- Improved microbial gene identification with GLIMMER
A L Delcher
Department of Computer Science, Loyola College in Maryland, Baltimore, MD 21210, USA
Nucleic Acids Res 27:4636-41. 1999
..When the analysis is restricted to genes that have significant homology to genes in other organisms, GLIMMER misses <1% of known genes...
- Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)
S D Bentley
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Nature 417:141-7. 2002
..The genome sequence will greatly increase our understanding of microbial life in the soil as well as aiding the generation of new drug candidates by genetic engineering...
- Genes required for mycobacterial growth defined by high density mutagenesis
Christopher M Sassetti
Department of Immunology and Infectious Diseases, Harvard School of Public Health, Harvard Medical School, Boston, MA 02115, USA
Mol Microbiol 48:77-84. 2003
- Small CRISPR RNAs guide antiviral defense in prokaryotes
Stan J J Brouns
Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, Netherlands
Science 321:960-4. 2008
..Our results demonstrate that the formation of mature guide RNAs by the CRISPR RNA endonuclease subunit of Cascade is a mechanistic requirement for antiviral defense...
- The complete genome sequence of Escherichia coli K-12
F R Blattner
Laboratory of Genetics, University of Wisconsin Madison, 445 Henry Mall, Madison, WI 53706, USA
Science 277:1453-62. 1997
..The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer...
- Complete genome sequence of Salmonella enterica serovar Typhimurium LT2
Sidney Kimmel Cancer Center, 10835 Altman Row, San Diego, California 92121, USA
Nature 413:852-6. 2001
..Most of these homologues were previously unknown, and 50 may be exported to the periplasm or outer membrane, rendering them accessible as therapeutic or vaccine targets...
- Sex and virulence in Escherichia coli: an evolutionary perspective
Department of Molecular Biology, Schumannstrasse 21 22, Max Planck Institut für Infektionsbiologie, 10117 Berlin, Germany
Mol Microbiol 60:1136-51. 2006
..This long-term pattern of evolution was observed in genes distributed throughout the genome, and thereby is the likely result of episodic selection for strains that can escape the host immune response...
- The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae
Derrick H Lenz
Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
Cell 118:69-82. 2004
..We propose that Hfq, together with these sRNAs, creates an ultrasensitive regulatory switch that controls the critical transition into the high cell density, quorum-sensing mode...
- Complete genome sequence of a virulent isolate of Streptococcus pneumoniae
The Institute for Genomic Research (TIGR, 9712 Medical Center Drive, Rockville, MD 20850, USA
Science 293:498-506. 2001
..Comparative genome hybridization with DNA arrays revealed strain differences in S. pneumoniae that could contribute to differences in virulence and antigenicity...
- GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
School of Biology and School of Mathematics, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA
Nucleic Acids Res 29:2607-18. 2001
..These motifs were shown to possess a significant variability, the functional and evolutionary connections of which are discussed...
- Environmental genome shotgun sequencing of the Sargasso Sea
J Craig Venter
Institute for Biological Energy Alternatives, 1901 Research Boulevard, Rockville, MD 20850, USA
Science 304:66-74. 2004
..2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity...
- An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutants
Nicole T Liberati
Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
Proc Natl Acad Sci U S A 103:2833-8. 2006
..Comparison of the genes disrupted in the PA14 transposon insertion library with an independently constructed insertion library in P. aeruginosa strain PAO1 provides an estimate of the number of P. aeruginosa essential genes...
- Comprehensive transposon mutant library of Pseudomonas aeruginosa
Michael A Jacobs
Department of Medicine, University of Washington Genome Center, Box 352145, Seattle, WA 98195 2145, USA
Proc Natl Acad Sci U S A 100:14339-44. 2003
..The transposons used to generate the mutant collection have added features that should facilitate downstream studies of gene expression, protein localization, epistasis, and chromosome engineering...
- Diversity of the human intestinal microbial flora
Paul B Eckburg
Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Room S 169, 300 Pasteur Drive, Stanford CA 94305 5107, USA
Science 308:1635-8. 2005
..We discovered significant intersubject variability and differences between stool and mucosa community composition. Characterization of this immensely diverse ecosystem is the first step in elucidating its role in health and disease...
