-
1
-
-
0035853296
-
Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains
-
DOI 10.1006/jmbi.2001.4508
-
Anantharaman V, Koonin EV, Aravind L. (2001). Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains. J Mol Biol 307: 1271-1292. (Pubitemid 33027639)
-
(2001)
Journal of Molecular Biology
, vol.307
, Issue.5
, pp. 1271-1292
-
-
Anantharaman, V.1
Koonin, E.V.2
Aravind, L.3
-
2
-
-
0000756743
-
Carotenoid genetics and biochemistry
-
Cane DE (ed. Elsevier: Amsterdam, The Netherlands
-
Armstrong G. (1999). Carotenoid genetics and biochemistry. In: Cane DE (ed.). Isoprenoids Including Carotenoids and Steroids vol. 2. Elsevier: Amsterdam, The Netherlands. pp 321-352.
-
(1999)
Isoprenoids Including Carotenoids and Steroids
, vol.2
, pp. 321-352
-
-
Armstrong, G.1
-
3
-
-
0036183336
-
Chemical and catalytic mechanisms of carboxyl transfer reactions in biotindependent enzymes
-
Attwood PV, Wallace JC. (2002). Chemical and catalytic mechanisms of carboxyl transfer reactions in biotindependent enzymes. Acc Chem Res 35: 113-120.
-
(2002)
Acc Chem Res
, vol.35
, pp. 113-120
-
-
Attwood, P.V.1
Wallace, J.C.2
-
4
-
-
0034665853
-
Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea
-
Béjè O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP et al. (2000) Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea. Science 289, 1902-1906.
-
(2000)
Science
, vol.289
, pp. 1902-1906
-
-
Béjè, O.1
Aravind, L.2
Koonin, E.V.3
Suzuki, M.T.4
Hadd, A.5
Nguyen, L.P.6
-
5
-
-
0035859080
-
Proteorhodopsin phototrophy in the ocean
-
DOI 10.1038/35081051
-
Béjè O, Spudich EN, Spudich JL, Leclerc M, DeLong EF. (2001) Proteorhodopsin phototrophy in the ocean. Nature, 411, 786-789. (Pubitemid 32588098)
-
(2001)
Nature
, vol.411
, Issue.6839
, pp. 786-789
-
-
Beja, O.1
Spudich, E.N.2
Spudich, J.L.3
Leclerc, M.4
DeLong, E.F.5
-
6
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Statist Soc B 57: 289-300.
-
(1995)
J R Statist Soc B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
7
-
-
33745114416
-
Bacteriorhodopsin-like proteins of eubacteria and fungi: The extent of conservation of the haloarchaeal proton-pumping mechanism
-
DOI 10.1039/b514537f
-
Brown LS, Jung K-H. (2006). Bacteriorhodopsin-like proteins of eubacteria and fungi: The extent of conservation of the haloarchaeal proton-pumping mechanism. Photochem Photobiol Sci 5: 538-546. (Pubitemid 43885917)
-
(2006)
Photochemical and Photobiological Sciences
, vol.5
, Issue.6
, pp. 538-546
-
-
Brown, L.S.1
Jung, K.-H.2
-
8
-
-
0028485650
-
Molecular structure and enzymatic function of lycopene cyclase from the cyanobacterium Synechococcus sp strain PCC7942
-
Cunningham FX, Sun Z, Chamovitz D, Hirschberg J, Gantt E. (1994). Molecular structure and enzymatic function of lycopene cyclase from the cyanobacterium Synechococcus sp strain PCC7942. Plant Cell 6: 1107-1121.
