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1.
PLoS Biol ; 4(6): e188, 2006 Jun.
Article in English | MEDLINE | ID: mdl-16729848

ABSTRACT

Mutualistic intracellular symbiosis between bacteria and insects is a widespread phenomenon that has contributed to the global success of insects. The symbionts, by provisioning nutrients lacking from diets, allow various insects to occupy or dominate ecological niches that might otherwise be unavailable. One such insect is the glassy-winged sharpshooter (Homalodisca coagulata), which feeds on xylem fluid, a diet exceptionally poor in organic nutrients. Phylogenetic studies based on rRNA have shown two types of bacterial symbionts to be coevolving with sharpshooters: the gamma-proteobacterium Baumannia cicadellinicola and the Bacteroidetes species Sulcia muelleri. We report here the sequencing and analysis of the 686,192-base pair genome of B. cicadellinicola and approximately 150 kilobase pairs of the small genome of S. muelleri, both isolated from H. coagulata. Our study, which to our knowledge is the first genomic analysis of an obligate symbiosis involving multiple partners, suggests striking complementarity in the biosynthetic capabilities of the two symbionts: B. cicadellinicola devotes a substantial portion of its genome to the biosynthesis of vitamins and cofactors required by animals and lacks most amino acid biosynthetic pathways, whereas S. muelleri apparently produces most or all of the essential amino acids needed by its host. This finding, along with other results of our genome analysis, suggests the existence of metabolic codependency among the two unrelated endosymbionts and their insect host. This dual symbiosis provides a model case for studying correlated genome evolution and genome reduction involving multiple organisms in an intimate, obligate mutualistic relationship. In addition, our analysis provides insight for the first time into the differences in symbionts between insects (e.g., aphids) that feed on phloem versus those like H. coagulata that feed on xylem. Finally, the genomes of these two symbionts provide potential targets for controlling plant pathogens such as Xylella fastidiosa, a major agroeconomic problem, for which H. coagulata and other sharpshooters serve as vectors of transmission.


Subject(s)
Aphids/metabolism , Aphids/microbiology , Bacteroidetes/metabolism , Symbiosis/genetics , Symbiosis/physiology , Amino Acids/biosynthesis , Amino Acids/deficiency , Animals , Coenzymes/biosynthesis , Evolution, Molecular , Forecasting , Genes, Bacterial , Genome, Bacterial , Genomics/methods , Metabolic Networks and Pathways , Models, Biological , Molecular Sequence Data , Phylogeny , Polymorphism, Single Nucleotide , Sequence Analysis, DNA/methods , Vitamins/biosynthesis
2.
Proc Natl Acad Sci U S A ; 100(18): 10181-6, 2003 Sep 02.
Article in English | MEDLINE | ID: mdl-12928499

ABSTRACT

We report the complete genome sequence of the model bacterial pathogen Pseudomonas syringae pathovar tomato DC3000 (DC3000), which is pathogenic on tomato and Arabidopsis thaliana. The DC3000 genome (6.5 megabases) contains a circular chromosome and two plasmids, which collectively encode 5,763 ORFs. We identified 298 established and putative virulence genes, including several clusters of genes encoding 31 confirmed and 19 predicted type III secretion system effector proteins. Many of the virulence genes were members of paralogous families and also were proximal to mobile elements, which collectively comprise 7% of the DC3000 genome. The bacterium possesses a large repertoire of transporters for the acquisition of nutrients, particularly sugars, as well as genes implicated in attachment to plant surfaces. Over 12% of the genes are dedicated to regulation, which may reflect the need for rapid adaptation to the diverse environments encountered during epiphytic growth and pathogenesis. Comparative analyses confirmed a high degree of similarity with two sequenced pseudomonads, Pseudomonas putida and Pseudomonas aeruginosa, yet revealed 1,159 genes unique to DC3000, of which 811 lack a known function.