- A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes
Daniel H Haft
The Institute for Genomic Research, Rockville, Maryland, USA
PLoS Comput Biol 1:e60. 2005
..It is evident from this analysis that CRISPR/cas loci are larger, more complex, and more heterogeneous than previously appreciated...
- Essential genes of a minimal bacterium
John I Glass
Synthetic Biology Group, J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
Proc Natl Acad Sci U S A 103:425-30. 2006
..Genes encoding proteins of unknown function constitute 28% of the essential protein-coding genes set. Disruption of some genes accelerated M. genitalium growth...
- An efficient recombination system for chromosome engineering in Escherichia coli
Gene Regulation and Chromosome Biology Laboratory and Mouse Cancer Genetics Program, National Cancer Institute, Division of Basic Science, National Cancer Institute Frederick Cancer Research and Development Center, Frederick, MD 21702, USA
Proc Natl Acad Sci U S A 97:5978-83. 2000
..This system will be especially useful for the engineering of large bacterial plasmids such as those from bacterial artificial chromosome libraries...
- PCR-targeted Streptomyces gene replacement identifies a protein domain needed for biosynthesis of the sesquiterpene soil odor geosmin
Department of Molecular Microbiology, John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom
Proc Natl Acad Sci U S A 100:1541-6. 2003
- A new evolutionary scenario for the Mycobacterium tuberculosis complex
Unite de Genetique Moleculaire Bacterienne, Laboratoire de Génomique des Microorganismes Pathogènes, and Centre National de Référence des Mycobactéries, Institut Pasteur, 25 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
Proc Natl Acad Sci U S A 99:3684-9. 2002
..bovis lineage separated from the M. tuberculosis lineage. This observation suggests that the common ancestor of the tubercle bacilli resembled M. tuberculosis or M. canettii and could well have been a human pathogen already...
- Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the Dictyostelium host model system
Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
Proc Natl Acad Sci U S A 103:1528-33. 2006
..Thus, the genes encoding the VAS-related, type VI secretion system likely play an important conserved function in microbial pathogenesis and represent an additional class of targets for vaccine and antimicrobial drug-based therapies...
- Microbial minimalism: genome reduction in bacterial pathogens
Nancy A Moran
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
Cell 108:583-6. 2002
..Complete genome sequences are providing an understanding of how extreme genome reduction affects evolutionary directions and metabolic capabilities of obligate pathogens and symbionts...
- Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays
Jonathan A Bernstein
Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 99:9697-702. 2002
..Our results identify previously unsuspected features of mRNA decay at a global level and also indicate that generalizations about decay derived from the study of individual gene transcripts may have limited applicability...
- Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes
Deo Prakash Pandey
Department of Biochemistry and Molecular Biology, University of Southern Denmark DK 5230 Odense M, Denmark
Nucleic Acids Res 33:966-76. 2005
- Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms
M C Maiden
Wellcome Trust Centre for the Epidemiology of Infectious Disease, Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
Proc Natl Acad Sci U S A 95:3140-5. 1998
- Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements
The Institute for Genomic Research, Rockville, Maryland, USA
PLoS Biol 2:E69. 2004
..With the availability of the complete genomes of both species and excellent genetic tools for the host, the wMel-D. melanogaster symbiosis is now an ideal system for studying the biology and evolution of Wolbachia infections...
- Identification of genes that are associated with DNA repeats in prokaryotes
Department of Infectious Diseases and Immunology, Bacteriology Division, Veterinary Faculty, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
Mol Microbiol 43:1565-75. 2002
..The spatial coherence of CRISPR and cas genes may stimulate new research on the genesis and biological role of these repeats and genes...
- The composite genome of the legume symbiont Sinorhizobium meliloti
UMR6061-CNRS, , , , F-35043 Rennes Cedex, France
Science 293:668-72. 2001
..The genome sequence will be useful in understanding the dynamics of interkingdom associations and of life in soil environments...