-
(1994)
Plant Cell
, vol.6
, pp. 1107-1121
-
-
Cunningham, F.X.1
Sun, Z.2
Chamovitz, D.3
Hirschberg, J.4
Gantt, E.5
-
9
-
-
0242331634
-
Proteorhodopsin genes are distributed among divergent marine bacterial taxa
-
DOI 10.1073/pnas.2133554100
-
de la Torre JR, Christianson LM, Béjè O, Suzuki MT, Karl DM, Heidelberg J et al. (2003). Proteorhodopsin genes are distributed among divergent marine bacterial taxa. Proc Natl Acad Sci USA 100: 12830-12835. (Pubitemid 37339985)
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.22
, pp. 12830-12835
-
-
De La Torre, J.R.1
Christianson, L.M.2
Beja, O.3
Suzuki, M.T.4
Karl, D.M.5
Heidelberg, J.6
DeLong, E.F.7
-
10
-
-
66149119261
-
The microbial ocean from genomes to biomes
-
DeLong EF. (2009). The microbial ocean from genomes to biomes. Nature 459: 200-206.
-
(2009)
Nature
, vol.459
, pp. 200-206
-
-
DeLong, E.F.1
-
11
-
-
77951701764
-
Light-driven proton pump proteorhodopsin enhances bacterial survival during tough times
-
DeLong EF, Béjè O. (2010). Light-driven proton pump proteorhodopsin enhances bacterial survival during tough times. PLoS Biol 8.
-
(2010)
PLoS Biol
, vol.8
-
-
DeLong, E.F.1
Béjè, O.2
-
12
-
-
0032441150
-
Cluster analysis and display of genome-wide expression patterns
-
DOI 10.1073/pnas.95.25.14863
-
Eisen MB, Spellman PT, Brown PO, Botstein D. (1998). Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95: 14863-14868. (Pubitemid 29003722)
-
(1998)
Proceedings of the National Academy of Sciences of the United States of America
, vol.95
, Issue.25
, pp. 14863-14868
-
-
Eisen, M.B.1
Spellman, P.T.2
Brown, P.O.3
Botstein, D.4
-
13
-
-
32844465575
-
Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea
-
DOI 10.1038/nature04435, PII NATURE04435
-
Frigaard N-U, Martinez A, Mincer TJ, DeLong EF. (2006). Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea. Nature 439: 847-850. (Pubitemid 43255702)
-
(2006)
Nature
, vol.439
, Issue.7078
, pp. 847-850
-
-
Frigaard, N.-U.1
Martinez, A.2
Mincer, T.J.3
DeLong, E.F.4
-
14
-
-
72549115429
-
Phylogenetic and transcriptional analyses of a tetrachloroethene- dechlorinating 'Dehalococcoides' enrichment culture TUT2264 and its reductive-dehalogenase genes
-
Futamata H, Kaiya S, Sugawara M, Hiraishi A. (2009). Phylogenetic and transcriptional analyses of a tetrachloroethene-dechlorinating 'Dehalococcoides' enrichment culture TUT2264 and its reductive-dehalogenase genes. Microbes Environ 24: 330-337.
-
(2009)
Microbes Environ
, vol.24
, pp. 330-337
-
-
Futamata, H.1
Kaiya, S.2
Sugawara, M.3
Hiraishi, A.4
-
15
-
-
58149191274
-
Rfam: Updates to the RNA families database
-
Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S et al. (2009). Rfam: Updates to the RNA families database. Nucleic Acids Res 37: D136-D140.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Gardner, P.P.1
Daub, J.2
Tate, J.G.3
Nawrocki, E.P.4
Kolbe, D.L.5
Lindgreen, S.6
-
16
-
-
0035171382
-
Emerging views on tmRNA-mediated protein tagging and ribosome rescue
-
DOI 10.1046/j.1365-2958.2001.02701.x
-
Gillet R, Felden B. (2001). Emerging views on tmRNAmediated protein tagging and ribosome rescue. Mol Microbiol 42: 879-885. (Pubitemid 33078373)
-
(2001)
Molecular Microbiology
, vol.42
, Issue.4
, pp. 879-885
-
-
Gillet, R.1
Felden, B.2
-
17
-
-
27744438187
-
Proteorhodopsin in the ubiquitous marine bacterium SAR11
-
DOI 10.1038/nature04032, PII N04032
-
Giovannoni SJ, Bibbs L, Cho J-C, Stapels MD, Desiderio R, Vergin KL et al. (2005). Proteorhodopsin in the ubiquitous marine bacterium SAR11. Nature 438: 82-85. (Pubitemid 41599823)
-
(2005)
Nature
, vol.438
, Issue.7064
, pp. 82-85
-
-
Giovannoni, S.J.1
Bibbs, L.2
Cho, J.-C.3
Stapels, M.D.4
Desiderio, R.5
Vergin, K.L.6
Rappe, M.S.7
Laney, S.8
Wilhelm, L.J.9
Tripp, H.J.10
Mathur, E.J.11
Barofsky, D.F.12
-
18
-
-
0036804709
-
BLUF: A novel FAD-binding domain involved in sensory transduction in microorganisms
-
DOI 10.1016/S0968-0004(02)02181-3, PII S0968000402021813
-
Gomelsky M, Klug G. (2002). BLUF: A novel FAD-binding domain involved in sensory transduction in microorganisms. Trends Biochem Sci 27: 497-500. (Pubitemid 35279589)
-
(2002)
Trends in Biochemical Sciences
, vol.27
, Issue.10
, pp. 497-500
-
-
Gomelsky, M.1
Klug, G.2
-
19
-
-
77951706049
-
Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation
-
Gómez-Consarnau L, Akram N, Lindell K, Pedersen A, Neutze R, Milton DL et al. (2010). Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation. PLoS Biol 8: E1000358.
