Gonzalez JM

References (7)

Title : Analysis of three genomes within the thermophilic bacterial species Caldanaerobacter subterraneus with a focus on carbon monoxide dehydrogenase evolution and hydrolase diversity - Sant'Anna_2015_BMC.Genomics_16_757
Author(s) : Sant'Anna FH , Lebedinsky AV , Sokolova TG , Robb FT , Gonzalez JM
Ref : BMC Genomics , 16 :757 , 2015
Abstract : BACKGROUND: The Caldanaerobacter subterraneus species includes thermophilic fermentative bacteria able to grow on carbohydrates substrates with acetate and L-alanine as the main products. In this study, comprehensive analysis of three genomes of C. subterraneus subspecies was carried in order to identify genes encoding key metabolic enzymes and to document the genomic basis for the evolution of these organisms.
METHODS: Average nucleotide identity and in silico DNA relatedness were estimated for the studied C. subterraneus genomes. Genome synteny was evaluated using R2CAT software. Protein conservation was analyzed using mGenome Subtractor. Horizontal gene transfer was predicted through the GOHTAM pipeline (using tetranucleotide composition) and phylogenetic analyses (by maximum likelihood). Hydrolases were identified through the MEROPS and CAZy platforms.
RESULTS: The three genomes of C. subterraneus showed high similarity, although there are substantial differences in their gene composition and organization. Each subspecies possesses a gene cluster encoding a carbon monoxide dehydrogenase (CODH) and an energy converting hydrogenase (ECH). The CODH gene is associated with an operon that resembles the Escherichia coli hydrogenase hyc/hyf operons, a novel genetic context distinct from that found in archetypical hydrogenogenic carboxydotrophs. Apart from the CODH-associated hydrogenase, these bacteria also contain other hydrogenases, encoded by ech and hyd genes. An Mbx ferredoxin:NADP oxidoreductase homolog similar to that originally described in the archaeon Pyrococcus furiosus was uniquely encoded in the C. subterraneus subsp. yonseiensis genome. Compositional analysis demonstrated that some genes of the CODH-ECH and mbx operons present distinct sequence patterns in relation to the majority of the other genes of each genome. Phylogenetic reconstructions of the genes from these operons and those from the ech operon are incongruent to the species tree. Notably, the cooS gene of C. subterraneus subsp. pacificus and its homologs in C. subterraneus subsp. tengcongensis and C. subterraneus subsp. yonseiensis form distinct clades. The strains have diverse hydrolytic enzymes and they appear to be proteolytic and glycolytic. Divergent glycosidases from 14 families, among them amylases, chitinases, alpha-glucosidases, beta-glucosidases, and cellulases, were identified. Each of the three genomes also contains around 100 proteases from 50 subfamilies, as well about ten different esterases.
CONCLUSIONS: Genomic information suggests that multiple horizontal gene transfers conferred the adaptation of C. subterraneus subspecies to extreme niches throughout the carbon monoxide utilization and hydrogen production. The variety of hydrolases found in their genomes indicate the versatility of the species in obtaining energy and carbon from diverse substrates, therefore these organisms constitute a remarkable resource of enzymes with biotechnological potential.
ESTHER : Sant'Anna_2015_BMC.Genomics_16_757
PubMedSearch : Sant'Anna_2015_BMC.Genomics_16_757
PubMedID: 26446804

Title : Draft Genome of the Marine Gammaproteobacterium Halomonas titanicae - Sanchez-Porro_2013_Genome.Announc_1_e0008313
Author(s) : Sanchez-Porro C , de la Haba RR , Cruz-Hernandez N , Gonzalez JM , Reyes-Guirao C , Navarro-Sampedro L , Carballo M , Ventosa A
Ref : Genome Announc , 1 :e0008313 , 2013
Abstract : Halomonas titanicae strain BH1 is a heterotrophic, aerobic marine bacterium which was isolated from rusticles of the RMS Titanic wreck. Here we report the draft genome sequence of this halophilic gammaproteobacterium.
ESTHER : Sanchez-Porro_2013_Genome.Announc_1_e0008313
PubMedSearch : Sanchez-Porro_2013_Genome.Announc_1_e0008313
PubMedID: 23516210
Gene_locus related to this paper: 9gamm-l9ub00 , 9gamm-l9ud02

