Chakraborty T

References (7)

Title : Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes - Hain_2012_BMC.Genomics_13_144
Author(s) : Hain T , Ghai R , Billion A , Kuenne CT , Steinweg C , Izar B , Mohamed W , Mraheil MA , Domann E , Schaffrath S , Karst U , Goesmann A , Oehm S , Puhler A , Merkl R , Vorwerk S , Glaser P , Garrido P , Rusniok C , Buchrieser C , Goebel W , Chakraborty T
Ref : BMC Genomics , 13 :144 , 2012
Abstract : BACKGROUND: Listeria monocytogenes is a food-borne pathogen that causes infections with a high-mortality rate and has served as an invaluable model for intracellular parasitism. Here, we report complete genome sequences for two L. monocytogenes strains belonging to serotype 4a (L99) and 4b (CLIP80459), and transcriptomes of representative strains from lineages I, II, and III, thereby permitting in-depth comparison of genome- and transcriptome -based data from three lineages of L. monocytogenes. Lineage III, represented by the 4a L99 genome is known to contain strains less virulent for humans.
RESULTS: The genome analysis of the weakly pathogenic L99 serotype 4a provides extensive evidence of virulence gene decay, including loss of several important surface proteins. The 4b CLIP80459 genome, unlike the previously sequenced 4b F2365 genome harbours an intact inlB invasion gene. These lineage I strains are characterized by the lack of prophage genes, as they share only a single prophage locus with other L. monocytogenes genomes 1/2a EGD-e and 4a L99. Comparative transcriptome analysis during intracellular growth uncovered adaptive expression level differences in lineages I, II and III of Listeria, notable amongst which was a strong intracellular induction of flagellar genes in strain 4a L99 compared to the other lineages. Furthermore, extensive differences between strains are manifest at levels of metabolic flux control and phosphorylated sugar uptake. Intriguingly, prophage gene expression was found to be a hallmark of intracellular gene expression. Deletion mutants in the single shared prophage locus of lineage II strain EGD-e 1/2a, the lma operon, revealed severe attenuation of virulence in a murine infection model. CONCLUSION: Comparative genomics and transcriptome analysis of L. monocytogenes strains from three lineages implicate prophage genes in intracellular adaptation and indicate that gene loss and decay may have led to the emergence of attenuated lineages.
ESTHER : Hain_2012_BMC.Genomics_13_144
PubMedSearch : Hain_2012_BMC.Genomics_13_144
PubMedID: 22530965
Gene_locus related to this paper: lismo-LMO0110 , lismo-LMO0493 , lismo-LMO0580 , lismo-LMO0950 , lismo-LMO0951 , lismo-LMO1128 , lismo-LMO1258 , lismo-LMO2089 , lismo-LMO2433 , lismo-LMO2578 , lismo-LMO2755 , lismo-metx

Title : Complete genome sequence of the animal pathogen Listeria ivanovii, which provides insights into host specificities and evolution of the genus Listeria - Buchrieser_2011_J.Bacteriol_193_6787
Author(s) : Buchrieser C , Rusniok C , Garrido P , Hain T , Scortti M , Lampidis R , Karst U , Chakraborty T , Cossart P , Kreft J , Vazquez-Boland JA , Goebel W , Glaser P
Ref : Journal of Bacteriology , 193 :6787 , 2011
Abstract : We report the complete and annotated genome sequence of the animal pathogen Listeria ivanovii subsp. ivanovii strain PAM 55 (serotype 5), isolated in 1997 in Spain from an outbreak of abortion in sheep. The sequence and its analysis are available at an interactive genome browser at the Institut Pasteur (http:\/\/genolist.pasteur.fr/LivaList/).
ESTHER : Buchrieser_2011_J.Bacteriol_193_6787
PubMedSearch : Buchrieser_2011_J.Bacteriol_193_6787
PubMedID: 22072644
Gene_locus related to this paper: lisip-g2zat3 , lismo-LMO2452 , lisip-g2zf96 , lisiv-a0a097bbs7

Title : Complete genome sequence of Listeria seeligeri, a nonpathogenic member of the genus Listeria - Steinweg_2010_J.Bacteriol_192_1473
Author(s) : Steinweg C , Kuenne CT , Billion A , Mraheil MA , Domann E , Ghai R , Barbuddhe SB , Karst U , Goesmann A , Puhler A , Weisshaar B , Wehland J , Lampidis R , Kreft J , Goebel W , Chakraborty T , Hain T
Ref : Journal of Bacteriology , 192 :1473 , 2010
Abstract : We report the complete and annotated genome sequence of the nonpathogenic Listeria seeligeri SLCC3954 serovar 1/2b type strain harboring the smallest completely sequenced genome of the genus Listeria.
ESTHER : Steinweg_2010_J.Bacteriol_192_1473
PubMedSearch : Steinweg_2010_J.Bacteriol_192_1473
PubMedID: 20061480
Gene_locus related to this paper: lisin-LIN0976 , lismo-LMO2452 , lismo-metx , lisss-d3ulc5 , lisss-d3unw0 , lisss-d3urb3 , lisss-d3urc9

