Publications (34)502.02 Total impact
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Article: Evolution of sensory complexity recorded in a myxobacterial genome.
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ABSTRACT: Myxobacteria are single-celled, but social, eubacterial predators. Upon starvation they build multicellular fruiting bodies using a developmental program that progressively changes the pattern of cell movement and the repertoire of genes expressed. Development terminates with spore differentiation and is coordinated by both diffusible and cell-bound signals. The growth and development of Myxococcus xanthus is regulated by the integration of multiple signals from outside the cells with physiological signals from within. A collection of M. xanthus cells behaves, in many respects, like a multicellular organism. For these reasons M. xanthus offers unparalleled access to a regulatory network that controls development and that organizes cell movement on surfaces. The genome of M. xanthus is large (9.14 Mb), considerably larger than the other sequenced delta-proteobacteria. We suggest that gene duplication and divergence were major contributors to genomic expansion from its progenitor. More than 1,500 duplications specific to the myxobacterial lineage were identified, representing >15% of the total genes. Genes were not duplicated at random; rather, genes for cell-cell signaling, small molecule sensing, and integrative transcription control were amplified selectively. Families of genes encoding the production of secondary metabolites are overrepresented in the genome but may have been received by horizontal gene transfer and are likely to be important for predation.Proceedings of the National Academy of Sciences 10/2006; 103(41):15200-5. · 9.68 Impact Factor -
Article: Genome of Geobacter sulfurreducens: metal reduction in subsurface environments.
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ABSTRACT: The complete genome sequence of Geobacter sulfurreducens, a delta-proteobacterium, reveals unsuspected capabilities, including evidence of aerobic metabolism, one-carbon and complex carbon metabolism, motility, and chemotactic behavior. These characteristics, coupled with the possession of many two-component sensors and many c-type cytochromes, reveal an ability to create alternative, redundant, electron transport networks and offer insights into the process of metal ion reduction in subsurface environments. As well as playing roles in the global cycling of metals and carbon, this organism clearly has the potential for use in bioremediation of radioactive metals and in the generation of electricity.Science 01/2004; 302(5652):1967-9. · 31.20 Impact Factor -
Article: Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440
Environmental Microbiology 06/2003; 5(7):630 - 630. · 5.84 Impact Factor -
Article: Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis.
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ABSTRACT: The complete genome sequence of Enterococcus faecalis V583, a vancomycin-resistant clinical isolate, revealed that more than a quarter of the genome consists of probable mobile or foreign DNA. One of the predicted mobile elements is a previously unknown vanB vancomycin-resistance conjugative transposon. Three plasmids were identified, including two pheromone-sensing conjugative plasmids, one encoding a previously undescribed pheromone inhibitor. The apparent propensity for the incorporation of mobile elements probably contributed to the rapid acquisition and dissemination of drug resistance in the enterococci.Science 04/2003; 299(5615):2071-4. · 31.20 Impact Factor -
Article: Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440.
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ABSTRACT: Pseudomonas putida is a metabolically versatile saprophytic soil bacterium that has been certified as a biosafety host for the cloning of foreign genes. The bacterium also has considerable potential for biotechnological applications. Sequence analysis of the 6.18 Mb genome of strain KT2440 reveals diverse transport and metabolic systems. Although there is a high level of genome conservation with the pathogenic Pseudomonad Pseudomonas aeruginosa (85% of the predicted coding regions are shared), key virulence factors including exotoxin A and type III secretion systems are absent. Analysis of the genome gives insight into the non-pathogenic nature of P. putida and points to potential new applications in agriculture, biocatalysis, bioremediation and bioplastic production.Environmental Microbiology 01/2003; 4(12):799-808. · 5.84 Impact Factor -
Article: Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains.
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ABSTRACT: Virulence and immunity are poorly understood in Mycobacterium tuberculosis. We sequenced the complete genome of the M. tuberculosis clinical strain CDC1551 and performed a whole-genome comparison with the laboratory strain H37Rv in order to identify polymorphic sequences with potential relevance to disease pathogenesis, immunity, and evolution. We found large-sequence and single-nucleotide polymorphisms in numerous genes. Polymorphic loci included a phospholipase C, a membrane lipoprotein, members of an adenylate cyclase gene family, and members of the PE/PPE gene family, some of which have been implicated in virulence or the host immune response. Several gene families, including the PE/PPE gene family, also had significantly higher synonymous and nonsynonymous substitution frequencies compared to the genome as a whole. We tested a large sample of M. tuberculosis clinical isolates for a subset of the large-sequence and single-nucleotide polymorphisms and found widespread genetic variability at many of these loci. We performed phylogenetic and epidemiological analysis to investigate the evolutionary relationships among isolates and the origins of specific polymorphic loci. A number of these polymorphisms appear to have occurred multiple times as independent events, suggesting that these changes may be under selective pressure. Together, these results demonstrate that polymorphisms among M. tuberculosis strains are more extensive than initially anticipated, and genetic variation may have an important role in disease pathogenesis and immunity.Journal of Bacteriology 11/2002; 184(19):5479-90. · 3.83 Impact Factor -
Article: A cut above: discovery of an alternative excision repair pathway in bacteria
Proceedings of the National Academy of Sciences 04/2002; 99(5):2581-3. · 9.68 Impact Factor -
Article: The genome of the natural genetic engineer Agrobacterium tumefaciens C58.