-
(2010)
PLoS Biol
, vol.8
-
-
Gómez-Consarnau, L.1
Akram, N.2
Lindell, K.3
Pedersen, A.4
Neutze, R.5
Milton, D.L.6
-
20
-
-
33846238031
-
Light stimulates growth of proteorhodopsin-containing marine Flavobacteria
-
DOI 10.1038/nature05381, PII NATURE05381
-
Gómez-Consarnau L, González JM, Coll-Lladó M, Gourdon P, Pascher T, Neutze R et al. (2007). Light stimulates growth of proteorhodopsin-containing marine Flavobacteria. Nature 445: 210-213. (Pubitemid 46095725)
-
(2007)
Nature
, vol.445
, Issue.7124
, pp. 210-213
-
-
Gomez-Consarnau, L.1
Gonzalez, J.M.2
Coll-Llado, M.3
Gourdon, P.4
Pascher, T.5
Neutze, R.6
Pedros-Alio, C.7
Pinhassi, J.8
-
21
-
-
47249148362
-
Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria)
-
DOI 10.1073/pnas.0712027105
-
González JM, Fernández-Gómez B, Fernèndez- Guerra A, Gómez-Consarnau L, Sánchez O, Coll-Lladó M et al. (2008). Genome analysis of the proteorhodopsincontaining marine bacterium Polaribacter sp. MED152 (Flavobacteria). Proc Natl Acad Sci USA 105: 8724-8729. (Pubitemid 351987747)
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, Issue.25
, pp. 8724-8729
-
-
Gonzalez, J.M.1
Fernandez-Gomez, B.2
Fernandez-Guerra, A.3
Gomez-Consarnau, L.4
Sanchez, O.5
Coll-Llado, M.6
Del Campo, J.7
Escudero, L.8
Rodriguez-Martinez, R.9
Alonso-Saez, L.10
Latasa, M.11
Paulsen, I.12
Nedashkovskaya, O.13
Lekunberri, I.14
Pinhassi, J.15
Pedros-Alio, C.16
-
23
-
-
3242719687
-
Phosphoenolpyruvate carboxylase: A new era of structural biology
-
DOI 10.1146/annurev.arplant.55.031903.141619
-
Izui K, Matsumura H, Furumoto T, Kai Y. (2004). Phosphoenolpyruvate carboxylase: A new era of structural biology. Annu Rev Plant Biol 55: 69-84. (Pubitemid 38940926)
-
(2004)
Annual Review of Plant Biology
, vol.55
, pp. 69-84
-
-
Izui, K.1
Matsumura, H.2
Furumoto, T.3
Kai, Y.4
-
24
-
-
48249150656
-
Structure, mechanism and regulation of pyruvate carboxylase
-
Jitrapakdee S, St Maurice M, Rayment I, Cleland WW, Wallace JC, Attwood PV. (2008). Structure, mechanism and regulation of pyruvate carboxylase. Biochem J 413: 369-387.