- A genomic view of the human-Bacteroides thetaiotaomicron symbiosis
Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, MO 63110, USA
Science 299:2074-6. 2003
..These and other expanded paralogous groups shed light on the molecular mechanisms underlying symbiotic host-bacterial relationships in our intestine...
- Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus
M C Enright
Wellcome Trust Centre for the Epidemiology of Infectious Disease, Department of Zoology, Oxford University, Oxford OX1 3FY
J Clin Microbiol 38:1008-15. 2000
..MLST provides an unambiguous method for assigning MRSA and MSSA isolates to known clones or assigning them as novel clones via the Internet...
- DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes
Department of Epidemiology and Biostatistics, Tianjin Cancer Institute and Hospital, Tianjin 300060, China
Nucleic Acids Res 37:D455-8. 2009
..These updates not only represent significant advances of DEG, but also represent the rapid progress of the essential-gene field. DEG is freely available at the website http://tubic.tju.edu.cn/deg or http://www.essentialgene.org...
- Deletion of RD1 from Mycobacterium tuberculosis mimics bacille Calmette-Guérin attenuation
Kaeryn N Lewis
Department of Pediatrics, University of Washington, Seattle 98195, USA
J Infect Dis 187:117-23. 2003
..Therefore, it was concluded that genes within or controlled by RD1 are essential for MTB virulence and that loss of RD1 was important in BCG attenuation...
- Identification of a pathogenicity island required for Salmonella survival in host cells
Department of Biology, University of Rochester, NY 14627, USA
Proc Natl Acad Sci U S A 93:7800-4. 1996
..The "pathogenicity island" harboring the spi genes may encode the virulence determinants that set Salmonella apart from other enteric pathogens...
- Pseudomonas biofilm formation and antibiotic resistance are linked to phenotypic variation
Department of Genetics, Harvard Medical School, Massahusetts General Hospital, Boston, MA 02114, USA
Nature 416:740-3. 2002
..Compounds that affect PvrR function could have an important role in the treatment of CF infections...
- Community structure and metabolism through reconstruction of microbial genomes from the environment
Gene W Tyson
Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA
Nature 428:37-43. 2004
..Analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment...
- The population genetics of ecological specialization in evolving Escherichia coli populations
V S Cooper
Center for Microbial Ecology, Michigan State University, East Lansing 48824, USA
Nature 407:736-9. 2000
..Thus, antagonistic pleiotropy appears more important than mutation accumulation for the decay of unused catabolic functions in these populations...
- Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria
P W Postma
E C Slater Institute, University of Amsterdam, The Netherlands
Microbiol Rev 57:543-94. 1993
..In gram-positive bacteria, it has been demonstrated that HPr can be phosphorylated by ATP on a serine residue and this modification may perform a regulatory function...
- Analysis of a complete library of putative drug transporter genes in Escherichia coli
Department of Cell Membrane Biology, Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
J Bacteriol 183:5803-12. 2001
..Of these 20 ORFs, cusA, yegMNO, ydgFE, yceE, yceL, yidY, and ybjYZ are novel drug resistance genes. The fsr, bcr, yjiO, ydhE, acrD, and yhiUV genes gave broader resistance spectra than previously reported...
- Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients
Zackary I Johnson
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 15 Vassar Street 48 419, Cambridge, MA 02139, USA
Science 311:1737-40. 2006
..Light, nutrients, and competitor abundances also appeared to play a role in shaping different distributions...
- Essential genes are more evolutionarily conserved than are nonessential genes in bacteria
I King Jordan
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Genome Res 12:962-8. 2002
..knockout data to compare the rates of evolution and the levels of selection for essential versus nonessential bacterial genes. In contrast to the results obtained for eukaryotic genes, essential bacterial genes appear to be more ..
- The bacterial species challenge: making sense of genetic and ecological diversity
Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK
Science 323:741-6. 2009
..The resulting data may help to discriminate among the many theories of prokaryotic species that have been produced to date...