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ABSTRACT: The 5.67-megabase genome of the plant pathogen Agrobacterium tumefaciens C58 consists of a circular chromosome, a linear chromosome, and two plasmids. Extensive orthology and nucleotide colinearity between the genomes of A. tumefaciens and the plant symbiont Sinorhizobium meliloti suggest a recent evolutionary divergence. Their similarities include metabolic, transport, and regulatory systems that promote survival in the highly competitive rhizosphere; differences are apparent in their genome structure and virulence gene complement. Availability of the A. tumefaciens sequence will facilitate investigations into the molecular basis of pathogenesis and the evolutionary divergence of pathogenic and symbiotic lifestyles.Science 01/2002; 294(5550):2317-23. · 31.20 Impact Factor -
Article: Lateral gene transfer or viral colonization?
Science 09/2001; 293(5532):1048. · 31.20 Impact Factor -
Article: Complete genome sequence of a virulent isolate of Streptococcus pneumoniae.
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ABSTRACT: The 2,160,837-base pair genome sequence of an isolate of Streptococcus pneumoniae, a Gram-positive pathogen that causes pneumonia, bacteremia, meningitis, and otitis media, contains 2236 predicted coding regions; of these, 1440 (64%) were assigned a biological role. Approximately 5% of the genome is composed of insertion sequences that may contribute to genome rearrangements through uptake of foreign DNA. Extracellular enzyme systems for the metabolism of polysaccharides and hexosamines provide a substantial source of carbon and nitrogen for S. pneumoniae and also damage host tissues and facilitate colonization. A motif identified within the signal peptide of proteins is potentially involved in targeting these proteins to the cell surface of low-guanine/cytosine (GC) Gram-positive species. Several surface-exposed proteins that may serve as potential vaccine candidates were identified. Comparative genome hybridization with DNA arrays revealed strain differences in S. pneumoniae that could contribute to differences in virulence and antigenicity.Science 08/2001; 293(5529):498-506. · 31.20 Impact Factor -
Article: Microbial genes in the human genome: lateral transfer or gene loss?
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ABSTRACT: The human genome was analyzed for evidence that genes had been laterally transferred into the genome from prokaryotic organisms. Protein sequence comparisons of the proteomes of human, fruit fly, nematode worm, yeast, mustard weed, eukaryotic parasites, and all completed prokaryote genomes were performed, and all genes shared between human and each of the other groups of organisms were collected. About 40 genes were found to be exclusively shared by humans and bacteria and are candidate examples of horizontal transfer from bacteria to vertebrates. Gene loss combined with sample size effects and evolutionary rate variation provide an alternative, more biologically plausible explanation.Science 07/2001; 292(5523):1903-6. · 31.20 Impact Factor -
Article: Sequence and analysis of the Arabidopsis genome.
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ABSTRACT: The comprehensive analysis of the genome sequence of the plant Arabidopsis thaliana has been completed recently. The genome sequence and associated analyses provide the foundations for rapid progress in many fields of plant research, such as the exploitation of genetic variation in Arabidopsis ecotypes, the assessment of the transcriptome and proteome, and the association of genome changes at the sequence level with evolutionary processes. Nevertheless, genome sequencing and analysis are only the first steps towards a new plant biology. Much remains to be done to refine the analysis of encoded genes, to define the functions of encoded proteins systematically, and to establish new generations of databases to capture and relate diverse data sets generated in widely distributed laboratories.Current Opinion in Plant Biology 05/2001; 4(2):105-10. · 9.27 Impact Factor -
Article: Complete genome sequence of Caulobacter crescentus.
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ABSTRACT: The complete genome sequence of Caulobacter crescentus was determined to be 4,016,942 base pairs in a single circular chromosome encoding 3,767 genes. This organism, which grows in a dilute aquatic environment, coordinates the cell division cycle and multiple cell differentiation events. With the annotated genome sequence, a full description of the genetic network that controls bacterial differentiation, cell growth, and cell cycle progression is within reach. Two-component signal transduction proteins are known to play a significant role in cell cycle progression. Genome analysis revealed that the C. crescentus genome encodes a significantly higher number of these signaling proteins (105) than any bacterial genome sequenced thus far. Another regulatory mechanism involved in cell cycle progression is DNA methylation. The occurrence of the recognition sequence for an essential DNA methylating enzyme that is required for cell cycle regulation is severely limited and shows a bias to intergenic regions. The genome contains multiple clusters of genes encoding proteins essential for survival in a nutrient poor habitat. Included are those involved in chemotaxis, outer membrane channel function, degradation of aromatic ring compounds, and the breakdown of plant-derived carbon sources, in addition to many extracytoplasmic function sigma factors, providing the organism with the ability to respond to a wide range of environmental fluctuations. C. crescentus is, to our knowledge, the first free-living alpha-class proteobacterium to be sequenced and will serve as a foundation for exploring the biology of this group of bacteria, which includes the obligate endosymbiont and human pathogen Rickettsia prowazekii, the plant pathogen Agrobacterium tumefaciens, and the bovine and human pathogen Brucella abortus.Proceedings of the National Academy of Sciences 04/2001; 98(7):4136-41. · 9.68 Impact Factor -
Article: Genome of Thermotoga maritima MSB8.