-
(2008)
Biochem J
, vol.413
, pp. 369-387
-
-
Jitrapakdee, S.1
St Maurice, M.2
Rayment, I.3
Cleland, W.W.4
Wallace, J.C.5
Attwood, P.V.6
-
25
-
-
53849117142
-
Biology of trans-translation
-
Keiler KC. (2008). Biology of trans-translation. Annu Rev Microbiol 62: 133-151.
-
(2008)
Annu Rev Microbiol
, vol.62
, pp. 133-151
-
-
Keiler, K.C.1
-
26
-
-
71249149524
-
Light-dependent growth and proteorhodopsin expression by Flavobacteria and SAR11 in experiments with Delaware coastal waters
-
Lami R, Cottrell MT, Campbell BJ, Kirchman DL. (2009). Light-dependent growth and proteorhodopsin expression by Flavobacteria and SAR11 in experiments with Delaware coastal waters. Environ Microbiol 11: 3201-3209.
-
(2009)
Environ Microbiol
, vol.11
, pp. 3201-3209
-
-
Lami, R.1
Cottrell, M.T.2
Campbell, B.J.3
Kirchman, D.L.4
-
27
-
-
34248151050
-
Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host
-
DOI 10.1073/pnas.0611470104
-
Martinez A, Bradley AS, Waldbauer JR, Summons RE, DeLong EF. (2007). Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host. Proc Natl Acad Sci USA 104: 5590-5595. (Pubitemid 47175725)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.13
, pp. 5590-5595
-
-
Martinez, A.1
Bradley, A.S.2
Waldbauer, J.R.3
Summons, R.E.4
DeLong, E.F.5
-
28
-
-
78049286743
-
Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea
-
McCarren J, Becker JW, Repeta DJ, Shi Y, Young CR, Malmstrom RR et al. (2010). Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. Proc Natl Acad Sci USA 107: 16420-16427.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 16420-16427
-
-
McCarren, J.1
Becker, J.W.2
Repeta, D.J.3
Shi, Y.4
Young, C.R.5
Malmstrom, R.R.6
-
29
-
-
33947101507
-
Proteorhodopsin photosystem gene clusters exhibit co-evolutionary trends and shared ancestry among diverse marine microbial phyla
-
DOI 10.1111/j.1462-2920.2006.01203.x
-
McCarren J, DeLong EF. (2007). Proteorhodopsin photosystem gene clusters exhibit co-evolutionary trends and shared ancestry among diverse marine microbial phyla. Environ Microbiol 9: 846-858. (Pubitemid 46397080)
-
(2007)
Environmental Microbiology
, vol.9
, Issue.4
, pp. 846-858
-
-
McCarren, J.1
DeLong, E.F.2
-
30
-
-
34247103448
-
The tmRNA system for translational surveillance and ribosome rescue
-
Moore SD, Sauer RT. (2007). The tmRNA system for translational surveillance and ribosome rescue. Annu Rev Biochem 76: 101-124.
-
(2007)
Annu Rev Biochem
, vol.76
, pp. 101-124
-
-
Moore, S.D.1
Sauer, R.T.2
-
31
-
-
34548725601
-
Resourceful heterotrophs make the most of light in the coastal ocean
-
DOI 10.1038/nrmicro1746, PII NRMICRO1746
-
Moran MA, Miller WL. (2007). Resourceful heterotrophs make the most of light in the coastal ocean. Nat Rev Microbiol 5: 792-800. (Pubitemid 47423767)
-
(2007)
Nature Reviews Microbiology
, vol.5
, Issue.10
, pp. 792-800
-
-
Moran, M.A.1
Miller, W.L.2
-
32
-
-
33646361583
-
GenePattern 2.0
-
Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP. (2006). GenePattern 2.0. Nat Genet 38: 500-501.