- Multilocus sequence typing system for Campylobacter jejuni
K E Dingle
Wellcome Trust Centre for the Epidemiology of Infectious Disease, Department of Zoology, University of Oxford, Oxford OX1 3FY, United Kingdom
J Clin Microbiol 39:14-23. 2001
..Application of this approach to further isolate collections will enable an integrated global picture of C. jejuni epidemiology to be established and will permit more detailed studies of the population genetics of this organism...
- Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome"
Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Proc Natl Acad Sci U S A 102:13950-5. 2005
..Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactiae pan-genome is vast and that unique genes will continue to be identified even after sequencing hundreds of genomes...
- SOS response promotes horizontal dissemination of antibiotic resistance genes
John W Beaber
Department of Microbiology, Tufts University School of Medicine and Howard Hughes Medical Institute, 136 Harrison Avenue, Boston, Massachusetts 02111, USA
Nature 427:72-4. 2004
..Thus, we present a mechanism by which therapeutic agents can promote the spread of antibiotic resistance genes...
- The genome of Rhizobium leguminosarum has recognizable core and accessory components
J Peter W Young
Department of Biology, University of York, York, UK
Genome Biol 7:R34. 2006
..We have sequenced the genome of R. leguminosarum biovar viciae strain 3841...
- Entry of L. monocytogenes into cells is mediated by internalin, a repeat protein reminiscent of surface antigens from gram-positive cocci
J L Gaillard
Laboratoire de Microbiologie, Faculte de Medecine Necker Enfants Malades, Paris, France
Cell 65:1127-41. 1991
..As evidenced by Southern blot analysis, inlA is part of a gene family. One of them is the gene situated directly downstream of inlA, called inlB, which also encodes a leucine-rich repeat protein...
- Yersinia pestis--etiologic agent of plague
R D Perry
Department of Microbiology and Immunology, University of Kentucky, Lexington 40536, USA
Clin Microbiol Rev 10:35-66. 1997
..These areas of research have provide new insights into the host-parasite relationship. This review will update our present understanding of the history, etiology, epidemiology, clinical aspects, and public health issues of plague...
- The Listeria transcriptional landscape from saprophytism to virulence
Institut Pasteur, Unité des Interactions Bactéries Cellules, F 75015 Paris, France
Nature 459:950-6. 2009
..Together, our data unravel successive and coordinated global transcriptional changes during infection and point to previously unknown regulatory mechanisms in bacteria...
- CRISPR provides acquired resistance against viruses in prokaryotes
Danisco USA Inc, 3329 Agriculture Drive, Madison, WI 53716, USA
Science 315:1709-12. 2007
..Thus, CRISPR, together with associated cas genes, provided resistance against phages, and resistance specificity is determined by spacer-phage sequence similarity...
- Determination of the core of a minimal bacterial gene set
Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Apartat Oficial 2085, 46071 Valencia, Spain
Microbiol Mol Biol Rev 68:518-37, table of contents. 2004
..The main features of such a minimal gene set, as well as the metabolic functions that must be present in the hypothetical minimal cell, are discussed...
- Widespread selection for local RNA secondary structure in coding regions of bacterial genes
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Genome Res 13:2042-51. 2003
..These results are interpreted in terms of possible roles of RNA structures in RNA processing, regulation of mRNA stability, and translational control...
- Genome-wide screen for Salmonella genes required for long-term systemic infection of the mouse
Trevor D Lawley
Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
PLoS Pathog 2:e11. 2006
- Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition
The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
J Bacteriol 187:6488-98. 2005
..With access to a fifth complete pseudomonad genome sequence, we were able to identify 3,567 ORFs that likely comprise the core Pseudomonas genome and 365 ORFs that are P. syringae specific...
- Inactivation of the dlt operon in Staphylococcus aureus confers sensitivity to defensins, protegrins, and other antimicrobial peptides
Mikrobielle Genetik, Universitat Tubingen, Waldhäuser Strasse 70 8, 72076 Tubingen, Germany
J Biol Chem 274:8405-10. 1999
..We propose a role of the D-alanine-esterified teichoic acids which occur in many pathogenic bacteria in the protection against human and animal defense systems...
