Overbeek R

References (9)

Title : Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus - Bolotin_2004_Nat.Biotechnol_22_1554
Author(s) : Bolotin A , Quinquis B , Renault P , Sorokin A , Ehrlich SD , Kulakauskas S , Lapidus A , Goltsman E , Mazur M , Pusch GD , Fonstein M , Overbeek R , Kyprides N , Purnelle B , Prozzi D , Ngui K , Masuy D , Hancy F , Burteau S , Boutry M , Delcour J , Goffeau A , Hols P
Ref : Nat Biotechnol , 22 :1554 , 2004
Abstract : The lactic acid bacterium Streptococcus thermophilus is widely used for the manufacture of yogurt and cheese. This dairy species of major economic importance is phylogenetically close to pathogenic streptococci, raising the possibility that it has a potential for virulence. Here we report the genome sequences of two yogurt strains of S. thermophilus. We found a striking level of gene decay (10% pseudogenes) in both microorganisms. Many genes involved in carbon utilization are nonfunctional, in line with the paucity of carbon sources in milk. Notably, most streptococcal virulence-related genes that are not involved in basic cellular processes are either inactivated or absent in the dairy streptococcus. Adaptation to the constant milk environment appears to have resulted in the stabilization of the genome structure. We conclude that S. thermophilus has evolved mainly through loss-of-function events that remarkably mirror the environment of the dairy niche resulting in a severely diminished pathogenic potential.
ESTHER : Bolotin_2004_Nat.Biotechnol_22_1554
PubMedSearch : Bolotin_2004_Nat.Biotechnol_22_1554
PubMedID: 15543133
Gene_locus related to this paper: strt1-q5lz16 , strt1-q5lza1 , strt2-q5m420 , strtr-pepx

Title : The genome of Methanosarcina mazei: evidence for lateral gene transfer between Bacteria and Archaea. -
Author(s) : Deppenmeier U , Johann A , Hartsch T , Merkl R , Martinez-Arias R , Henne A , Wiezer A , Baeumer S , Brueggemann H , Lienard T , Christmann A , Boemecke M , Bhattacharyya A , Lykidis A , Overbeek R , Klenk H-P , Fritz H-J
Ref : J Mol Microbiol Biotechnol , 4 :453 , 2002
PubMedID: 12125824
Gene_locus related to this paper: metma-MM0529 , metma-MM1373 , metma-MM2426 , metma-MM2553 , metma-MM2650 , metma-MM3122 , metma-MM3198 , metma-MM3308 , metma-q8pw23

Title : Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586 - Kapatral_2002_J.Bacteriol_184_2005
Author(s) : Kapatral V , Anderson I , Ivanova N , Reznik G , Los T , Lykidis A , Bhattacharyya A , Bartman A , Gardner W , Grechkin G , Zhu L , Vasieva O , Chu L , Kogan Y , Chaga O , Goltsman E , Bernal A , Larsen N , D'Souza M , Walunas T , Pusch G , Haselkorn R , Fonstein M , Kyrpides N , Overbeek R
Ref : Journal of Bacteriology , 184 :2005 , 2002
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, H(2)S, 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.
ESTHER : Kapatral_2002_J.Bacteriol_184_2005
PubMedSearch : Kapatral_2002_J.Bacteriol_184_2005
PubMedID: 11889109
Gene_locus related to this paper: fusnn-FN0616 , fusnn-FN0752 , fusnu-FN0280 , fusnu-FN0484 , fusnu-FN0852 , fusnu-FN1062 , fusnu-FN1128 , fusnu-FN1345 , fusnv-q7p2e5 , fusnv-q7p338

