Kerlavage AR

References (5)

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

Title : The complete genome sequence of the gastric pathogen Helicobacter pylori. - Tomb_1997_Nature_388_539
Author(s) : Tomb J-F , White O , Kerlavage AR , Clayton RA , Sutton GG , Fleischmann RD , Ketchum KA , Klenk H-P , Gill S , Dougherty BA , Nelson K , Quackenbush J , Zhou L , Kirkness EF , Peterson S , Loftus B , Richardson D , Dodson R , Khalak HG , Glodek A , McKenney K , FitzGerald LM , Lee N , Adams MD , Hickey EK , Berg DE , Gocayne JD , Utterback TR , Peterson JD , Kelley JM , Cotton MD , Weidman JM , Fujii C , Bowman C , Watthey L , Wallin E , Hayes WS , Borodovsky M , Karp PD , Smith HO , Fraser CM , Venter JC
Ref : Nature , 388 :539 , 1997
Abstract : Helicobacter pylori, strain 26695, has a circular genome of 1,667,867 base pairs and 1,590 predicted coding sequences. Sequence analysis indicates that H. pylori has well-developed systems for motility, for scavenging iron, and for DNA restriction and modification. Many putative adhesins, lipoproteins and other outer membrane proteins were identified, underscoring the potential complexity of host-pathogen interaction. Based on the large number of sequence-related genes encoding outer membrane proteins and the presence of homopolymeric tracts and dinucleotide repeats in coding sequences, H. pylori, like several other mucosal pathogens, probably uses recombination and slipped-strand mispairing within repeats as mechanisms for antigenic variation and adaptive evolution. Consistent with its restricted niche, H. pylori has a few regulatory networks, and a limited metabolic repertoire and biosynthetic capacity. Its survival in acid conditions depends, in part, on its ability to establish a positive inside-membrane potential in low pH.
ESTHER : Tomb_1997_Nature_388_539
PubMedSearch : Tomb_1997_Nature_388_539
PubMedID: 9252185
Gene_locus related to this paper: helpy-HP0739 , helpy-o25061

Title : Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi - Fraser_1997_Nature_390_580
Author(s) : Fraser CM , Casjens S , Huang WM , Sutton GG , Clayton R , Lathigra R , White O , Ketchum KA , Dodson R , Hickey EK , Gwinn M , Dougherty B , Tomb JF , Fleischmann RD , Richardson D , Peterson J , Kerlavage AR , Quackenbush J , Salzberg S , Hanson M , van Vugt R , Palmer N , Adams MD , Gocayne J , Weidman J , Utterback T , Watthey L , McDonald L , Artiach P , Bowman C , Garland S , Fujii C , Cotton MD , Horst K , Roberts K , Hatch B , Smith HO , Venter JC
Ref : Nature , 390 :580 , 1997
Abstract : The genome of the bacterium Borrelia burgdorferi B31, the aetiologic agent of Lyme disease, contains a linear chromosome of 910,725 base pairs and at least 17 linear and circular plasmids with a combined size of more than 533,000 base pairs. The chromosome contains 853 genes encoding a basic set of proteins for DNA replication, transcription, translation, solute transport and energy metabolism, but, like Mycoplasma genitalium, it contains no genes for cellular biosynthetic reactions. Because B. burgdorferi and M. genitalium are distantly related eubacteria, we suggest that their limited metabolic capacities reflect convergent evolution by gene loss from more metabolically competent progenitors. Of 430 genes on 11 plasmids, most have no known biological function; 39% of plasmid genes are paralogues that form 47 gene families. The biological significance of the multiple plasmid-encoded genes is not clear, although they may be involved in antigenic variation or immune evasion.
ESTHER : Fraser_1997_Nature_390_580
PubMedSearch : Fraser_1997_Nature_390_580
PubMedID: 9403685
Gene_locus related to this paper: borbu-BB0646

Title : The minimal gene complement of Mycoplasma genitalium - Fraser_1995_Science_270_397
Author(s) : Fraser CM , Gocayne JD , White O , Adams MD , Clayton RA , Fleischmann RD , Bult CJ , Kerlavage AR , Sutton G , Kelley JM , Fritchman RD , Weidman JF , Small KV , Sandusky M , Fuhrmann J , Nguyen D , Utterback TR , Saudek DM , Phillips CA , Merrick JM , Tomb JF , Dougherty BA , Bott KF , Hu PC , Lucier TS , Peterson SN , Smith HO , Hutchison CA, 3rd , Venter JC
Ref : Science , 270 :397 , 1995
Abstract : The complete nucleotide sequence (580,070 base pairs) of the Mycoplasma genitalium genome, the smallest known genome of any free-living organism, has been determined by whole-genome random sequencing and assembly. A total of only 470 predicted coding regions were identified that include genes required for DNA replication, transcription and translation, DNA repair, cellular transport, and energy metabolism. Comparison of this genome to that of Haemophilus influenzae suggests that differences in genome content are reflected as profound differences in physiology and metabolic capacity between these two organisms.
ESTHER : Fraser_1995_Science_270_397
PubMedSearch : Fraser_1995_Science_270_397
PubMedID: 7569993
Gene_locus related to this paper: mycge-esl1 , mycge-esl2 , mycge-esl3 , mycge-pip

Title : Whole-genome random sequencing and assembly of Haemophilus influenzae Rd - Fleischmann_1995_Science_269_496
Author(s) : Fleischmann RD , Adams MD , White O , Clayton RA , Kirkness EF , Kerlavage AR , Bult CJ , Tomb JF , Dougherty BA , Merrick JM , McKenney K , Sutton G , FitzHugh W , Fields C , Gocayne JD , Scott J , Shirley R , Liu LI , Glodek A , Kelley JM , Weidman JF , Phillips CA , Spriggs T , Hedblom E , Cotton MD , Utterback TR , Hanna MC , Nguyen DT , Saudek DM , Brandon RC , FineLD , Fritchman JL , Fuhrmann JL , Geoghagen NS , Gnehm CL , McDonald LA , Keith V , Small KV , Fraser CM , Smith HO , Venter JC
Ref : Science , 269 :496 , 1995
Abstract : An approach for genome analysis based on sequencing and assembly of unselected pieces of DNA from the whole chromosome has been applied to obtain the complete nucleotide sequence (1,830,137 base pairs) of the genome from the bacterium Haemophilus influenzae Rd. This approach eliminates the need for initial mapping efforts and is therefore applicable to the vast array of microbial species for which genome maps are unavailable. The H. influenzae Rd genome sequence (Genome Sequence DataBase accession number L42023) represents the only complete genome sequence from a free-living organism.
ESTHER : Fleischmann_1995_Science_269_496
PubMedSearch : Fleischmann_1995_Science_269_496
PubMedID: 7542800
Gene_locus related to this paper: haein-HI0193 , haein-metx , haein-pldb , haein-sfgh , haein-y1552 , haein-yfbb