Methods in Enzymology 02/2001; 330:169-80. · 2.04 Impact Factor -
Article: Horizontal gene transfer among microbial genomes: new insights from complete genome analysis.
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ABSTRACT: The determination and analysis of complete genome sequences has led to the suggestion that horizontal gene transfer may be much more extensive than previously appreciated. Many of these studies, however, rely on evidence that could be generated by forces other than gene transfer including selection, variable evolutionary rates, and biased sampling.Current Opinion in Genetics & Development 01/2001; 10(6):606-11. · 8.09 Impact Factor -
Article: Assessing evolutionary relationships among microbes from whole-genome analysis.
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ABSTRACT: The determination and analysis of complete genome sequences have recently enabled many major advances to be made in the area of microbial evolutionary biology. These include the determination of the first genome of a Crenarchaeota, the suggestion that horizontal gene transfer may be the rule rather than the exception, and revelations about how genomes evolve on short timescales.Current Opinion in Microbiology 11/2000; 3(5):475-80. · 7.93 Impact Factor -
Article: Microbial genome sequencing.
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ABSTRACT: Complete genome sequences of 30 microbial species have been determined during the past five years, and work in progress indicates that the complete sequences of more than 100 further microbial species will be available in the next two to four years. These results have revealed a tremendous amount of information on the physiology and evolution of microbial species, and should provide novel approaches to the diagnosis and treatment of infectious disease.Nature 09/2000; 406(6797):799-803. · 36.28 Impact Factor -
Article: DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae.
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ABSTRACT: Here we determine the complete genomic sequence of the gram negative, gamma-Proteobacterium Vibrio cholerae El Tor N16961 to be 4,033,460 base pairs (bp). The genome consists of two circular chromosomes of 2,961,146 bp and 1,072,314 bp that together encode 3,885 open reading frames. The vast majority of recognizable genes for essential cell functions (such as DNA replication, transcription, translation and cell-wall biosynthesis) and pathogenicity (for example, toxins, surface antigens and adhesins) are located on the large chromosome. In contrast, the small chromosome contains a larger fraction (59%) of hypothetical genes compared with the large chromosome (42%), and also contains many more genes that appear to have origins other than the gamma-Proteobacteria. The small chromosome also carries a gene capture system (the integron island) and host 'addiction' genes that are typically found on plasmids; thus, the small chromosome may have originally been a megaplasmid that was captured by an ancestral Vibrio species. The V. cholerae genomic sequence provides a starting point for understanding how a free-living, environmental organism emerged to become a significant human bacterial pathogen.Nature 09/2000; 406(6795):477-83. · 36.28 Impact Factor -
Article: Genome data: what do we learn?
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ABSTRACT: Genome sequence information has continued to accumulate at a spectacular pace during the past year. Details of the sequence and gene content of human chromosome 22 were published. The sequencing and annotation of the first two Arabidopsis thaliana chromosomes was completed. The sequence of chromosome 3 from Plasmodium falciparum, the second sequenced malaria chromosome, was reported, as was that of chromosome 1 from Leishmania major. The complete genomic sequences of five microbes were reported. Approaches to using data from completely sequenced microbial genomes in phylogenetic studies are being explored, as is the application of microarrays to whole genome expression analysis.Current Opinion in Structural Biology 07/2000; 10(3):343-8. · 9.42 Impact Factor -
Article: Microbial genome sequencing 2000: new insights into physiology, evolution and expression analysis.
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ABSTRACT: The complete genome sequence has been reported for 24 microbial organisms. The genome organization and gene content of these organisms has revealed an incredible diversity. Nearly half of the open reading frames identified by these sequencing projects are for potential genes with no known biological function. Efforts to make evolutionary sense and biological sense of the gene content of these organisms have been initiated. The greatest future challenge of genomics will be to determine function for the unknown genes.Research in Microbiology 04/2000; 151(2):79-84. · 2.76 Impact Factor
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Institutions
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1999–2004
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St Joseph Medical Center (MD, USA)
Towson, MD, USA
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2002
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National Institutes of Health
- Molecular Targets Laboratory
Bethesda, MD, USA
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1994–1999
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Stanford University
Palo Alto, CA, USA
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