115-nt long stem-loop structure as compared to the ITS1s of other enterococci, only one out of the 3 ITS1s of E. hirae ATCC 9790, was found to contain a similar 107-nt long stem-loop structure. The ITS1 of strain E27 is 100% identical to that of E. faecium ATCC 19434T, except that the 115-nt additional fragment is absent. This strongly suggests the existence of lateral DNA transfer or DNA recombination events at a hot spot position of the ITS1s from E. faecium and E. hirae. Small and large ITS1 nucleotide sequence determination for strain E27 generalized the notion of two kinds of ITSs in enterococci: one with a tRNA(Ala) gene, one without tRNA gene. To complete strain E27 characterization, its 23S rRNA sequence was established. This is the first complete 23S rRNA nucleotide sequence determined for an enterococcal species.
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Affiliation(s)
- A Naimi
- Maturation des ARN et Enzymologie Moléculaire, UMR 7567 CNRS-Université Henri Poincaré, Vandoeuvre-Lès-Nancy, France
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20
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Nour M. 16S-23S and 23S-5S intergenic spacer regions of lactobacilli: nucleotide sequence, secondary structure and comparative analysis. Res Microbiol 1998; 149:433-48. [PMID: 9766243 DOI: 10.1016/s0923-2508(98)80326-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Lactobacilli have been used as industrial starters for a long time, but in several cases their identification was, and still is, neither easy nor reliable. The aim of the present work was to examine whether the intergenic spacer regions could be of value in the identification of Lactobacillus species. For that purpose, the polymerase chain reaction (PCR) was used to amplify 16S-23S and 23S-5S spacer regions of Lactobacillus (L.) acidophilus, L. delbrueckii subsp. bulgaricus, L. casei, L. helveticus and L. curvatus. The PCR products were directly sequenced, and two forms of ribosomal RNA (rrn) operons were identified in each species studied: one with tandem tRNA(Ile)/tRNA(Ala) genes and the other one without tRNA genes. Our study revealed that the rrn operons of Lactobacillus species studied comprise the genes of 16S, 23S and 5S rRNA, in that order. Only the tRNA genes and the rRNA processing stems are highly conserved in spacer regions of lactobacilli. The divergence between the lactobacilli spacer region sequences arises from insertions and deletions of short sequences. These sequences could be interesting candidates for the development of species-specific probes. Theoretical RNA/RNA secondary structure models of the interaction between the two spacer region sequences were constructed. In conclusion, the two spacer region sequences may prove to be a useful alternative to 16S and 23S rDNA sequencing for designing species-specific probes and for establishing phylogenetic relationships between closely related species such as L. curvatus and L. casei or L. acidophilus and L. helveticus.
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MESH Headings
- Base Sequence
- Fermentation/genetics
- Lactobacillus/genetics
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 5S/genetics
- RNA, Transfer, Ala/genetics
- RNA, Transfer, Ile/genetics
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Affiliation(s)
- M Nour
- Département des Sciences Biologiques (Microbiologie), Faculté des Sciences de Monastir, Tunisia
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21
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Zhang YB, Greenberg B, Lacks SA. Analysis of a Streptococcus pneumoniae gene encoding signal peptidase I and overproduction of the enzyme. Gene 1997; 194:249-55. [PMID: 9272867 DOI: 10.1016/s0378-1119(97)00198-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The spi gene of Streptococcus pneumoniae was cloned and its nucleotide sequence was determined. It encodes a protein of 204 amino acids that is homologous to bacterial signal peptidase I proteins. The S. pneumoniae protein contains all of the conserved amino acid sequence motifs previously identified in this enzyme from both prokaryotic and eukaryotic sources. Sequence comparisons revealed several additional motifs characteristic of the enzyme. The cloned S. pneumoniae gene complemented an Escherichia coli mutant defective in its leader peptidase gene. Expression of the spi gene in S. pneumoniae appeared to be essential for viability. The cloned gene was shown to produce a polypeptide of approximately 20 kDa. Overproduction of the S. pneumoniae spi gene in an E. coli expression system gave a native protein product, soluble in the presence of a non-ionic detergent, which should be amenable to structural determination.