-
(2006)
Nat Genet
, vol.38
, pp. 500-501
-
-
Reich, M.1
Liefeld, T.2
Gould, J.3
Lerner, J.4
Tamayo, P.5
Mesirov, J.P.6
-
33
-
-
23944505538
-
New insights into metabolic properties of marine bacteria encoding proteorhodopsins
-
Sabehi G, Loy A, Jung KH, Partha R, Spudich JL, Isaacson T et al. (2005). New insights into metabolic properties of marine bacteria encoding proteorhodopsins. PLoS Biol 3: E273.
-
(2005)
PLoS Biol
, vol.3
-
-
Sabehi, G.1
Loy, A.2
Jung, K.H.3
Partha, R.4
Spudich, J.L.5
Isaacson, T.6
-
34
-
-
66149130975
-
Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column
-
Shi Y, Tyson GW, DeLong EF. (2009). Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature 459: 266-269.
-
(2009)
Nature
, vol.459
, pp. 266-269
-
-
Shi, Y.1
Tyson, G.W.2
DeLong, E.F.3
-
35
-
-
84889439782
-
Microbial rhodopsin: Phylogenetic and functional diversity
-
Briggs WR, Spudich JL (eds Wiley-VCH Verlag GmbH & Co KGaA: Weinheim, Germany
-
Spudich JL, Jung KH. (2005). Microbial rhodopsin: Phylogenetic and functional diversity. In: Briggs WR, Spudich JL (eds). Handbook of Photosensory Receptors. Wiley-VCH Verlag GmbH & Co KGaA: Weinheim, Germany. pp 1-24.
-
(2005)
Handbook of Photosensory Receptors.
, pp. 1-24
-
-
Spudich, J.L.1
Jung, K.H.2
-
36
-
-
77954086440
-
Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics
-
Stewart FJ, Ottesen EA, DeLong EF. (2010). Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics. ISME J 4: 896-907.
-
(2010)
ISME J
, vol.4
, pp. 896-907
-
-
Stewart, F.J.1
Ottesen, E.A.2
DeLong, E.F.3
-
37
-
-
34247488726
-
The SAR92 clade: An abundant coastal clade of culturable marine bacteria possessing proteorhodopsin
-
DOI 10.1128/AEM.02559-06
-
Stingl U, Desiderio RA, Cho J-C, Vergin KL, Giovannoni SJ. (2007). The SAR92 clade: An abundant coastal clade of culturable marine bacteria possessing proteorhodopsin. Appl Environ Microbiol 73: 2290-2296. (Pubitemid 46649521)
-
(2007)
Applied and Environmental Microbiology
, vol.73
, Issue.7
, pp. 2290-2296
-
-
Stingl, U.1
Desiderio, R.A.2
Cho, J.-C.3
Vergin, K.L.4
Giovannoni, S.J.5
-
39
-
-
0032990441
-
PAS domains: Internal sensors of oxygen, redox potential, and light
-
Taylor BL, Zhulin IB. (1999). PAS domains: Internal sensors of oxygen, redox potential, and light. Microbiol Mol Biol Rev 63: 479-506. (Pubitemid 29264980)
-
(1999)
Microbiology and Molecular Biology Reviews
, vol.63
, Issue.2
, pp. 479-506
-
-
Taylor, B.L.1
Zhulin, I.B.2
-
40
-
-
0020427791
-
+ pump in the marine bacterium vibrio alginolyticus
-
Tokuda H, Unemoto T. (1982). Characterization of the respiration- dependent Na+ pump in the marine bacterium Vibrio alginolyticus. J Biol Chem 257: 10007-10014. (Pubitemid 13250998)
-
(1982)
Journal of Biological Chemistry
, vol.257
, Issue.17
, pp. 10007-10014
-
-
Tokuda, H.1
Unemoto, T.2
-
41
-
-
33847770775
-
Light-powering Escherichia coli with proteorhodopsin
-
DOI 10.1073/pnas.0611035104
-
Walter JM, Greenfield D, Bustamante C, Liphardt J. (2007). Light-powering Escherichia coli with proteorhodopsin. Proc Natl Acad Sci USA 104: 2408-2412. (Pubitemid 46391410)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.7
, pp. 2408-2412
-
-
Walter, J.M.1
Greenfield, D.2
Bustamante, C.3
Liphardt, J.4
|