Feldman RA

References (3)

Title : Comparative genomics of DNA fragments from six Antarctic marine planktonic bacteria - Grzymski_2006_Appl.Environ.Microbiol_72_1532
Author(s) : Grzymski JJ , Carter BJ , DeLong EF , Feldman RA , Ghadiri A , Murray AE
Ref : Applied Environmental Microbiology , 72 :1532 , 2006
Abstract : Six environmental fosmid clones from Antarctic coastal water bacterioplankton were completely sequenced. The genome fragments harbored small-subunit rRNA genes that were between 85 and 91% similar to those of their nearest cultivated relatives. The six fragments span four phyla, including the Gemmatimonadetes, Proteobacteria (alpha and gamma), Bacteroidetes, and high-G+C gram-positive bacteria. Gene-finding and annotation analyses identified 244 total open reading frames. Amino acid comparisons of 123 and 113 Antarctic bacterial amino acid sequences to mesophilic homologs from G+C-specific and SwissProt/UniProt databases, respectively, revealed widespread adaptation to the cold. The most significant changes in these Antarctic bacterial protein sequences included a reduction in salt-bridge-forming residues such as arginine, glutamic acid, and aspartic acid, reduced proline contents, and a reduction in stabilizing hydrophobic clusters. Stretches of disordered amino acids were significantly longer in the Antarctic sequences than in the mesophilic sequences. These characteristics were not specific to any one phylum, COG role category, or G+C content and imply that underlying genotypic and biochemical adaptations to the cold are inherent to life in the permanently subzero Antarctic waters.
ESTHER : Grzymski_2006_Appl.Environ.Microbiol_72_1532
PubMedSearch : Grzymski_2006_Appl.Environ.Microbiol_72_1532
PubMedID: 16461708
Gene_locus related to this paper: 9bact-q2py51

Title : Bacterial rhodopsin: evidence for a new type of phototrophy in the sea - Beja_2000_Science_289_1902
Author(s) : Beja O , Aravind L , Koonin EV , Suzuki MT , Hadd A , Nguyen LP , Jovanovich SB , Gates CM , Feldman RA , Spudich JL , Spudich EN , DeLong EF
Ref : Science , 289 :1902 , 2000
Abstract : Extremely halophilic archaea contain retinal-binding integral membrane proteins called bacteriorhodopsins that function as light-driven proton pumps. So far, bacteriorhodopsins capable of generating a chemiosmotic membrane potential in response to light have been demonstrated only in halophilic archaea. We describe here a type of rhodopsin derived from bacteria that was discovered through genomic analyses of naturally occuring marine bacterioplankton. The bacterial rhodopsin was encoded in the genome of an uncultivated gamma-proteobacterium and shared highest amino acid sequence similarity with archaeal rhodopsins. The protein was functionally expressed in Escherichia coli and bound retinal to form an active, light-driven proton pump. The new rhodopsin exhibited a photochemical reaction cycle with intermediates and kinetics characteristic of archaeal proton-pumping rhodopsins. Our results demonstrate that archaeal-like rhodopsins are broadly distributed among different taxa, including members of the domain Bacteria. Our data also indicate that a previously unsuspected mode of bacterially mediated light-driven energy generation may commonly occur in oceanic surface waters worldwide.
ESTHER : Beja_2000_Science_289_1902
PubMedSearch : Beja_2000_Science_289_1902
PubMedID: 10988064
Gene_locus related to this paper: bacte-AF279106.13 , prb01-lipas , prb01-Q9F7Q5

Title : The complete genome of the hyperthermophilic bacterium Aquifex aeolicus - Deckert_1998_Nature_392_353
Author(s) : Deckert G , Warren PV , Gaasterland T , Young WG , Lenox AL , Graham DE , Overbeek R , Snead MA , Keller M , Aujay M , Huber R , Feldman RA , Short JM , Olsen GJ , Swanson RV
Ref : Nature , 392 :353 , 1998
Abstract : Aquifex aeolicus was one of the earliest diverging, and is one of the most thermophilic, bacteria known. It can grow on hydrogen, oxygen, carbon dioxide, and mineral salts. The complex metabolic machinery needed for A. aeolicus to function as a chemolithoautotroph (an organism which uses an inorganic carbon source for biosynthesis and an inorganic chemical energy source) is encoded within a genome that is only one-third the size of the E. coli genome. Metabolic flexibility seems to be reduced as a result of the limited genome size. The use of oxygen (albeit at very low concentrations) as an electron acceptor is allowed by the presence of a complex respiratory apparatus. Although this organism grows at 95 degrees C, the extreme thermal limit of the Bacteria, only a few specific indications of thermophily are apparent from the genome. Here we describe the complete genome sequence of 1,551,335 base pairs of this evolutionarily and physiologically interesting organism.
ESTHER : Deckert_1998_Nature_392_353
PubMedSearch : Deckert_1998_Nature_392_353
PubMedID: 9537320
Gene_locus related to this paper: aquae-AQ.1571 , aquae-aq327 , aquae-aq2138 , aquae-dlhh