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Affiliation(s)
- Y B Zhang
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
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22
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Zhang YB, Ayalew S, Lacks SA. The rnhB gene encoding RNase HII of Streptococcus pneumoniae and evidence of conserved motifs in eucaryotic genes. J Bacteriol 1997; 179:3828-36. [PMID: 9190796 PMCID: PMC179189 DOI: 10.1128/jb.179.12.3828-3836.1997] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A single RNase H enzyme was detected in extracts of Streptococcus pneumoniae. The gene encoding this enzyme was cloned and expressed in Escherichia coli, as demonstrated by its ability to complement a double-mutant rnhA recC strain. Sequence analysis of the cloned DNA revealed an open reading frame of 290 codons that encodes a polypeptide of 31.9 kDa. The predicted protein exhibits a low level of homology (19% identity of amino acid residues) to RNase HII encoded by rnhB of E. coli. Identification of the S. pneumoniae RNase HII translation start site by amino-terminal sequencing of the protein and of mRNA start sites by primer extension with reverse transcriptase showed that the major transcript encoding rnhB begins at the protein start site. Comparison of the S. pneumoniae and E. coli RNase HII sequences and sequences of other, putative bacterial rnhB gene products surmised from sequencing data revealed three conserved motifs. Use of these motifs to search for homologous genes in eucaryotes demonstrated the presence of rnhB genes in a yeast and a roundworm. Partial rnhB gene sequences were detected among expressed sequences of mouse and human cells. From these data, it appears that RNase HII is universally present in living cells.
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Affiliation(s)
- Y B Zhang
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA
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23
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Naïmi A, Beck G, Branlant C. Primary and secondary structures of rRNA spacer regions in enterococci. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 3):823-834. [PMID: 9084166 DOI: 10.1099/00221287-143-3-823] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The 16S-23S and 23S-5S rRNA spacer DNA regions (spacer regions 1 and 2, respectively) from Enterococcus faecalis, Enterococcus faecium, Enterococcus hirae, Enterococcus durans and Enterococcus mundtii were amplified by PCR. Their nucleotide sequences were established and a secondary structure model showing the interaction between the two spacer regions was built. Whereas lactococci and Streptococcus sensu stricto are characterized by a single type of spacer region 1, the enterococci show a high degree of variability in this region; thus the spacer regions 1 with and without tRNA(Ala) were characterized. However, as shown for lactococci and Streptococcus sensu stricto, the tRNA(Ala) gene does not encode the 3'-terminal CCA trinucleotide. A putative antitermination signal is found downstream from the tRNA(Ala) gene. Based on comparison with Lactococcus lactis and Streptococcus thermophilus, a double-stranded processing stem is proposed. In E, hirae, one of the three different types of spacer region 1 contains no tRNA(Ala), but displays a 107 nt insertion that forms a long stem-loop structure. A similar insertion (115 nt in length) was found in E. faecium and base compensatory mutations preserve the ability to form the long stem-loop structure. Such insertions may correspond to mobile intervening sequences, as found in the 23S rRNA coding sequences of some Gram-negative bacteria. The spacer regions 1 and 2 from the three subgroups of streptococci were compared, and except for the tRNA(Ala) gene and the double-stranded processing sites, little similarity was found, which opens large possibilities for future development of DNA-based typing methods.
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Affiliation(s)
- Afaf Naïmi
- Laboratoire d'Enzymologie et de Génie Génétiqe, URA CNRS 457, Université; de Nancy I, Bld des Aiguillettes, BP 239-54506 Vandoeuvre-Lés-Nancy Cedex, France
| | - Geneviéve Beck
- Laboratoire d'Enzymologie et de Génie Génétiqe, URA CNRS 457, Université; de Nancy I, Bld des Aiguillettes, BP 239-54506 Vandoeuvre-Lés-Nancy Cedex, France
| | - Christiane Branlant
- Laboratoire d'Enzymologie et de Génie Génétiqe, URA CNRS 457, Université; de Nancy I, Bld des Aiguillettes, BP 239-54506 Vandoeuvre-Lés-Nancy Cedex, France
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24
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Dintilhac A, Claverys JP. The adc locus, which affects competence for genetic transformation in Streptococcus pneumoniae, encodes an ABC transporter with a putative lipoprotein homologous to a family of streptococcal adhesins. Res Microbiol 1997; 148:119-31. [PMID: 9765793 DOI: 10.1016/s0923-2508(97)87643-7] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
To identify new components involved in the phenomenon of transformation in Streptococcus pneumoniae, a library of potential mutants has been generated by random insertion of an erythromycin resistance gene. Transformation-deficient mutants were screened using an in situ colony transformation test. The adc locus, which was identified in this search, was cloned and sequenced. Sequence analysis revealed a putative operon of three ORFs (adcC, adcB and adcA) with homology to ATP-binding cassette (ABC) transport operons encoding streptococcal adhesins such as ScaA of S. gordonii and FimA of S. parasanguis. adcA can encode a lipoprotein of 313 amino acid residues containing a putative metal-binding site. The polypeptide shows about 30% sequence identity with ScaA and FimA. We discuss evidence which leads us to propose that AdcA, together with a set of 14 proteins including ScaA, FimA and homologous adhesins, defines a new family of external solute-binding proteins, cluster 9, specific for metals.