Title : Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation - Gomez-Consarnau_2010_PLoS.Biol_8_e1000358
Author(s) : Gomez-Consarnau L , Akram N , Lindell K , Pedersen A , Neutze R , Milton DL , Gonzalez JM , Pinhassi J
Ref : PLoS Biol , 8 :e1000358 , 2010
Abstract : Proteorhodopsins are globally abundant photoproteins found in bacteria in the photic zone of the ocean. Although their function as proton pumps with energy-yielding potential has been demonstrated, the ecological role of proteorhodopsins remains largely unexplored. Here, we report the presence and function of proteorhodopsin in a member of the widespread genus Vibrio, uncovered through whole-genome analysis. Phylogenetic analysis suggests that the Vibrio strain AND4 obtained proteorhodopsin through lateral gene transfer, which could have modified the ecology of this marine bacterium. We demonstrate an increased long-term survival of AND4 when starved in seawater exposed to light rather than held in darkness. Furthermore, mutational analysis provides the first direct evidence, to our knowledge, linking the proteorhodopsin gene and its biological function in marine bacteria. Thus, proteorhodopsin phototrophy confers a fitness advantage to marine bacteria, representing a novel mechanism for bacterioplankton to endure frequent periods of resource deprivation at the ocean's surface.
ESTHER : Gomez-Consarnau_2010_PLoS.Biol_8_e1000358
PubMedSearch : Gomez-Consarnau_2010_PLoS.Biol_8_e1000358
PubMedID: 20436956
Gene_locus related to this paper: 9vibr-a8tap9 , 9vibr-a8taz0 , 9vibr-a8tbi9 , vibha-d0x5c8 , vibhb-a7n5i4 , vibhb-bioh , vibpa-VP2790 , 9vibr-a8tcc0 , 9vibr-a8t3b5 , 9vibr-a8tbz0 , 9vibr-a8t606

Title : Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria) - Gonzalez_2008_Proc.Natl.Acad.Sci.U.S.A_105_8724
Author(s) : Gonzalez JM , Fernandez-Gomez B , Fernandez-Guerra A , Gomez-Consarnau L , Sanchez O , Coll-Llado M , Del Campo J , Escudero L , Rodriguez-Martinez R , Alonso-Saez L , Latasa M , Paulsen I , Nedashkovskaya O , Lekunberri I , Pinhassi J , Pedros-Alio C
Ref : Proc Natl Acad Sci U S A , 105 :8724 , 2008
Abstract : Analysis of marine cyanobacteria and proteobacteria genomes has provided a profound understanding of the life strategies of these organisms and their ecotype differentiation and metabolisms. However, a comparable analysis of the Bacteroidetes, the third major bacterioplankton group, is still lacking. In the present paper, we report on the genome of Polaribacter sp. strain MED152. On the one hand, MED152 contains a substantial number of genes for attachment to surfaces or particles, gliding motility, and polymer degradation. This agrees with the currently assumed life strategy of marine Bacteroidetes. On the other hand, it contains the proteorhodopsin gene, together with a remarkable suite of genes to sense and respond to light, which may provide a survival advantage in the nutrient-poor sun-lit ocean surface when in search of fresh particles to colonize. Furthermore, an increase in CO(2) fixation in the light suggests that the limited central metabolism is complemented by anaplerotic inorganic carbon fixation. This is mediated by a unique combination of membrane transporters and carboxylases. This suggests a dual life strategy that, if confirmed experimentally, would be notably different from what is known of the two other main bacterial groups (the autotrophic cyanobacteria and the heterotrophic proteobacteria) in the surface oceans. The Polaribacter genome provides insights into the physiological capabilities of proteorhodopsin-containing bacteria. The genome will serve as a model to study the cellular and molecular processes in bacteria that express proteorhodopsin, their adaptation to the oceanic environment, and their role in carbon-cycling.
ESTHER : Gonzalez_2008_Proc.Natl.Acad.Sci.U.S.A_105_8724
PubMedSearch : Gonzalez_2008_Proc.Natl.Acad.Sci.U.S.A_105_8724
PubMedID: 18552178
Gene_locus related to this paper: 9flao-a2twv7 , 9flao-a2tyd0 , 9flao-a2tyx8 , 9flao-a2tzk2 , 9flao-a2tzs0 , 9flao-a2u1x6 , 9flao-a2u1z3 , 9flao-a2u1z4 , 9flao-a2u306

Title : Light stimulates growth of proteorhodopsin-containing marine Flavobacteria - Gomez-Consarnau_2007_Nature_445_210
Author(s) : Gomez-Consarnau L , Gonzalez JM , Coll-Llado M , Gourdon P , Pascher T , Neutze R , Pedros-Alio C , Pinhassi J
Ref : Nature , 445 :210 , 2007
Abstract : Proteorhodopsins are bacterial light-dependent proton pumps. Their discovery within genomic material from uncultivated marine bacterioplankton caused considerable excitement because it indicated a potential phototrophic function within these organisms, which had previously been considered strictly chemotrophic. Subsequent studies established that sequences encoding proteorhodopsin are broadly distributed throughout the world's oceans. Nevertheless, the role of proteorhodopsins in native marine bacteria is still unknown. Here we show, from an analysis of the complete genomes of three marine Flavobacteria, that cultivated bacteria in the phylum Bacteroidetes, one of the principal components of marine bacterioplankton, contain proteorhodopsin. Moreover, growth experiments in both natural and artificial seawater (low in labile organic matter, which is typical of the world's oceans) establish that exposure to light results in a marked increase in the cell yield of one such bacterium (Dokdonia sp. strain MED134) when compared with cells grown in darkness. Thus, our results show that the phototrophy conferred by proteorhodopsin can provide critical amounts of energy, not only for respiration and maintenance but also for active growth of marine bacterioplankton in their natural environment.
ESTHER : Gomez-Consarnau_2007_Nature_445_210
PubMedSearch : Gomez-Consarnau_2007_Nature_445_210
PubMedID: 17215843
Gene_locus related to this paper: 9flao-a2tns8 , 9flao-a2tp95 , 9flao-a2tqj4 , 9flao-a2trk4 , 9flao-a2tsw3 , 9flao-a2twv7 , 9flao-a2tyd0 , 9flao-a2tyx8 , 9flao-a2tzk2 , 9flao-a2tzs0 , 9flao-a2u1x6 , 9flao-a2u1z3 , 9flao-a2u1z4 , 9flao-a2u306 , leebm-a3xkj0 , leebm-a3xl40 , leebm-a3xl92 , leebm-a3xqu3 , 9flao-a2u0w9 , leebm-a3xlk2