- Efflux-mediated heavy metal resistance in prokaryotes
Dietrich H Nies
Institute of Microbiology, Molecular Microbiology, Martin Luther University Halle Wittenberg, Kurt Mothes Strasse 3, 06099 Halle Saale, Germany
FEMS Microbiol Rev 27:313-39. 2003
..Possession of the latter systems makes a bacterium heavy metal resistant...
- Riboswitches in eubacteria sense the second messenger cyclic di-GMP
Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
Science 321:411-3. 2008
..In addition, sequences matching the consensus for cyclic di-GMP riboswitches are present in the genome of a bacteriophage...
- Sampling the antibiotic resistome
Vanessa M D'Costa
Antimicrobial Research Centre, Department of Biochemistry and Biomedical Sciences, McMaster University, Ontario, Canada, L8N 3Z5
Science 311:374-7. 2006
..They are a reservoir of resistance determinants that can be mobilized into the microbial community. Study of this reservoir could provide an early warning system for future clinically relevant antibiotic resistance mechanisms...
- Community genomics among stratified microbial assemblages in the ocean's interior
Edward F DeLong
Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Science 311:496-503. 2006
..Comparative genomic analyses of stratified microbial communities have the potential to provide significant insight into higher-order community organization and dynamics...
- Chitin induces natural competence in Vibrio cholerae
Karin L Meibom
Division of Infectious Diseases and Geographic Medicine, Department of Microbiology and Immunology, and Stanford Institute for the Environment, Stanford University, Stanford, CA 94305, USA
Science 310:1824-7. 2005
- Molecular correlates of host specialization in Staphylococcus aureus
Department of Microbiology, Veterinary Pathobiology and Biomedical Genomics Center, University of Minnesota, Saint Paul, Minnesota, United States of America
PLoS ONE 2:e1120. 2007
..aureus clonal groups associated with human and ruminant infection. However, the molecular basis of host specialization in S. aureus is not understood...
- Regulation of a Bacillus subtilis mobile genetic element by intercellular signaling and the global DNA damage response
Jennifer M Auchtung
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Proc Natl Acad Sci U S A 102:12554-9. 2005
..The dual regulation of ICEBs1 allows for passive propagation in the host cell until either the potential mating partners lacking ICEBs1 are present or the host cell is in distress...
- The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates
David A Rasko
Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, 20 Penn Street, Baltimore, MD 21201, USA
J Bacteriol 190:6881-93. 2008
..This comparative study of the species E. coli, while descriptive, should provide the basis for future functional work on this important group of pathogens...
- Negative autoregulation speeds the response times of transcription networks
Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
J Mol Biol 323:785-93. 2002
..This agrees with an analytical solution of a mathematical model for negative autoregulation. This may help in understanding the function of negative autoregulation, which appears in over 40% of known transcription factors in E.coli...
- Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters
The Institute for Genomic Research, Rockville, Maryland, USA
PLoS Biol 4:e188. 2006
..coagulata and other sharpshooters serve as vectors of transmission...
- The role of RelMtb-mediated adaptation to stationary phase in long-term persistence of Mycobacterium tuberculosis in mice
John L Dahl
Tuberculosis Research Section, National Institute of Allergy and Infectious Disease, 12441 Parklawn Drive, Rockville, MD 20852, USA
Proc Natl Acad Sci U S A 100:10026-31. 2003
..Thus, RelMtb is critical for the successful establishment of persistent infection in mice by altering the expression of antigenic and enzymatic factors that may contribute to successful latent infection...
- Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence
Pathogen Molecular Department, London School of Hygiene and Tropical Medicine, UK
BMC Genomics 8:162. 2007
..We now describe the complete re-annotation and re-analysis of the C. jejuni NCTC11168 genome using current database information, novel tools and annotation techniques not used during the original annotation...
- Global transcriptomic analysis of Cyanothece 51142 reveals robust diurnal oscillation of central metabolic processes
Department of Biology, Washington University, St Louis, MO 63130, USA
Proc Natl Acad Sci U S A 105:6156-61. 2008
..These studies provide a comprehensive picture of how a physiologically relevant diurnal light-dark cycle influences the metabolism in a photosynthetic bacterium...