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Affiliation(s)
- A Dintilhac
- Laboratoire de Microbiologie et Génétique moléculaire CNRS-UPR 9007, Université Paul Sabatier, Toulouse, France
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25
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Le Jeune C, Lonvaud-Funel A. Sequence of DNA 16S/23S spacer region of Leuconostoc oenos (Oenococcus oeni): application to strain differentiation. Res Microbiol 1997; 148:79-86. [PMID: 9404508 DOI: 10.1016/s0923-2508(97)81903-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Leuconostoc oenos is involved in malolactic fermentation occurring during wine-making. An increasing number of wines are being inoculated with malolactic starters to control the process, and the identification and differentiation of selected strains are now indispensable both for quality control of production and for commercial purposes. In the present work we evaluated the potential use of the intergenic regions of three L. oenos strains for their differentiation. The three 16S/23S rRNA intergenic spacers were amplified in vitro by PCR, and sequences were compared. The spacer sequence was highly conserved in all strains. Inside this spacer, a tRNA-Ala gene containing an 18-bp sequence stretch which is conserved in all tRNA genes was discovered. This sequence, together with random primers, was used for characterization of ten L. oenos strains by PCR.
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Affiliation(s)
- C Le Jeune
- Institut d'Oenologie, Unité Associée Université de Bordeaux II/INRA, Talence, France
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26
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Martín AC, López R, García P. Analysis of the complete nucleotide sequence and functional organization of the genome of Streptococcus pneumoniae bacteriophage Cp-1. J Virol 1996; 70:3678-87. [PMID: 8648702 PMCID: PMC190243 DOI: 10.1128/jvi.70.6.3678-3687.1996] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Cp-1, a bacteriophage infecting Streptococcus pneumoniae, has a linear double-stranded DNA genome, with a terminal protein covalently linked to its 5' ends, that replicates by the protein-priming mechanism. We describe here the complete DNA sequence and transcriptional map of the Cp-1 genome. These analyses have led to the firm assignment of 10 genes and the localization of 19 additional open reading frames in the 19,345-bp Cp-1 DNA. Striking similarities and differences between some of these proteins and those of the Bacillus subtilis phage phi 29, a system that also replicates its DNA by the protein-priming mechanism, have been revealed. The genes coding for structural proteins and assembly factors are located in the central part of the Cp-1 genome. Several proteins corresponding to the predicted gene products were identified by in vitro and in vivo expression of the cloned genes. Mature major head protein from the virion particles results from hydrolysis of the primary gene product at the His-49 residue, whereas the phage gene is expressed in Escherichia coli without modification. We have also identified two open reading frames coding for proteins that show high degrees of similarity to the N- and C-terminal regions, respectively, of the single tail protein identified in phi 29. Sequencing and primer extension analysis suggest transcription of a small RNA showing a secondary structure similar to that of the prohead RNA required for the ATP-dependent packaging of phi 29 DNA. On the basis of its temporal expression, transcription of the Cp-1 genome takes place in two stages, early and late. Combined Northern (RNA) blot and primer extension experiments allowed us to map the 5' initiation sites of the transcripts, and we found that only three genes were transcribed from right to left. These analyses reveal that there are also noticeable differences between Cp-l and phi 29 in transcriptional organization. Considered together, the observations reported here provide new tangible evidence on phylogenetic relationships between B. subtilis and S. pneumoniae.
