Gerstein M

References (3)

Title : New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis - Smith_2007_Genes.Dev_21_601
Author(s) : Smith MG , Gianoulis TA , Pukatzki S , Mekalanos JJ , Ornston LN , Gerstein M , Snyder M
Ref : Genes Dev , 21 :601 , 2007
Abstract : Acinetobacter baumannii has emerged as an important and problematic human pathogen as it is the causative agent of several types of infections including pneumonia, meningitis, septicemia, and urinary tract infections. We explored the pathogenic content of this harmful pathogen using a combination of DNA sequencing and insertional mutagenesis. The genome of this organism was sequenced using a strategy involving high-density pyrosequencing, a novel, rapid method of high-throughput sequencing. Excluding the rDNA repeats, the assembled genome is 3,976,746 base pairs (bp) and has 3830 ORFs. A significant fraction of ORFs (17.2%) are located in 28 putative alien islands, indicating that the genome has acquired a large amount of foreign DNA. Consistent with its role in pathogenesis, a remarkable number of the islands (16) contain genes implicated in virulence, indicating the organism devotes a considerable portion of its genes to pathogenesis. The largest island contains elements homologous to the Legionella/Coxiella Type IV secretion apparatus. Type IV secretion systems have been demonstrated to be important for virulence in other organisms and thus are likely to help mediate pathogenesis of A. baumannii. Insertional mutagenesis generated avirulent isolates of A. baumannii and verified that six of the islands contain virulence genes, including two novel islands containing genes that lacked homology with others in the databases. The DNA sequencing approach described in this study allows the rapid elucidation of the DNA sequence of any microbe and, when combined with genetic screens, can identify many novel genes important for microbial pathogenesis.
ESTHER : Smith_2007_Genes.Dev_21_601
PubMedSearch : Smith_2007_Genes.Dev_21_601
PubMedID: 17344419
Gene_locus related to this paper: acib1-e8pgf8 , acib3-metx , acib5-b7iaz7 , aciba-d0c661 , aciba-d0c992 , aciba-k6lkl9 , aciba-q76hj1 , acibc-b2huf4 , acibc-b2i0a2 , acibc-b2i0w9 , acibc-b2i2b0 , acibt-a3m1g6 , acibt-a3m5r6 , acibt-a3m5t3 , acibt-a3m5x2 , acibt-a3m5z0 , acibt-a3m7c7 , acibt-a3m627 , acibt-a3m707 , acibt-a3mab8 , aciby-b0v723 , acica-d0s0a7 , aciba-f5iht4 , aciba-a0a009wzt4

Title : Functional profiling of the Saccharomyces cerevisiae genome - Giaever_2002_Nature_418_387
Author(s) : Giaever G , Chu AM , Ni L , Connelly C , Riles L , Veronneau S , Dow S , Lucau-Danila A , Anderson K , Andre B , Arkin AP , Astromoff A , El-Bakkoury M , Bangham R , Benito R , Brachat S , Campanaro S , Curtiss M , Davis K , Deutschbauer A , Entian KD , Flaherty P , Foury F , Garfinkel DJ , Gerstein M , Gotte D , Guldener U , Hegemann JH , Hempel S , Herman Z , Jaramillo DF , Kelly DE , Kelly SL , Kotter P , LaBonte D , Lamb DC , Lan N , Liang H , Liao H , Liu L , Luo C , Lussier M , Mao R , Menard P , Ooi SL , Revuelta JL , Roberts CJ , Rose M , Ross-Macdonald P , Scherens B , Schimmack G , Shafer B , Shoemaker DD , Sookhai-Mahadeo S , Storms RK , Strathern JN , Valle G , Voet M , Volckaert G , Wang CY , Ward TR , Wilhelmy J , Winzeler EA , Yang Y , Yen G , Youngman E , Yu K , Bussey H , Boeke JD , Snyder M , Philippsen P , Davis RW , Johnston M
Ref : Nature , 418 :387 , 2002
Abstract : Determining the effect of gene deletion is a fundamental approach to understanding gene function. Conventional genetic screens exhibit biases, and genes contributing to a phenotype are often missed. We systematically constructed a nearly complete collection of gene-deletion mutants (96% of annotated open reading frames, or ORFs) of the yeast Saccharomyces cerevisiae. DNA sequences dubbed 'molecular bar codes' uniquely identify each strain, enabling their growth to be analysed in parallel and the fitness contribution of each gene to be quantitatively assessed by hybridization to high-density oligonucleotide arrays. We show that previously known and new genes are necessary for optimal growth under six well-studied conditions: high salt, sorbitol, galactose, pH 8, minimal medium and nystatin treatment. Less than 7% of genes that exhibit a significant increase in messenger RNA expression are also required for optimal growth in four of the tested conditions. Our results validate the yeast gene-deletion collection as a valuable resource for functional genomics.
ESTHER : Giaever_2002_Nature_418_387
PubMedSearch : Giaever_2002_Nature_418_387
PubMedID: 12140549

Title : Subcellular localization of the yeast proteome - Kumar_2002_Genes.Dev_16_707
Author(s) : Kumar A , Agarwal S , Heyman JA , Matson S , Heidtman M , Piccirillo S , Umansky L , Drawid A , Jansen R , Liu Y , Cheung KH , Miller P , Gerstein M , Roeder GS , Snyder M
Ref : Genes Dev , 16 :707 , 2002
Abstract : Protein localization data are a valuable information resource helpful in elucidating eukaryotic protein function. Here, we report the first proteome-scale analysis of protein localization within any eukaryote. Using directed topoisomerase I-mediated cloning strategies and genome-wide transposon mutagenesis, we have epitope-tagged 60% of the Saccharomyces cerevisiae proteome. By high-throughput immunolocalization of tagged gene products, we have determined the subcellular localization of 2744 yeast proteins. Extrapolating these data through a computational algorithm employing Bayesian formalism, we define the yeast localizome (the subcellular distribution of all 6100 yeast proteins). We estimate the yeast proteome to encompass approximately 5100 soluble proteins and >1000 transmembrane proteins. Our results indicate that 47% of yeast proteins are cytoplasmic, 13% mitochondrial, 13% exocytic (including proteins of the endoplasmic reticulum and secretory vesicles), and 27% nuclear/nucleolar. A subset of nuclear proteins was further analyzed by immunolocalization using surface-spread preparations of meiotic chromosomes. Of these proteins, 38% were found associated with chromosomal DNA. As determined from phenotypic analyses of nuclear proteins, 34% are essential for spore viability--a percentage nearly twice as great as that observed for the proteome as a whole. In total, this study presents experimentally derived localization data for 955 proteins of previously unknown function: nearly half of all functionally uncharacterized proteins in yeast. To facilitate access to these data, we provide a searchable database featuring 2900 fluorescent micrographs at http:\/\/
ESTHER : Kumar_2002_Genes.Dev_16_707
PubMedSearch : Kumar_2002_Genes.Dev_16_707
PubMedID: 11914276
Gene_locus related to this paper: yeast-mgll