Zhulin IB

References (6)

Title : Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments - Wisniewski-Dye_2011_PLoS.Genet_7_e1002430
Author(s) : Wisniewski-Dye F , Borziak K , Khalsa-Moyers G , Alexandre G , Sukharnikov LO , Wuichet K , Hurst GB , McDonald WH , Robertson JS , Barbe V , Calteau A , Rouy Z , Mangenot S , Prigent-Combaret C , Normand P , Boyer M , Siguier P , Dessaux Y , Elmerich C , Condemine G , Krishnen G , Kennedy I , Paterson AH , Gonzalez V , Mavingui P , Zhulin IB
Ref : PLoS Genet , 7 :e1002430 , 2011
Abstract : Fossil records indicate that life appeared in marine environments approximately 3.5 billion years ago (Gyr) and transitioned to terrestrial ecosystems nearly 2.5 Gyr. Sequence analysis suggests that "hydrobacteria" and "terrabacteria" might have diverged as early as 3 Gyr. Bacteria of the genus Azospirillum are associated with roots of terrestrial plants; however, virtually all their close relatives are aquatic. We obtained genome sequences of two Azospirillum species and analyzed their gene origins. While most Azospirillum house-keeping genes have orthologs in its close aquatic relatives, this lineage has obtained nearly half of its genome from terrestrial organisms. The majority of genes encoding functions critical for association with plants are among horizontally transferred genes. Our results show that transition of some aquatic bacteria to terrestrial habitats occurred much later than the suggested initial divergence of hydro- and terrabacterial clades. The birth of the genus Azospirillum approximately coincided with the emergence of vascular plants on land.
ESTHER : Wisniewski-Dye_2011_PLoS.Genet_7_e1002430
PubMedSearch : Wisniewski-Dye_2011_PLoS.Genet_7_e1002430
PubMedID: 22216014
Gene_locus related to this paper: azobr-g8al65 , azol4-g7zc95 , azol4-g7zc98 , azol4-g7zfp9 , azol4-g7zcr5 , azobr-g8b0i6

Title : The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota - Anderson_2009_BMC.Genomics_10_145
Author(s) : Anderson IJ , Dharmarajan L , Rodriguez J , Hooper S , Porat I , Ulrich LE , Elkins JG , Mavromatis K , Sun H , Land M , Lapidus A , Lucas S , Barry K , Huber H , Zhulin IB , Whitman WB , Mukhopadhyay B , Woese C , Bristow J , Kyrpides N
Ref : BMC Genomics , 10 :145 , 2009
Abstract : BACKGROUND: Staphylothermus marinus is an anaerobic, sulfur-reducing peptide fermenter of the archaeal phylum Crenarchaeota. It is the third heterotrophic, obligate sulfur reducing crenarchaeote to be sequenced and provides an opportunity for comparative analysis of the three genomes.
RESULTS: The 1.57 Mbp genome of the hyperthermophilic crenarchaeote Staphylothermus marinus has been completely sequenced. The main energy generating pathways likely involve 2-oxoacid:ferredoxin oxidoreductases and ADP-forming acetyl-CoA synthases. S. marinus possesses several enzymes not present in other crenarchaeotes including a sodium ion-translocating decarboxylase likely to be involved in amino acid degradation. S. marinus lacks sulfur-reducing enzymes present in the other two sulfur-reducing crenarchaeotes that have been sequenced -- Thermofilum pendens and Hyperthermus butylicus. Instead it has three operons similar to the mbh and mbx operons of Pyrococcus furiosus, which may play a role in sulfur reduction and/or hydrogen production. The two marine organisms, S. marinus and H. butylicus, possess more sodium-dependent transporters than T. pendens and use symporters for potassium uptake while T. pendens uses an ATP-dependent potassium transporter. T. pendens has adapted to a nutrient-rich environment while H. butylicus is adapted to a nutrient-poor environment, and S. marinus lies between these two extremes. CONCLUSION: The three heterotrophic sulfur-reducing crenarchaeotes have adapted to their habitats, terrestrial vs. marine, via their transporter content, and they have also adapted to environments with differing levels of nutrients. Despite the fact that they all use sulfur as an electron acceptor, they are likely to have different pathways for sulfur reduction.
ESTHER : Anderson_2009_BMC.Genomics_10_145
PubMedSearch : Anderson_2009_BMC.Genomics_10_145
PubMedID: 19341479

Title : Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction - Anderson_2008_J.Bacteriol_190_2957
Author(s) : Anderson I , Rodriguez J , Susanti D , Porat I , Reich C , Ulrich LE , Elkins JG , Mavromatis K , Lykidis A , Kim E , Thompson LS , Nolan M , Land M , Copeland A , Lapidus A , Lucas S , Detter C , Zhulin IB , Olsen GJ , Whitman W , Mukhopadhyay B , Bristow J , Kyrpides N
Ref : Journal of Bacteriology , 190 :2957 , 2008
Abstract : We report the complete genome of Thermofilum pendens, a deeply branching, hyperthermophilic member of the order Thermoproteales in the archaeal kingdom Crenarchaeota. T. pendens is a sulfur-dependent, anaerobic heterotroph isolated from a solfatara in Iceland. It is an extracellular commensal, requiring an extract of Thermoproteus tenax for growth, and the genome sequence reveals that biosynthetic pathways for purines, most amino acids, and most cofactors are absent. In fact, T. pendens has fewer biosynthetic enzymes than obligate intracellular parasites, although it does not display other features that are common among obligate parasites and thus does not appear to be in the process of becoming a parasite. It appears that T. pendens has adapted to life in an environment rich in nutrients. T. pendens was known previously to utilize peptides as an energy source, but the genome revealed a substantial ability to grow on carbohydrates. T. pendens is the first crenarchaeote and only the second archaeon found to have a transporter of the phosphotransferase system. In addition to fermentation, T. pendens may obtain energy from sulfur reduction with hydrogen and formate as electron donors. It may also be capable of sulfur-independent growth on formate with formate hydrogen lyase. Additional novel features are the presence of a monomethylamine:corrinoid methyltransferase, the first time that this enzyme has been found outside the Methanosarcinales, and the presence of a presenilin-related protein. The predicted highly expressed proteins do not include proteins encoded by housekeeping genes and instead include ABC transporters for carbohydrates and peptides and clustered regularly interspaced short palindromic repeat-associated proteins.
ESTHER : Anderson_2008_J.Bacteriol_190_2957
PubMedSearch : Anderson_2008_J.Bacteriol_190_2957
PubMedID: 18263724
Gene_locus related to this paper: thepd-a1s004