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Affiliation(s)
- A C Martín
- Consejo Superior de Investigaciones Científicas, Madrid, Spain
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27
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Cuny C, Claus H, Witte W. Discrimination of S. aureus strains by PCR for r-RNA gene spacer size polymorphism and comparison to SmaI macrorestriction patterns. ZENTRALBLATT FUR BAKTERIOLOGIE : INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY 1996; 283:466-76. [PMID: 8737944 DOI: 10.1016/s0934-8840(96)80123-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The size polymorphism of the internal spacer between the 16 S and the 23 S r-RNA genes was studied in S. aureus with the aid of PCR. The patterns of corresponding PCR products were compared with SmaI-generated macrorestriction patterns for definite propagating strains of S. aureus typing phages, for strains with phage pattern 29, phage-group II patterns, phage pattern 94, 96, phage pattern 95 and epidemic methicillin-resistant strains (MRSA). The spacer length polymorphism did not prove to be as discriminative as genomic DNA fragment patterns. However, as shown for S. aureus with phage patterns 29; group II; 94, 96; 95 and also for 4 out of 6 epidemic MRSA, unique patterns of r-RNA gene spacers probably indicate a relatedness among strains which is also suggested by SmaI macrorestriction patterns.
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Affiliation(s)
- C Cuny
- Robert Koch Institute, Wernigerode Branch, Germany
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28
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Gürtler V, Stanisich VA. New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. MICROBIOLOGY (READING, ENGLAND) 1996; 142 ( Pt 1):3-16. [PMID: 8581168 DOI: 10.1099/13500872-142-1-3] [Citation(s) in RCA: 566] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Volker Gürtler
- Department of Microbiology, Austin and Repatriation Medical Centre (Repatriation Campus), Heidelberg West 3081, Victoria, Australia
| | - Vilma A Stanisich
- School of Microbiology, La Trobe University, Bundoora 3083, Victoria, Australia
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29
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Hall LM, Duke B, Urwin G. An approach to the identification of the pathogens of bacterial meningitis by the polymerase chain reaction. Eur J Clin Microbiol Infect Dis 1995; 14:1090-4. [PMID: 8681987 DOI: 10.1007/bf01590946] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A combination of universal and species-specific primers was used to detect and differentiate by nested polymerase chain reaction (PCR) the four species most commonly causing bacterial meningitis. Primers recognising conserved sequences in the 16S and 23S ribosomal RNA genes were employed to amplify the 16S-23S spacer region from Neisseria meningitidis, Haemophilus influenzae (type b), Streptococcus pneumoniae, and Streptococcus agalactiae (group B streptococcus). The sequence of the most abundant spacer product was determined in each case and used to deduce species-specific primers. A nested PCR using universal primers in the first round and a species-specific primer in the second were able to detect and distinguish between the four common pathogens, in the presence of human DNA. Streptococcus pneumoniae DNA was detected in the cerebrospinal fluid of a meningitis patient with negative culture and Gram-stain results.
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Affiliation(s)
- L M Hall
- Department of Medical Microbiology, London Hospital Medical College, UK
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30
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Nour M, Naimi A, Beck G, Branlant C. 16S-23S and 23S-5S intergenic spacer regions of Streptococcus thermophilus and Streptococcus salivarius, primary and secondary structure. Curr Microbiol 1995; 31:270-8. [PMID: 7580797 DOI: 10.1007/bf00314579] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The 16S-23S intergenic spacer region (spacer region 1) of Streptococcus salivarius, S. thermophilus, and Lactococcus lactis subsp. cremoris and the 23S-5S intergenic spacer region (spacer region 2) of S. salivarius and L. lactis subsp. cremoris were sequenced and compared with the spacer regions 1 and 2 of other streptococci. A high degree of intraspecific conservation was observed for S. thermophilus and L. lactis, and very similar sequences were found for S. salivarius and S. thermophilus. Whereas spacer region 1 is highly conserved in the genus Streptococcus sensu-stricto, only the tRNA gene and the rRNA processing stems are highly conserved in the three genera: Streptococcus sensu-stricto, Lactococcus, and Enterococcus. The presence of a unique tRNA(Ala) gene without the 3' terminal CCA sequence seems to be a general feature of the streptococci spacer region 1. A secondary structure model was built to show the interaction between the spacer regions 1 and 2 of S. thermophilus and S. salivarius. The rapid evolution of spacer region 1 in streptococci is in part due to insertions and deletions of small RNA stem/loop structures.
