Showing papers by "Nikos C. Kyrpides published in 2002"

The genome sequence of the facultative intracellular pathogen Brucella melitensis

Abstract: Brucella melitensis is a facultative intracellular bacterial pathogen that causes abortion in goats and sheep and Malta fever in humans. The genome of B. melitensis strain 16M was sequenced and found to contain 3,294,935 bp distributed over two circular chromosomes of 2,117,144 bp and 1,177,787 bp encoding 3,197 ORFs. By using the bioinformatics suite ERGO, 2,487 (78%) ORFs were assigned functions. The origins of replication of the two chromosomes are similar to those of other α-proteobacteria. Housekeeping genes, including those involved in DNA replication, transcription, translation, core metabolism, and cell wall biosynthesis, are distributed on both chromosomes. Type I, II, and III secretion systems are absent, but genes encoding sec-dependent, sec-independent, and flagella-specific type III, type IV, and type V secretion systems as well as adhesins, invasins, and hemolysins were identified. Several features of the B. melitensis genome are similar to those of the symbiotic Sinorhizobium meliloti.

Genome Sequence and Analysis of the Oral Bacterium Fusobacterium nucleatum Strain ATCC 25586

Abstract: We present a complete DNA sequence and metabolic analysis of the dominant oral bacterium Fusobacterium nucleatum. Although not considered a major dental pathogen on its own, this anaerobe facilitates the aggregation and establishment of several other species including the dental pathogens Porphyromonas gingivalis and Bacteroides forsythus. The F. nucleatum strain ATCC 25586 genome was assembled from shotgun sequences and analyzed using the ERGO bioinformatics suite (http://www.integratedgenomics.com). The genome contains 2.17 Mb encoding 2,067 open reading frames, organized on a single circular chromosome with 27% GC content. Despite its taxonomic position among the gram-negative bacteria, several features of its core metabolism are similar to that of gram-positive Clostridium spp., Enterococcus spp., and Lactococcus spp. The genome analysis has revealed several key aspects of the pathways of organic acid, amino acid, carbohydrate, and lipid metabolism. Nine very-high-molecular-weight outer membrane proteins are predicted from the sequence, none of which has been reported in the literature. More than 137 transporters for the uptake of a variety of substrates such as peptides, sugars, metal ions, and cofactors have been identified. Biosynthetic pathways exist for only three amino acids: glutamate, aspartate, and asparagine. The remaining amino acids are imported as such or as di- or oligopeptides that are subsequently degraded in the cytoplasm. A principal source of energy appears to be the fermentation of glutamate to butyrate. Additionally, desulfuration of cysteine and methionine yields ammonia, H2S, methyl mercaptan, and butyrate, which are capable of arresting fibroblast growth, thus preventing wound healing and aiding penetration of the gingival epithelium. The metabolic capabilities of F. nucleatum revealed by its genome are therefore consistent with its specialized niche in the mouth.

Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains

Abstract: Xylella fastidiosa (Xf) causes wilt disease in plants and is responsible for major economic and crop losses globally. Owing to the public importance of this phytopathogen we embarked on a comparative analysis of the complete genome of Xf pv citrus and the partial genomes of two recently sequenced strains of this species: Xf pv almond and Xf pv oleander, which cause leaf scorch in almond and oleander plants, respectively. We report a reanalysis of the previously sequenced Xf 9a5c (CVC, citrus) strain and the two "gapped" Xf genomes revealing ORFs encoding critical functions in pathogenicity and conjugative transfer. Second, a detailed whole-genome functional comparison was based on the three sequenced Xf strains, identifying the unique genes present in each strain, in addition to those shared between strains. Third, an "in silico" cellular reconstruction of these organisms was made, based on a comparison of their core functional subsystems that led to a characterization of their conjugative transfer machinery, identification of potential differences in their adhesion mechanisms, and highlighting of the absence of a classical quorum-sensing mechanism. This study demonstrates the effectiveness of comparative analysis strategies in the interpretation of genomes that are closely related.

Draft Sequencing and Comparative Genomics of Xylella fastidiosa Strains Reveal Novel Biological Insights

Abstract: Xylella fastidiosa is a Gram-negative bacterium belonging to the gamma subgroup of the proteobacteria (Wells et al. 1987). This microorganism is an important plant pathogen causing many economically important crop diseases, such as Pierce's disease (PD) of grapevine and citrus variegated chlorosis in citrus (Moller et al. 1974; Purcell 1997). Almond leaf scorch was first described in 1974 (Moller et al. 1974), and electron microscope studies indicated the presence in almond of the same bacterium previously associated with PD of grapevines (Mircetich et al. 1976). Cross-inoculation studies showed that PD and the almond leaf scorch strains were pathogenic to both almond and grape (Davis and Thompson 1980). Oleander leaf scorch was first noticed in 1994 in southern California. The glassy-winged sharpshooter, Homalodisca coagulata, was found to be the vector for this bacterium. It is possible that several other varieties of sharpshooters can transmit X. fastidiosa between oleander plants (Purcell et al. 1999). The oleander leaf scorch strain could not be reisolated from grapevine in a greenhouse after inoculation using needle puncture (Purcell et al. 1999). This result provides evidence for host specificity among strains of X. fastidiosa. Previous studies classified X. fastidiosa as a single species, but differentiated members of the species, depending on such criteria as host specificity and pathogenicity (Hendson et al. 2001 and references therein). We define each strain of X. fastidiosa to be a pathovar for a specific plant, as suggested previously (Hendson et al. 2001). We will therefore refer throughout to the citrus, almond, and oleander strains as Xf pv citrus (XFA), Xf pv almond (XFX), and Xf pv oleander (XFY). The complete genome sequence of the X. fastidiosa 9a5c strain (XFA), which causes citrus variegated chlorosis , was recently published (Simpson et al. 2000). In this study, we report the gapped-genome sequences of Xf pv almond (Dixon strain) (XFX) and Xf pv oleander (Ann-1 strain) (XFY) and compare them to the complete genomic sequence of XFA. Here we present highlights of the first functional reconstruction of a phytopathogenic microbe based on the three sequenced genomes. This approach has led us to the identification of a putative drug target in the aerobic respiratory chain of this organism, as well as to a prediction of the specific growth requirements of this bacterium, which were used to develop a defined medium for optimal growth. Furthermore, based on a global alignment of the proteomes for these genomes, we identified a region in XFA that is absent in the other two genomes that potentially encodes host-specific functions. Comparisons of curated pathways and their components present in the complete XFA genome relative to the gapped XFY and XFX genomes allows the prediction of functions potentially missed during gapped-genome sequencing. Such an approach provides an added level of quality control to the analysis of sequenced genomes.