Title : Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes - Hain_2006_J.Bacteriol_188_7405
Author(s) : Hain T , Steinweg C , Kuenne CT , Billion A , Ghai R , Chatterjee SS , Domann E , Karst U , Goesmann A , Bekel T , Bartels D , Kaiser O , Meyer F , Puhler A , Weisshaar B , Wehland J , Liang C , Dandekar T , Lampidis R , Kreft J , Goebel W , Chakraborty T
Ref : Journal of Bacteriology , 188 :7405 , 2006
Abstract : We present the complete genome sequence of Listeria welshimeri, a nonpathogenic member of the genus Listeria. Listeria welshimeri harbors a circular chromosome of 2,814,130 bp with 2,780 open reading frames. Comparative genomic analysis of chromosomal regions between L. welshimeri, Listeria innocua, and Listeria monocytogenes shows strong overall conservation of synteny, with the exception of the translocation of an F(o)F(1) ATP synthase. The smaller size of the L. welshimeri genome is the result of deletions in all of the genes involved in virulence and of "fitness" genes required for intracellular survival, transcription factors, and LPXTG- and LRR-containing proteins as well as 55 genes involved in carbohydrate transport and metabolism. In total, 482 genes are absent from L. welshimeri relative to L. monocytogenes. Of these, 249 deletions are commonly absent in both L. welshimeri and L. innocua, suggesting similar genome evolutionary paths from an ancestor. We also identified 311 genes specific to L. welshimeri that are absent in the other two species, indicating gene expansion in L. welshimeri, including horizontal gene transfer. The species L. welshimeri appears to have been derived from early evolutionary events and an ancestor more compact than L. monocytogenes that led to the emergence of nonpathogenic Listeria spp.
ESTHER : Hain_2006_J.Bacteriol_188_7405
PubMedSearch : Hain_2006_J.Bacteriol_188_7405
PubMedID: 16936040
Gene_locus related to this paper: lisin-LIN0976 , lisin-LIN2544 , lismo-LMO2089 , lismo-LMO2452 , lismo-LMO2453 , lismo-metx , lisss-d3urb3 , lisw6-a0agy6 , lisw6-a0ajc8 , lisw6-a0am12

Title : Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora - Tauch_2005_J.Bacteriol_187_4671
Author(s) : Tauch A , Kaiser O , Hain T , Goesmann A , Weisshaar B , Albersmeier A , Bekel T , Bischoff N , Brune I , Chakraborty T , Kalinowski J , Meyer F , Rupp O , Schneiker S , Viehoever P , Puhler A
Ref : Journal of Bacteriology , 187 :4671 , 2005
Abstract : Corynebacterium jeikeium is a "lipophilic" and multidrug-resistant bacterial species of the human skin flora that has been recognized with increasing frequency as a serious nosocomial pathogen. Here we report the genome sequence of the clinical isolate C. jeikeium K411, which was initially recovered from the axilla of a bone marrow transplant patient. The genome of C. jeikeium K411 consists of a circular chromosome of 2,462,499 bp and the 14,323-bp bacteriocin-producing plasmid pKW4. The chromosome of C. jeikeium K411 contains 2,104 predicted coding sequences, 52% of which were considered to be orthologous with genes in the Corynebacterium glutamicum, Corynebacterium efficiens, and Corynebacterium diphtheriae genomes. These genes apparently represent the chromosomal backbone that is conserved between the four corynebacteria. Among the genes that lack an ortholog in the known corynebacterial genomes, many are located close to transposable elements or revealed an atypical G+C content, indicating that horizontal gene transfer played an important role in the acquisition of genes involved in iron and manganese homeostasis, in multidrug resistance, in bacterium-host interaction, and in virulence. Metabolic analyses of the genome sequence indicated that the "lipophilic" phenotype of C. jeikeium most likely originates from the absence of fatty acid synthase and thus represents a fatty acid auxotrophy. Accordingly, both the complete gene repertoire and the deduced lifestyle of C. jeikeium K411 largely reflect the strict dependence of growth on the presence of exogenous fatty acids. The predicted virulence factors of C. jeikeium K411 are apparently involved in ensuring the availability of exogenous fatty acids by damaging the host tissue.
ESTHER : Tauch_2005_J.Bacteriol_187_4671
PubMedSearch : Tauch_2005_J.Bacteriol_187_4671
PubMedID: 15968079
Gene_locus related to this paper: corjk-q4jsq8 , corjk-q4jst9 , corjk-q4jt28 , corjk-q4jt69 , corjk-q4jta2 , corjk-q4jth4 , corjk-q4jti5 , corjk-q4ju26 , corjk-q4jug4 , corjk-q4juz4 , corjk-q4jv41 , corjk-q4jvr2 , corjk-q4jwi5 , corjk-q4jwq5 , corjk-q4jwu9 , corjk-q4jx57 , corjk-q4jx58 , corjk-q4jxf4 , corjk-q4jxg1 , corjk-q4jxi0 , corjk-q4jxk5 , corjk-q4jxw6 , corjk-q4jxx7 , corjk-q4jy17 , corjk-q4jy19 , corjk-q4jy21 , corjk-q4jy22 , corjk-q4jyd0 , corjk-q4jyf2