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MESH Headings
- Base Sequence
- Conserved Sequence
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Lactococcus lactis/chemistry
- Lactococcus lactis/genetics
- Molecular Sequence Data
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Transfer, Ala/genetics
- Sequence Homology, Nucleic Acid
- Streptococcus/chemistry
- Streptococcus/genetics
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Affiliation(s)
- M Nour
- Laboratoire d'Enzymologie et de Génie Génétique, Université de Nancy I, URA CNRS 457, Vandoeuvre-Les-Nancy, France
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31
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Bentley RW, Leigh JA. Determination of 16S ribosomal RNA gene copy number in Streptococcus uberis, S. agalactiae, S. dysgalactiae and S. parauberis. FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY 1995; 12:1-7. [PMID: 8580896 DOI: 10.1111/j.1574-695x.1995.tb00167.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Species-specific oligonucleotide probes and a universal oligonucleotide probe derived from sequences of 16S rRNA were hybridised to chromosomal DNA from Streptococcus agalactiae, S. dysgalactiae, S. parauberis and S. uberis following digestion with EcoRI. Due to the presence of a unique EcoRI site in each 16S rRNA gene, the number of hybridised fragments was indicative of the number of 16S rRNA genes. Southern hybridisation indicated six 16S rRNA genes in ten isolates of S. agalactiae, five genes in ten isolates of S. uberis, five genes in six isolates and six in another isolate of S. dysgalactiae, and six genes in four isolates of S. parauberis. For a fifth isolate of S. parauberis, six 16S rRNA genes were indicated by the universal probe but only five when hybridised to the species-specific probe, indicating sequence variation (microheterogeneity) within the probe target region.
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Affiliation(s)
- R W Bentley
- Institute for Animal Health, Newbury, Berkshire, UK
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32
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Whiley RA, Duke B, Hardie JM, Hall LMC. Heterogeneity among 16S-23S rRNA intergenic spacers of species within the 'Streptococcus milleri group'. MICROBIOLOGY (READING, ENGLAND) 1995; 141 ( Pt 6):1461-1467. [PMID: 7545512 DOI: 10.1099/13500872-141-6-1461] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The 16S-23S rRNA intergenic spacer has been suggested as a suitable region of the bacterial genome from which to derive useful taxonomic information, particularly with regard to identification at the species level. To investigate this approach as an aid to the identification of the three species comprising the 'Streptococcus milleri group' (SMG), the spacers of isolates of Streptococcus intermedius, Streptococcus anginosus and Streptococcus constellatus were amplified by PCR and length polymorphisms determined by agarose gel electrophoresis. Phenotypically atypical isolates which had been identified presumptively as belonging to these three species were also included. Spacers from two representatives of each spacer length found within the three SMG species were sequenced. 16S-23S rRNA intergenic spacer length polymorphisms allowed discrimination between S. anginosus (350 bp or 450 bp amplification product) and S. constellatus (380 bp amplification product), species that are difficult to differentiate phenotypically. S. intermedius (330 bp or 450 bp amplification product) and S. anginosus (350 bp or 450 bp amplification product) were not reliably distinguished by this method but are phenotypically distinct. Sequencing data demonstrated that the spacers had a central region of highly variable length flanked by conserved regions which included a single tRNA(Ala) gene. Polymorphism in the length of the 16S-23S spacer determined by PCR provides a rapid and useful adjunct to strain identification for S. anginosus and S. constellatus, which are not readily differentiated phenotypically.
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MESH Headings
- Base Sequence
- DNA, Bacterial/genetics
- DNA, Ribosomal/genetics
- Genes, Bacterial
- Molecular Sequence Data
- Polymerase Chain Reaction
- Polymorphism, Restriction Fragment Length
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- Sequence Alignment
- Sequence Homology, Nucleic Acid
- Species Specificity
- Streptococcus/classification
- Streptococcus/genetics
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Affiliation(s)
- R A Whiley
- Departments of Oral Microbiology, The London Hospital Medical College,Turner Street, London E1 2AD,UK
| | - B Duke
- Departments of Medical Microbiology, The London Hospital Medical College,Turner Street, London E1 2AD,UK
| | - J M Hardie
- Departments of Oral Microbiology, The London Hospital Medical College,Turner Street, London E1 2AD,UK
| | - L M C Hall
- Departments of Medical Microbiology, The London Hospital Medical College,Turner Street, London E1 2AD,UK
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Lacks SA, Greenberg B, Sabelnikov AG. Possible regulation of DNA methyltransferase expression by RNA processing in Streptococcus pneumoniae. Gene X 1995; 157:209-12. [PMID: 7541761 DOI: 10.1016/0378-1119(94)00481-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Atypical ribosome-binding sites lacking Shine-Dalgarno sequences appear to be used for translation of the DpnM and DpnA DNA methyltransferases of the DpnII restriction system. Preliminary results indicate that the 5'-endpoints of DpnII system mRNAs result from degradation of the original transcript. These tentative findings serve as the basis for a possible regulatory model that would accommodate the DpnII cassette either as a single copy in the chromosome or on a multicopy plasmid.