- The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal transfer among prokaryotes
James S Godde
Department of Biology, Monmouth College, Monmouth, IL 61462, USA
J Mol Evol 62:718-29. 2006
..We suggest a mechanism by which this HGT has occurred, namely, that the CRISPR loci can be carried between cells on megaplasmids > or = 40 kb in length...
- Molecular mechanisms of antibacterial multidrug resistance
Michael N Alekshun
Schering Plough Research Institute, Kenilworth, NJ 07033, USA
Cell 128:1037-50. 2007
..Once established, multidrug-resistant organisms persist and spread worldwide, causing clinical failures in the treatment of infections and public health crises...
- The genome of the natural genetic engineer Agrobacterium tumefaciens C58
D W Wood
Department of Microbiology, University of Washington, 1959 NE Pacific Street, Box 357242, Seattle, WA 98195, USA
Science 294:2317-23. 2001
..Availability of the A. tumefaciens sequence will facilitate investigations into the molecular basis of pathogenesis and the evolutionary divergence of pathogenic and symbiotic lifestyles...
- Mycobacterium tuberculosis invasion of macrophages: linking bacterial gene expression to environmental cues
Kyle H Rohde
Cornell University, College of Veterinary Medicine, Department of Microbiology and Immunology, Ithaca, NY 14853, USA
Cell Host Microbe 2:352-64. 2007
..Finally, there are marked species-specific differences in the response of Mtb and M. bovis BCG to intraphagosomal cues...
- GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses
School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
Nucleic Acids Res 33:W451-4. 2005
..A database of reannotations of >1000 viral genomes by the GeneMarkS program is also available from the web site. The GeneMark website is frequently updated to provide the latest versions of the software and gene models...
- Quorum-sensing regulators control virulence gene expression in Vibrio cholerae
Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
Proc Natl Acad Sci U S A 99:3129-34. 2002
..Together these data suggest a role for quorum sensing in modulating expression of blocks of virulence genes in a reciprocal fashion in vivo...
- Stochastic gene expression in a single cell
Michael B Elowitz
Laboratory of Cancer Biology, Center for Studies in Physics and Biology, Rockefeller University, New York, NY 10021, USA
Science 297:1183-6. 2002
..These results establish a quantitative foundation for modeling noise in genetic networks and reveal how low intracellular copy numbers of molecules can fundamentally limit the precision of gene regulation...
- Individual RD1-region genes are required for export of ESAT-6/CFP-10 and for virulence of Mycobacterium tuberculosis
Kristi M Guinn
Department of Pathobiology, University of Washington, Seattle, WA 98195, USA
Mol Microbiol 51:359-70. 2004
..Our results indicate that RD1 genes work together to form a single virulence determinant, and argue that RD1 encodes a novel specialized secretion system that is required for pathogenesis of MTB...
- Host cell killing and bacterial conjugation require overlapping sets of genes within a 22-kb region of the Legionella pneumophila genome
Department of Microbiology, College of Physicians and Surgeons of Columbia University, 701 West 168th Street, New York, NY 10032, USA
Proc Natl Acad Sci U S A 95:1669-74. 1998
..It is possible either that small plasmids can take advantage of an existing secretion system to be mobilized or that DNA transfer is required for human macrophage killing by L. pneumophila...
- Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis
Institute for Hygiene and Microbiology, University of Wurzburg, Josef Schneider Strasse 2, 97080 Wurzburg, Germany
Proc Natl Acad Sci U S A 105:3473-8. 2008
..meningitidis has emerged as an unencapsulated human commensal from a common ancestor with Neisseria gonorrhoeae and Neisseria lactamica and consecutively acquired the genes responsible for capsule synthesis via horizontal gene transfer...
- Attenuation of Pseudomonas aeruginosa virulence by quorum sensing inhibitors
BioCentrum DTU, Technical University of Denmark, DK 2800 Lyngby, Denmark
EMBO J 22:3803-15. 2003
..aeruginosa biofilms increased bacterial susceptibility to tobramycin and SDS. In a mouse pulmonary infection model, the drug inhibited quorum sensing of the infecting bacteria and promoted their clearance by the mouse immune response...