Title : Identification of a hypothetical membrane protein interactor of ribosomal phosphoprotein P0 - Aruna_2004_J.Biosci_29_33
Author(s) : Aruna K , Chakraborty T , Nambeesan S , Mannan AB , Sehgal A , Bhalchandara SR , Sharma S
Ref : J Biosci , 29 :33 , 2004
Abstract : The ribosomal phosphoprotein P0 of the human malarial parasite Plasmodium falciparum (PfP0) has been identified as a protective surface protein. In Drosophila, P0 protein functions in the nucleus. The ribosomal function of P0 is mediated at the stalk of the large ribosomal subunit at the GTPase centre, where the elongation factor eEF2 binds. The multiple roles of the P0 protein presumably occur through interactions with other proteins. To identify such interacting protein domains, a yeast two-hybrid screen was carried out. Out of a set of sixty clones isolated, twelve clones that interacted strongly with both PfP0 and the Saccharomyces cerevisiae P0 (ScP0) protein were analysed. These belonged to three broad classes: namely (i) ribosomal proteins; (ii) proteins involved in nucleotide binding; and (iii) hypothetical integral membrane proteins. One of the strongest interactors (clone 67B) mapped to the gene YFL034W which codes for a hypothetical integral membrane protein, and is conserved amongst several eukaryotic organisms. The insert of clone 67B was expressed as a recombinant protein, and immunoprecipitaion (IP) reaction with anti-P0 antibodies pulled down this protein along with PfP0 as well as ScP0 protein. Using deletion constructions, the domain of ScP0, which interacted with clone 67B, was mapped to 60-148 amino acids. It is envisaged that the surface localization of P0 protein may be mediated through interactions with putative YFL034W-like proteins in P. falciparum.
ESTHER : Aruna_2004_J.Biosci_29_33
PubMedSearch : Aruna_2004_J.Biosci_29_33
PubMedID: 15286401
Gene_locus related to this paper: yeast-yfd4

Title : Comparative genomics of Listeria species - Glaser_2001_Science_294_849
Author(s) : Glaser P , Frangeul L , Buchrieser C , Rusniok C , Amend A , Baquero F , Berche P , Bloecker H , Brandt P , Chakraborty T , Charbit A , Chetouani F , Couve E , de Daruvar A , Dehoux P , Domann E , Dominguez-Bernal G , Duchaud E , Durant L , Dussurget O , Entian KD , Fsihi H , Portillo FG , Garrido P , Gautier L , Goebel W , Gomez-Lopez N , Hain T , Hauf J , Jackson D , Jones LM , Kaerst U , Kreft J , Kuhn M , Kunst F , Kurapkat G , Madueno E , Maitournam A , Vicente JM , Ng E , Nedjari H , Nordsiek G , Novella S , de Pablos B , Perez-Diaz JC , Purcell R , Remmel B , Rose M , Schlueter T , Simoes N , Tierrez A , Vazquez-Boland JA , Voss H , Wehland J , Cossart P
Ref : Science , 294 :849 , 2001
Abstract : Listeria monocytogenes is a food-borne pathogen with a high mortality rate that has also emerged as a paradigm for intracellular parasitism. We present and compare the genome sequences of L. monocytogenes (2,944,528 base pairs) and a nonpathogenic species, L. innocua (3,011,209 base pairs). We found a large number of predicted genes encoding surface and secreted proteins, transporters, and transcriptional regulators, consistent with the ability of both species to adapt to diverse environments. The presence of 270 L. monocytogenes and 149 L. innocua strain-specific genes (clustered in 100 and 63 islets, respectively) suggests that virulence in Listeria results from multiple gene acquisition and deletion events.
ESTHER : Glaser_2001_Science_294_849
PubMedSearch : Glaser_2001_Science_294_849
PubMedID: 11679669
Gene_locus related to this paper: lisin-LIN0589 , lisin-LIN0754 , lisin-LIN0850 , lisin-LIN0949 , lisin-LIN0950 , lisin-LIN0976 , lisin-LIN1094 , lisin-LIN1546 , lisin-LIN1782 , lisin-LIN2180 , lisin-LIN2214 , lisin-LIN2363 , lisin-LIN2527 , lisin-LIN2544 , lisin-LIN2547 , lisin-LIN2722 , lisin-LIN2825 , lisin-LIN2898 , lismc-c1l0d9 , lismo-LMO0110 , lismo-LMO0493 , lismo-LMO0580 , lismo-LMO0752 , lismo-LMO0760 , lismo-LMO0857 , lismo-LMO0950 , lismo-LMO0951 , lismo-LMO0977 , lismo-LMO1128 , lismo-LMO1258 , lismo-LMO1511 , lismo-LMO1674 , lismo-LMO2074 , lismo-LMO2089 , lismo-LMO2109 , lismo-LMO2262 , lismo-LMO2433 , lismo-LMO2450 , lismo-LMO2452 , lismo-LMO2453 , lismo-LMO2578 , lismo-LMO2677 , lismo-LMO2755 , lismo-metx