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Affiliation(s)
- S A Lacks
- Brookhaven National Laboratory, Upton, NY 11973, USA
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34
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Roux V, Raoult D. The 16S-23S rRNA intergenic spacer region of Bartonella (Rochalimaea) species is longer than usually described in other bacteria. Gene 1995; 156:107-11. [PMID: 7737501 DOI: 10.1016/0378-1119(94)00919-j] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We amplified by polymerase chain reaction (PCR) and sequenced using an automated laser fluorescent DNA sequencer (Pharmacia) the intergenic spacer region (ITS) between the 16S and 23S rRNAs of the four species of Rochalimaea which were recently renamed Bartonella sp. We obtained DNA fragments of 1211, 1262, 1258 and 1529 bp for the reference species of B. quintana, B. henselae, B. vinsonii and B. elizabethae, respectively. The ITS of the four species are longer than previously reported in prokaryotes and contained the genes encoding isoleucine-tRNA (tRNA(Ile)) and alanine-tRNA (tRNA(Ala)). The sequences of the tRNA(Ala) genes are identical for the four Bartonella species, but the tRNA(Ile) gene sequence of B. quintana presents one mutation in comparison with the other species.
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MESH Headings
- Bartonella/genetics
- Bartonella quintana/genetics
- Base Composition
- Base Sequence
- DNA, Ribosomal/genetics
- Genes, Bacterial/genetics
- Molecular Sequence Data
- Nucleic Acid Conformation
- Polymerase Chain Reaction
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- RNA, Transfer, Ala/chemistry
- RNA, Transfer, Ala/genetics
- RNA, Transfer, Ile/chemistry
- RNA, Transfer, Ile/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- V Roux
- Unité des Rickettsies, CNRS EP J 0054, Faculté de Médecine, Marseille, France
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Lacks SA, Greenberg B, Lopez P. A cluster of four genes encoding enzymes for five steps in the folate biosynthetic pathway of Streptococcus pneumoniae. J Bacteriol 1995; 177:66-74. [PMID: 7798151 PMCID: PMC176557 DOI: 10.1128/jb.177.1.66-74.1995] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Two genes, sulB and sulC, in a folate biosynthetic gene cluster of Streptococcus pneumoniae were identified after determination of the DNA sequence between two previously reported genes, sulA and sulD, in a cloned segment of chromosomal DNA containing a mutation to sulfonamide resistance. The gene products, SulB and SulC, correspond to polypeptides of 49 and 21 kDa, respectively. SulC has GTP cyclohydrolase activity and catalyzes the first step in the folate biosynthetic pathway. SulB apparently has dihydrofolate synthetase activity in that it complements a folC mutant of Escherichia coli and thus catalyzes the last step in the pathway. Prior work showed that SulA, a dihydropteroate synthase, and SulD, a bifunctional enzyme, catalyze three intervening steps. Mapping of the mRNA transcribed from the operon was consistent with its beginning at a promoter with a -35 site (gTGtCc) and an extended -10 site (T-TG-TAaAAT) and its termination at the end of a hairpin structure, which would give a transcript 3,745 nucleotides in length. SulC showed a considerable conservation of sequence by comparison with proven or putative GTP cyclohydrolases from four unrelated species, with 38 to 53% of the residues being identical. A similar comparison of SulB with dihydrofolate synthetases showed an identity of only 26 to 37%. Overall, comparisons of the five folate biosynthetic enzymes in different species suggest that S. pneumoniae is related more closely to other gram-positive bacteria, less closely to eucaryotes, and least closely to the gram-negative E. coli. The varied arrangements of folate biosynthetic genes in different species imply an early evolutionary period of fluidity in genomic rearrangement.