Title : Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901 - Wu_2005_PLoS.Genet_1_e65
Author(s) : Wu M , Ren Q , Durkin AS , Daugherty SC , Brinkac LM , Dodson RJ , Madupu R , Sullivan SA , Kolonay JF , Haft DH , Nelson WC , Tallon LJ , Jones KM , Ulrich LE , Gonzalez JM , Zhulin IB , Robb FT , Eisen JA
Ref : PLoS Genet , 1 :e65 , 2005
Abstract : We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO) as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a "minimal" model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously.
ESTHER : Wu_2005_PLoS.Genet_1_e65
PubMedSearch : Wu_2005_PLoS.Genet_1_e65
PubMedID: 16311624
Gene_locus related to this paper: carhz-metx , carhz-q3abd5 , carhz-q3adp4

Title : Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment - Moran_2004_Nature_432_910
Author(s) : Moran MA , Buchan A , Gonzalez JM , Heidelberg JF , Whitman WB , Kiene RP , Henriksen JR , King GM , Belas R , Fuqua C , Brinkac L , Lewis M , Johri S , Weaver B , Pai G , Eisen JA , Rahe E , Sheldon WM , Ye W , Miller TR , Carlton J , Rasko DA , Paulsen IT , Ren Q , Daugherty SC , DeBoy RT , Dodson RJ , Durkin AS , Madupu R , Nelson WC , Sullivan SA , Rosovitz MJ , Haft DH , Selengut J , Ward N
Ref : Nature , 432 :910 , 2004
Abstract : Since the recognition of prokaryotes as essential components of the oceanic food web, bacterioplankton have been acknowledged as catalysts of most major biogeochemical processes in the sea. Studying heterotrophic bacterioplankton has been challenging, however, as most major clades have never been cultured or have only been grown to low densities in sea water. Here we describe the genome sequence of Silicibacter pomeroyi, a member of the marine Roseobacter clade (Fig. 1), the relatives of which comprise approximately 10-20% of coastal and oceanic mixed-layer bacterioplankton. This first genome sequence from any major heterotrophic clade consists of a chromosome (4,109,442 base pairs) and megaplasmid (491,611 base pairs). Genome analysis indicates that this organism relies upon a lithoheterotrophic strategy that uses inorganic compounds (carbon monoxide and sulphide) to supplement heterotrophy. Silicibacter pomeroyi also has genes advantageous for associations with plankton and suspended particles, including genes for uptake of algal-derived compounds, use of metabolites from reducing microzones, rapid growth and cell-density-dependent regulation. This bacterium has a physiology distinct from that of marine oligotrophs, adding a new strategy to the recognized repertoire for coping with a nutrient-poor ocean.
ESTHER : Moran_2004_Nature_432_910
PubMedSearch : Moran_2004_Nature_432_910
PubMedID: 15602564
Gene_locus related to this paper: silpo-q5lke5 , silpo-q5lke7 , silpo-q5lke8 , silpo-q5lkk5 , silpo-q5lkv2 , silpo-q5lln9 , silpo-q5llu0 , silpo-q5llu2 , silpo-q5llx5 , silpo-q5lm66 , silpo-q5lmb9 , silpo-q5lml9 , silpo-q5lnp6 , silpo-q5lp28 , silpo-q5lp48 , silpo-q5lp56 , silpo-q5lpa5 , silpo-q5lpf7 , silpo-q5lpy6 , silpo-q5lrk1 , silpo-q5lsn7 , silpo-q5ltb5 , silpo-q5ltk0 , silpo-q5ltm5 , silpo-q5ltw8 , silpo-q5ltw9 , silpo-q5ltx1 , silpo-q5ltx5 , silpo-q5lu02 , silpo-q5lv12 , silpo-q5lv17 , silpo-q5lv53 , silpo-q5lvg9 , silpo-q5lw35 , silpo-q5lwk9 , silpo-q5lws0