- A bacterial guanine nucleotide exchange factor activates ARF on Legionella phagosomes
Section of Microbial Pathogenesis, Yale University School of Medicine, Boyer Center for Molecular Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
Science 295:679-82. 2002
..pneumophila. Translocation of RalF protein through the phagosomal membrane is a dot/icm-dependent process. Thus, RalF is a substrate of the Dot/Icm secretion apparatus...
- Control of cell shape in bacteria: helical, actin-like filaments in Bacillus subtilis
L J Jones
Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
Cell 104:913-22. 2001
..The distribution of the proteins in different species of bacteria, and the similarity of their sequence to eukaryotic actins, suggest that the MreB-like proteins have a cytoskeletal, actin-like role in bacterial cell morphogenesis...
- A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease
M C Enright
Wellcome Trust Centre for the Epidemiology of Infectious Disease, Department of Zoology, University of Oxford, UK
Microbiology 144:3049-60. 1998
..A Web site for the molecular characterization of pneumococci by MLST is available (http ://mlst.zoo.ox.ac.uk)...
- A novel regulatory system required for pathogenicity of Xanthomonas campestris is mediated by a small diffusible signal molecule
C E Barber
Sainsbury Laboratory, John Innes Centre, Norwich Research Park, UK
Mol Microbiol 24:555-66. 1997
..DSF production is confined to certain xanthomonads. We propose a model for the DSF system, which represents a novel mechanism for regulating virulence factor synthesis in response to physiological or environmental changes...
- Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis
Integrated Genomics, Chicago, Illinois 60612, USA
Nature 423:87-91. 2003
..cereus and B. anthracis, and the genes that are unique for each species. We use the former to clarify the phylogeny of the cereus group, and the latter to determine plasmid-independent species-specific markers...
- A genome-scale analysis for identification of genes required for growth or survival of Haemophilus influenzae
Brian J Akerley
Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
Proc Natl Acad Sci U S A 99:966-71. 2002
..This genome-scale phenotypic analysis identifies potential roles for a large set of genes of unknown function...
- Two genetic loci produce distinct carbohydrate-rich structural components of the Pseudomonas aeruginosa biofilm matrix
Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
J Bacteriol 186:4457-65. 2004
..Either carbohydrate-rich matrix component appears to be sufficient for mature biofilm formation, and at least one of them is required for mature biofilm formation in P. aeruginosa strains PA14 and ZK2870...
- NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes
T Z DeSantis
Lawrence Berkeley National Laboratory, Center for Environmental Biotechnology, Berkeley, CA, USA
Nucleic Acids Res 34:W394-9. 2006
..The ability to align and categorize large sequence sets using a simple interface has enabled researchers with various experience levels to obtain bacterial and archaeal community profiles...
- DNA as a nutrient: novel role for bacterial competence gene homologs
S E Finkel
Department of Biological Sciences, University of Southern California, Los Angeles, California 90089 1340, USA
J Bacteriol 183:6288-93. 2001
..Homologs of these E. coli genes are present in many members of the gamma subclass of Proteobacteria, suggesting that the mechanisms for consumption of DNA may have been widely conserved during evolution...
- Bacterial heavy metal resistance: new surprises
Department of Microbiology and Immunology, University of Illinois, College of Medicine, Chicago 60612, USA
Annu Rev Microbiol 50:753-89. 1996
..Finally, the first bacterial metallothionein (which by definition is a small protein that binds metal cations by means of numerous cysteine thiolates) has been characterized in cyanobacteria...
- Comparative genomics of multidrug resistance in Acinetobacter baumannii
Pierre Edouard Fournier
Information Genomique et Structurale, Institute for Structural Biology and Microbiology, IBSM, Marseille, France
PLoS Genet 2:e7. 2006
..Whole-genome sequencing appears to be a fast and efficient approach to the exhaustive identification of resistance genes in epidemic infectious agents of clinical significance...