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Affiliation(s)
- S A Lacks
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973
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López de Felipe F, Corrales MA, López P. Comparative analysis of gene expression in Streptococcus pneumoniae and Lactococcus lactis. FEMS Microbiol Lett 1994; 122:289-95. [PMID: 7988870 DOI: 10.1111/j.1574-6968.1994.tb07182.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The pFL10 plasmid vector for translational fusions was constructed. pFL10 is based in the promiscuous pLS1 replicon and contains the pC194 cat gene deprived of its transcriptional promoter and Shine-Dalgarno (SD) sequence. Three promoters (Pcit, PpolA and PtetL) from Gram-positive bacteria, inserted in pFL10, were tested for their ability to drive transcription in Lactococcus lactis and Streptococcus pneumoniae. These promoters were coupled to the SD sequence of the lactococcal citP gene fused to the cat gene. Determination of the 5' ends of the three mRNAs by primer extension revealed the same start sites in both bacterial systems. However, it was observed a differential efficiency of promoter utilization by the RNA polymerases from the two hosts. The transcriptional behavior correlates with expression of the cat gene measured by determinations of chloramphenicol acetyltransferase (CAT) activity. Substitution of the SD of citP by that of the T7 phi 10 gene rendered a similar decrease of the CAT production in both bacterial systems.
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Sechi LA, Zuccon FM, Mortensen JE, Daneo-Moore L. Ribosomal RNA gene (rrn) organization in enterococci. FEMS Microbiol Lett 1994; 120:307-13. [PMID: 7521309 DOI: 10.1111/j.1574-6968.1994.tb07051.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A cloned 1.8-kb probe containing the 3' end of 16S ribosomal RNA and the 5' end of 23S ribosomal RNA from Enterococcus hirae was used to analyze various endonuclease digests of enterococci. In the ATCC strains tested we observed a remarkable conservation of the ApaI sites in the rrn operons, and a partial conservation of EcoRI sites. Using a number of other endonuclease digestions with the ApaI rrn probe, we estimate the number of rrn operons in enterococci to be between five and six.
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Affiliation(s)
- L A Sechi
- Department of Microbiology and Immunology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140
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Bingen EH, Denamur E, Elion J. Use of ribotyping in epidemiological surveillance of nosocomial outbreaks. Clin Microbiol Rev 1994; 7:311-27. [PMID: 7923052 PMCID: PMC358328 DOI: 10.1128/cmr.7.3.311] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Over the past few years, genotypic methods based on the study of bacterial DNA polymorphism have shown high discriminatory power for strain differentiation and superiority over most phenotypic methods commonly available in the clinical microbiology laboratory. Some of the methods used, however, required either a high level of technology and sophisticated equipment (e.g., pulsed-field gel electrophoresis) or species-specific reagents of restricted availability (randomly cloned DNA probes or gene-specific probes). Because ribotyping uses a universal probe (rRNA) and is a rather simple technology, particularly since the advent of nonradioactive labelling systems, it has been widely used for strain differentiation of most bacterial species involved in nosocomial outbreaks. In vitro and in vivo stability of the markers studied has been demonstrated. Although there may be limitation to this approach, ribotyping was found to be highly discriminative, particularly for typing members of the family Enterobacteriaceae, Pseudomonas cepacia, and Xanthomonas maltophilia. In many cases, it has improved the understanding of the mechanism of nosocomial acquisition of organisms by allowing a distinction between endogenous and exogenous infections. Among exogenous infections, it has distinguished between individual and epidemic strains, thus differentiating cross-infection from independent acquisition.
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Affiliation(s)
- E H Bingen
- Laboratoire de Microbiologie, Hôpital Robert Debré, Paris, France
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Sechi LA, Daneo-Moore L. Characterization of intergenic spacers in two rrn operons of Enterococcus hirae ATCC 9790. J Bacteriol 1993; 175:3213-9. [PMID: 8491737 PMCID: PMC204647 DOI: 10.1128/jb.175.10.3213-3219.1993] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Two DNA restriction enzyme fragments coding for the 3' termini of 16S rRNA, the 5' termini of 23S rRNA, and the intergenic spaces between them in Enterococcus hirae ATCC 9790 were cloned and sequenced. The intergenic space of one of these genes contains a tRNA(Ala) sequence, whereas the other does not. Nevertheless, the intergenic spaces contain several regions that exhibit high levels of sequence homology and are capable of forming structures with similar base pairs. An analysis of Southern blots of chromosomal DNA cut with one and two restriction enzymes indicated that E. hirae has a total of six rrn operons.