Subject(s)
Arabidopsis/microbiology , Genome, Bacterial , Pseudomonas/genetics , Solanum lycopersicum/microbiology , Base Sequence , Biological Transport , Molecular Sequence Data , Plant Growth Regulators/biosynthesis , Plasmids , Pseudomonas/metabolism , Pseudomonas/pathogenicity , Reactive Oxygen Species , Siderophores/biosynthesis , Virulence
3.
Nature ; 419(6906): 512-9, 2002 Oct 03.
Article in English | MEDLINE | ID: mdl-12368865

ABSTRACT

Species of malaria parasite that infect rodents have long been used as models for malaria disease research. Here we report the whole-genome shotgun sequence of one species, Plasmodium yoelii yoelii, and comparative studies with the genome of the human malaria parasite Plasmodium falciparum clone 3D7. A synteny map of 2,212 P. y. yoelii contiguous DNA sequences (contigs) aligned to 14 P. falciparum chromosomes reveals marked conservation of gene synteny within the body of each chromosome. Of about 5,300 P. falciparum genes, more than 3,300 P. y. yoelii orthologues of predominantly metabolic function were identified. Over 800 copies of a variant antigen gene located in subtelomeric regions were found. This is the first genome sequence of a model eukaryotic parasite, and it provides insight into the use of such systems in the modelling of Plasmodium biology and disease.


Subject(s)
Genome, Protozoan , Plasmodium yoelii/genetics , Animals , DNA, Protozoan , Disease Models, Animal , Humans , Malaria/parasitology , Multigene Family , Plasmodium falciparum/genetics , Recombination, Genetic , Rodentia , Sequence Alignment , Sequence Analysis, DNA , Species Specificity , Synteny , Telomere
4.
Proc Natl Acad Sci U S A ; 99(20): 13148-53, 2002 Oct 01.
Article in English | MEDLINE | ID: mdl-12271122

ABSTRACT

The 3.31-Mb genome sequence of the intracellular pathogen and potential bioterrorism agent, Brucella suis, was determined. Comparison of B. suis with Brucella melitensis has defined a finite set of differences that could be responsible for the differences in virulence and host preference between these organisms, and indicates that phage have played a significant role in their divergence. Analysis of the B. suis genome reveals transport and metabolic capabilities akin to soil/plant-associated bacteria. Extensive gene synteny between B. suis chromosome 1 and the genome of the plant symbiont Mesorhizobium loti emphasizes the similarity between this animal pathogen and plant pathogens and symbionts. A limited repertoire of genes homologous to known bacterial virulence factors were identified.


Subject(s)
Brucella/genetics , Genome, Bacterial , Alphaproteobacteria/genetics , Brucella/pathogenicity , Brucella melitensis/genetics , Chromosomes, Bacterial/ultrastructure , DNA Transposable Elements , Models, Genetic , Molecular Sequence Data , Open Reading Frames , Rhizobium/genetics
5.
Proc Natl Acad Sci U S A ; 99(19): 12391-6, 2002 Sep 17.
Article in English | MEDLINE | ID: mdl-12200547

ABSTRACT

The 2,160,267 bp genome sequence of Streptococcus agalactiae, the leading cause of bacterial sepsis, pneumonia, and meningitis in neonates in the U.S. and Europe, is predicted to encode 2,175 genes. Genome comparisons among S. agalactiae, Streptococcus pneumoniae, Streptococcus pyogenes, and the other completely sequenced genomes identified genes specific to the streptococci and to S. agalactiae. These in silico analyses, combined with comparative genome hybridization experiments between the sequenced serotype V strain 2603 V/R and 19 S. agalactiae strains from several serotypes using whole-genome microarrays, revealed the genetic heterogeneity among S. agalactiae strains, even of the same serotype, and provided insights into the evolution of virulence mechanisms.


Subject(s)
Genome, Bacterial , Streptococcus agalactiae/genetics , Streptococcus agalactiae/pathogenicity , Amino Acid Sequence , Biological Evolution , Humans , Molecular Sequence Data , Oligonucleotide Array Sequence Analysis , Phylogeny , Serotyping , Species Specificity , Streptococcal Infections/microbiology , Streptococcus agalactiae/classification , Streptococcus pneumoniae/genetics , Streptococcus pyogenes/genetics , Virulence/genetics
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