- A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes
Institute of Botany III, University of Dusseldorf, Dusseldorf, Germany
Mol Biol Evol 21:1643-60. 2004
..Among eubacteria and archaebacteria, proteobacterial and methanogen genomes, respectively, shared more similarity with the yeast genome than other prokaryotic genomes surveyed...
- Conjugative transfer by the virulence system of Legionella pneumophila
J P Vogel
Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA
Science 279:873-6. 1998
..The dot virulence genes encoded a large putative membrane complex that functioned as a secretion system that was able to transfer plasmid DNA from one cell to another...
- Type III protein secretion systems in bacterial pathogens of animals and plants
C J Hueck
Lehrstuhl fur Mikrobiologie, Biozentrum der Universität Würzburg, 97074 Wurzburg, Germany
Microbiol Mol Biol Rev 62:379-433. 1998
..and the plant pathogens Pseudomonas syringae, Erwinia spp., Ralstonia solanacearum, Xanthomonas campestris, and Rhizobium spp...
- GeneChip expression analysis of the iron starvation response in Pseudomonas aeruginosa: identification of novel pyoverdine biosynthesis genes
Urs A Ochsner
Department of Microbiology, Campus Box B 175, University of Colorado Health Sciences Center, 4200 East Ninth Avenue, Denver, CO 80262, USA
Mol Microbiol 45:1277-87. 2002
..The GeneChip proved to be a very useful tool for rapid gene expression analysis and identification of novel genes controlled by Fur or PvdS...
- Quorum sensing and swarming migration in bacteria
Centre of Microbial and Plant Genetics, K U Leuven, Kasteelpark Arenberg 20, 3001 Heverlee, Belgium
FEMS Microbiol Rev 28:261-89. 2004
..Here we also describe how quorum sensing may disperse existing biofilms and control the interaction between bacteria and higher organisms (such as the Rhizobium-bean symbiosis)...
- The cyanobacterial genome core and the origin of photosynthesis
Armen Y Mulkidjanian
School of Physics, University of Osnabruck, D 49069 Osnabruck, Germany
Proc Natl Acad Sci U S A 103:13126-31. 2006
..From procyanobacteria, photosynthesis spread to other phyla by way of lateral gene transfer...
- MetaGene: prokaryotic gene finding from environmental genome shotgun sequences
Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277 8562, Japan
Nucleic Acids Res 34:5623-30. 2006
..Applied to the Sargasso Sea dataset, MetaGene predicted almost all of the annotated genes and a notable number of novel genes. MetaGene can be applied to wide variety of metagenomic projects and expands the utility of metagenomics...
- The genome of a motile marine Synechococcus
Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093 0202, USA
Nature 424:1037-42. 2003
..On the basis of its genome, WH8102 is more of a generalist than two related marine cyanobacteria...
- Genome sequence of Lactobacillus helveticus, an organism distinguished by selective gene loss and insertion sequence element expansion
Moorepark Food Research Centre, Moorepark, Fermoy, Co Cork, Ireland
J Bacteriol 190:727-35. 2008
..helveticus genome. These data suggest a special unobtrusive relationship between the DPC 4571 genome and its mobile DNA complement...
- A highly efficient Escherichia coli-based chromosome engineering system adapted for recombinogenic targeting and subcloning of BAC DNA
E C Lee
Mouse Cancer Genetics Program, National Cancer Institute Frederick, Frederick, Maryland 21702, USA
Genomics 73:56-65. 2001
- Quorum sensing controls biofilm formation in Vibrio cholerae
Brian K Hammer
Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544 1014, USA
Mol Microbiol 50:101-4. 2003
..Bacterial biofilms could represent a complex habitat where such differentiation occurs...
- Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time
Bigelow Laboratory for Ocean Sciences, P O Box 475, West Boothbay Harbor, ME 04575 0475, USA
Proc Natl Acad Sci U S A 104:9052-7. 2007
..Compared with metagenomics, the power of our approach lies in the ability to detect metabolic genes in uncultured microorganisms directly, even when the metabolic and phylogenetic markers are located far apart on the chromosome...
- Patterns and implications of gene gain and loss in the evolution of Prochlorococcus
Gregory C Kettler
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
PLoS Genet 3:e231. 2007