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MESH Headings
- Base Sequence
- Cloning, Molecular
- DNA, Bacterial/metabolism
- DNA, Ribosomal/genetics
- DNA, Ribosomal/metabolism
- Deoxyribonucleases, Type II Site-Specific/metabolism
- Enterococcus/genetics
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- RNA, Transfer, Ala/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- rRNA Operon/genetics
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Affiliation(s)
- L A Sechi
- Department of Microbiology and Immunology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140
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Campbell KD, East AK, Thompson DE, Collins MD. Studies on the large subunit ribosomal RNA genes and intergenic spacer regions of non-proteolytic Clostridium botulinum types B, E and F. Res Microbiol 1993; 144:171-80. [PMID: 8210674 DOI: 10.1016/0923-2508(93)90042-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The large-subunit ribosomal ribonucleic acid (23S rRNA) genes of non-proteolytic (group II) strains of Clostridium botulinum toxin types B, E and F were amplified using the polymerase chain reaction (PCR), and cloned in Escherichia coli. Sequence determination showed that the 23S rRNA genes were 2910 nucleotides in length, and comparative analysis revealed approximately 99.5% sequence similarity. The 23S rRNA gene sequence of a strain phenotypically resembling non-proteolytic C. botulinum, except in not producing botulinal neurotoxin, was also determined and displayed 99.5% sequence similarity with those from toxigenic strains. A diagnostic sequence within the 23S rRNA characteristic for non-proteolytic C. botulinum was identified and used for the design of an oligonucleotide probe. Molecular hybridizations with PCR-amplified rDNA targets provided a precise and reliable method of identifying non-proteolytic (or Group II) C. botulinum and closely related non-toxigenic strains.
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Affiliation(s)
- K D Campbell
- Department of Microbiology, AFRC Institute of Food Research, Reading Laboratory, UK
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41
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East AK, Thompson DE, Collins MD. Analysis of operons encoding 23S rRNA of Clostridium botulinum type A. J Bacteriol 1992; 174:8158-62. [PMID: 1339427 PMCID: PMC207558 DOI: 10.1128/jb.174.24.8158-8162.1992] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Southern hybridization analysis of Clostridium botulinum type A chromosomal DNA indicated the presence of six copies of the 23S rRNA gene. Fragments of DNA encoding 23S rRNA were amplified by polymerase chain reaction and cloned in Escherichia coli. Three clones examined by restriction enzyme and sequence analysis were found to be derived from different operons. Sequence determination of the entire insert of two clones revealed nine nucleotide changes in the genes coding for 23S rRNA (99.7% sequence identity) between operons encoded on the same chromosome, showing microheterogeneity in the rRNA operons of this organism.
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Affiliation(s)
- A K East
- Department of Microbiology, AFRC Institute for Food Research, Reading, United Kingdom
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42
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Kostman JR, Edlind TD, LiPuma JJ, Stull TL. Molecular epidemiology of Pseudomonas cepacia determined by polymerase chain reaction ribotyping. J Clin Microbiol 1992; 30:2084-7. [PMID: 1380010 PMCID: PMC265447 DOI: 10.1128/jcm.30.8.2084-2087.1992] [Citation(s) in RCA: 164] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Traditional ribotyping detects genomic restriction fragment length polymorphisms by probing chromosomal DNA with rRNA. Although it is a powerful method for determining the molecular epidemiology of bacterial pathogens, technical difficulties limit its application. As an alternative, polymorphisms were sought in the 16S-23S spacer regions of bacterial rRNA genes by use of the polymerase chain reaction (PCR). Chromosomal DNA from isolates of Pseudomonas cepacia was used as a template in the PCR with oligonucleotide primers complementary to highly conserved sequences flanking the spacer regions of the rRNA genes. Length polymorphisms in the amplified DNA distinguished unrelated isolates of P. cepacia. Isolates of P. cepacia previously implicated in person-to-person transmission were shown to have identical amplification patterns. These data demonstrate the utility of this new PCR ribotyping method for determining the molecular epidemiology of bacterial species.
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Affiliation(s)
- J R Kostman
- Department of Medicine, Temple University Health Sciences Center, Philadelphia, Pennsylvania 19140
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43
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New nucleotide sequence data on the EMBL File Server. Nucleic Acids Res 1991; 19:6669-86. [PMID: 1754420 PMCID: PMC329281 DOI: 10.1093/nar/19.23.6669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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