Title : Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights - Bhattacharyya_2002_Genome.Res_12_1556
Author(s) : Bhattacharyya A , Stilwagen S , Reznik G , Feil H , Feil WS , Anderson I , Bernal A , D'Souza M , Ivanova N , Kapatral V , Larsen N , Los T , Lykidis A , Selkov E, Jr. , Walunas TL , Purcell A , Edwards RA , Hawkins T , Haselkorn R , Overbeek R , Kyrpides NC , Predki PF
Ref : Genome Res , 12 :1556 , 2002
Abstract : Draft sequencing is a rapid and efficient method for determining the near-complete sequence of microbial genomes. Here we report a comparative analysis of one complete and two draft genome sequences of the phytopathogenic bacterium, Xylella fastidiosa, which causes serious disease in plants, including citrus, almond, and oleander. We present highlights of an in silico analysis based on a comparison of reconstructions of core biological subsystems. Cellular pathway reconstructions have been used to identify a small number of genes, which are likely to reside within the draft genomes but are not captured in the draft assembly. These represented only a small fraction of all genes and were predominantly large and small ribosomal subunit protein components. By using this approach, some of the inherent limitations of draft sequence can be significantly reduced. Despite the incomplete nature of the draft genomes, it is possible to identify several phage-related genes, which appear to be absent from the draft genomes and not the result of insufficient sequence sampling. This region may therefore identify potential host-specific functions. Based on this first functional reconstruction of a phytopathogenic microbe, we spotlight an unusual respiration machinery as a potential target for biological control. We also predicted and developed a new defined growth medium for Xylella.
ESTHER : Bhattacharyya_2002_Genome.Res_12_1556
PubMedSearch : Bhattacharyya_2002_Genome.Res_12_1556
PubMedID: 12368248

Title : Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains - Bhattacharyya_2002_Proc.Natl.Acad.Sci.U.S.A_99_12403
Author(s) : Bhattacharyya A , Stilwagen S , Ivanova N , D'Souza M , Bernal A , Lykidis A , Kapatral V , Anderson I , Larsen N , Los T , Reznik G , Selkov E, Jr. , Walunas TL , Feil H , Feil WS , Purcell A , Lassez JL , Hawkins TL , Haselkorn R , Overbeek R , Predki PF , Kyrpides NC
Ref : Proceedings of the National Academy of Sciences of the United States of America , 99 :12403 , 2002
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.
ESTHER : Bhattacharyya_2002_Proc.Natl.Acad.Sci.U.S.A_99_12403
PubMedSearch : Bhattacharyya_2002_Proc.Natl.Acad.Sci.U.S.A_99_12403
PubMedID: 12205291

Title : The genome sequence of the facultative intracellular pathogen Brucella melitensis - DelVecchio_2002_Proc.Natl.Acad.Sci.U.S.A_99_443
Author(s) : DelVecchio VG , Kapatral V , Redkar RJ , Patra G , Mujer C , Los T , Ivanova N , Anderson I , Bhattacharyya A , Lykidis A , Reznik G , Jablonski L , Larsen N , D'Souza M , Bernal A , Mazur M , Goltsman E , Selkov E , Elzer PH , Hagius S , O'Callaghan D , Letesson JJ , Haselkorn R , Kyrpides N , Overbeek R
Ref : Proc Natl Acad Sci U S A , 99 :443 , 2002
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 alpha-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.
ESTHER : DelVecchio_2002_Proc.Natl.Acad.Sci.U.S.A_99_443
PubMedSearch : DelVecchio_2002_Proc.Natl.Acad.Sci.U.S.A_99_443
PubMedID: 11756688
Gene_locus related to this paper: brume-BMEI0552 , brume-BMEI0733 , brume-BMEI1044 , brume-BMEI1119 , brume-BMEI1365 , brume-BMEI1594 , brume-BMEI1608 , brume-BMEI1822 , brume-BMEI1884 , brume-BMEI1951 , brume-BMEI2011 , brume-BMEII0047 , brume-BMEII0306 , brume-BMEII0681 , brume-BMEII0989 , brume-dhE2 , brume-PCAD , brusu-BR0288 , brusu-BR1291 , brusu-BR1327