Title : Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T - Weiner_2008_PLoS.Genet_4_e1000087
Author(s) : Weiner RM , Taylor LE, 2nd , Henrissat B , Hauser L , Land M , Coutinho PM , Rancurel C , Saunders EH , Longmire AG , Zhang H , Bayer EA , Gilbert HJ , Larimer F , Zhulin IB , Ekborg NA , Lamed R , Richardson PM , Borovok I , Hutcheson S
Ref : PLoS Genet , 4 :e1000087 , 2008
Abstract : The marine bacterium Saccharophagus degradans strain 2-40 (Sde 2-40) is emerging as a vanguard of a recently discovered group of marine and estuarine bacteria that recycles complex polysaccharides. We report its complete genome sequence, analysis of which identifies an unusually large number of enzymes that degrade >10 complex polysaccharides. Not only is this an extraordinary range of catabolic capability, many of the enzymes exhibit unusual architecture including novel combinations of catalytic and substrate-binding modules. We hypothesize that many of these features are adaptations that facilitate depolymerization of complex polysaccharides in the marine environment. This is the first sequenced genome of a marine bacterium that can degrade plant cell walls, an important component of the carbon cycle that is not well-characterized in the marine environment.
ESTHER : Weiner_2008_PLoS.Genet_4_e1000087
PubMedSearch : Weiner_2008_PLoS.Genet_4_e1000087
PubMedID: 18516288
Gene_locus related to this paper: sacd2-q21f03 , sacd2-q21l72 , sacd2-q21ms2 , sacd2-q21ll5

Title : Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility - Chain_2006_Proc.Natl.Acad.Sci.U.S.A_103_15280
Author(s) : Chain PS , Denef VJ , Konstantinidis KT , Vergez LM , Agullo L , Reyes VL , Hauser L , Cordova M , Gomez L , Gonzalez M , Land M , Lao V , Larimer F , LiPuma JJ , Mahenthiralingam E , Malfatti SA , Marx CJ , Parnell JJ , Ramette A , Richardson P , Seeger M , Smith D , Spilker T , Sul WJ , Tsoi TV , Ulrich LE , Zhulin IB , Tiedje JM
Ref : Proc Natl Acad Sci U S A , 103 :15280 , 2006
Abstract : Burkholderia xenovorans LB400 (LB400), a well studied, effective polychlorinated biphenyl-degrader, has one of the two largest known bacterial genomes and is the first nonpathogenic Burkholderia isolate sequenced. From an evolutionary perspective, we find significant differences in functional specialization between the three replicons of LB400, as well as a more relaxed selective pressure for genes located on the two smaller vs. the largest replicon. High genomic plasticity, diversity, and specialization within the Burkholderia genus are exemplified by the conservation of only 44% of the genes between LB400 and Burkholderia cepacia complex strain 383. Even among four B. xenovorans strains, genome size varies from 7.4 to 9.73 Mbp. The latter is largely explained by our findings that >20% of the LB400 sequence was recently acquired by means of lateral gene transfer. Although a range of genetic factors associated with in vivo survival and intercellular interactions are present, these genetic factors are likely related to niche breadth rather than determinants of pathogenicity. The presence of at least eleven "central aromatic" and twenty "peripheral aromatic" pathways in LB400, among the highest in any sequenced bacterial genome, supports this hypothesis. Finally, in addition to the experimentally observed redundancy in benzoate degradation and formaldehyde oxidation pathways, the fact that 17.6% of proteins have a better LB400 paralog than an ortholog in a different genome highlights the importance of gene duplication and repeated acquirement, which, coupled with their divergence, raises questions regarding the role of paralogs and potential functional redundancies in large-genome microbes.
ESTHER : Chain_2006_Proc.Natl.Acad.Sci.U.S.A_103_15280
PubMedSearch : Chain_2006_Proc.Natl.Acad.Sci.U.S.A_103_15280
PubMedID: 17030797
Gene_locus related to this paper: burxl-metx , burxl-mhpc , burxl-q13fa9 , burxl-q13ha0 , burxl-q13mn9 , burxl-q13nr6 , burxl-q13ns4 , burxl-q13p13 , burxl-q13p37 , burxl-q13pg5 , burxl-q13ph5 , burxl-q13pw2 , burxl-q13q15 , burxl-q13qw4 , burxl-q13ri3 , burxl-q13ui7 , burxl-q13ul9 , burxl-q13uz6 , burxl-q13vd6 , burxl-q13xg6 , burxl-q146l5 , burxl-q13u43 , parxl-hboh

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