Title : The complete genome of the hyperthermophilic bacterium Aquifex aeolicus - Deckert_1998_Nature_392_353
Author(s) : Deckert G , Warren PV , Gaasterland T , Young WG , Lenox AL , Graham DE , Overbeek R , Snead MA , Keller M , Aujay M , Huber R , Feldman RA , Short JM , Olsen GJ , Swanson RV
Ref : Nature , 392 :353 , 1998
Abstract : Aquifex aeolicus was one of the earliest diverging, and is one of the most thermophilic, bacteria known. It can grow on hydrogen, oxygen, carbon dioxide, and mineral salts. The complex metabolic machinery needed for A. aeolicus to function as a chemolithoautotroph (an organism which uses an inorganic carbon source for biosynthesis and an inorganic chemical energy source) is encoded within a genome that is only one-third the size of the E. coli genome. Metabolic flexibility seems to be reduced as a result of the limited genome size. The use of oxygen (albeit at very low concentrations) as an electron acceptor is allowed by the presence of a complex respiratory apparatus. Although this organism grows at 95 degrees C, the extreme thermal limit of the Bacteria, only a few specific indications of thermophily are apparent from the genome. Here we describe the complete genome sequence of 1,551,335 base pairs of this evolutionarily and physiologically interesting organism.
ESTHER : Deckert_1998_Nature_392_353
PubMedSearch : Deckert_1998_Nature_392_353
PubMedID: 9537320
Gene_locus related to this paper: aquae-AQ.1571 , aquae-aq327 , aquae-aq2138 , aquae-dlhh

Title : The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus - Klenk_1997_Nature_390_364
Author(s) : Klenk HP , Clayton RA , Tomb JF , White O , Nelson KE , Ketchum KA , Dodson RJ , Gwinn M , Hickey EK , Peterson JD , Richardson DL , Kerlavage AR , Graham DE , Kyrpides NC , Fleischmann RD , Quackenbush J , Lee NH , Sutton GG , Gill S , Kirkness EF , Dougherty BA , McKenney K , Adams MD , Loftus B , Peterson S , Reich CI , McNeil LK , Badger JH , Glodek A , Zhou L , Overbeek R , Gocayne JD , Weidman JF , McDonald L , Utterback T , Cotton MD , Spriggs T , Artiach P , Kaine BP , Sykes SM , Sadow PW , D'Andrea KP , Bowman C , Fujii C , Garland SA , Mason TM , Olsen GJ , Fraser CM , Smith HO , Woese CR , Venter JC
Ref : Nature , 390 :364 , 1997
Abstract : Archaeoglobus fulgidus is the first sulphur-metabolizing organism to have its genome sequence determined. Its genome of 2,178,400 base pairs contains 2,436 open reading frames (ORFs). The information processing systems and the biosynthetic pathways for essential components (nucleotides, amino acids and cofactors) have extensive correlation with their counterparts in the archaeon Methanococcus jannaschii. The genomes of these two Archaea indicate dramatic differences in the way these organisms sense their environment, perform regulatory and transport functions, and gain energy. In contrast to M. jannaschii, A. fulgidus has fewer restriction-modification systems, and none of its genes appears to contain inteins. A quarter (651 ORFs) of the A. fulgidus genome encodes functionally uncharacterized yet conserved proteins, two-thirds of which are shared with M. jannaschii (428 ORFs). Another quarter of the genome encodes new proteins indicating substantial archaeal gene diversity.
ESTHER : Klenk_1997_Nature_390_364
PubMedSearch : Klenk_1997_Nature_390_364
PubMedID: 9389475
Gene_locus related to this paper: arcfu-AF0514 , arcfu-AF0675 , arcfu-AF1134 , arcfu-AF1563 , arcfu-AF1753 , arcfu-AF1763 , arcfu-est1 , arcfu-est2 , arcfu-est3 , arcfu-estea , arcfu-o28594 , arcfu-o29442 , arcfu-pcbd