Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. MED134

Gonzalez JM, Pinhassi J, Fernández-Gómez B, Coll-Llado M, Gonzalez-Velazquez M, Puigbo P, Jaenicke S, Gomez-Consarnau L, Fernandez-Guerra A, Goesmann A, Pedros-Alio C (2011)
Applied and Environmental Microbiology 77(24): 8676-8686.

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Autor*in
Gonzalez, Jose M.; Pinhassi, Jarone; Fernández-Gómez, Beatriz; Coll-Llado, Montserrat; Gonzalez-Velazquez, Monica; Puigbo, Pere; Jaenicke, SebastianUniBi; Gomez-Consarnau, Laura; Fernandez-Guerra, Antoni; Goesmann, AlexanderUniBi ; Pedros-Alio, Carlos
Einrichtung
Centrum für Biotechnologie > Institut für Bioinformatik
Technische Fakultät > Computational Genomics
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Erscheinungsjahr
2011
Zeitschriftentitel
Applied and Environmental Microbiology
Band
77
Ausgabe
24
Seite(n)
8676-8686
ISSN
0099-2240
Page URI
https://pub.uni-bielefeld.de/record/2447730

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Gonzalez JM, Pinhassi J, Fernández-Gómez B, et al. Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. MED134. Applied and Environmental Microbiology. 2011;77(24):8676-8686.
Gonzalez, J. M., Pinhassi, J., Fernández-Gómez, B., Coll-Llado, M., Gonzalez-Velazquez, M., Puigbo, P., Jaenicke, S., et al. (2011). Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. MED134. Applied and Environmental Microbiology, 77(24), 8676-8686. doi:10.1128/aem.06152-11
Gonzalez, Jose M., Pinhassi, Jarone, Fernández-Gómez, Beatriz, Coll-Llado, Montserrat, Gonzalez-Velazquez, Monica, Puigbo, Pere, Jaenicke, Sebastian, et al. 2011. “Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. MED134”. Applied and Environmental Microbiology 77 (24): 8676-8686.
Gonzalez, J. M., Pinhassi, J., Fernández-Gómez, B., Coll-Llado, M., Gonzalez-Velazquez, M., Puigbo, P., Jaenicke, S., Gomez-Consarnau, L., Fernandez-Guerra, A., Goesmann, A., et al. (2011). Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. MED134. Applied and Environmental Microbiology 77, 8676-8686.
Gonzalez, J.M., et al., 2011. Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. MED134. Applied and Environmental Microbiology, 77(24), p 8676-8686.
J.M. Gonzalez, et al., “Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. MED134”, Applied and Environmental Microbiology, vol. 77, 2011, pp. 8676-8686.
Gonzalez, J.M., Pinhassi, J., Fernández-Gómez, B., Coll-Llado, M., Gonzalez-Velazquez, M., Puigbo, P., Jaenicke, S., Gomez-Consarnau, L., Fernandez-Guerra, A., Goesmann, A., Pedros-Alio, C.: Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. MED134. Applied and Environmental Microbiology. 77, 8676-8686 (2011).
Gonzalez, Jose M., Pinhassi, Jarone, Fernández-Gómez, Beatriz, Coll-Llado, Montserrat, Gonzalez-Velazquez, Monica, Puigbo, Pere, Jaenicke, Sebastian, Gomez-Consarnau, Laura, Fernandez-Guerra, Antoni, Goesmann, Alexander, and Pedros-Alio, Carlos. “Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. MED134”. Applied and Environmental Microbiology 77.24 (2011): 8676-8686.

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Daten bereitgestellt von Europe PubMed Central.

"Candidatus Thermonerobacter thiotrophicus," A Non-phototrophic Member of the Bacteroidetes/Chlorobi With Dissimilatory Sulfur Metabolism in Hot Spring Mat Communities.
Thiel V, Garcia Costas AM, Fortney NW, Martinez JN, Tank M, Roden EE, Boyd ES, Ward DM, Hanada S, Bryant DA., Front Microbiol 9(), 2018
PMID: 30687241
Solar-panel and parasol strategies shape the proteorhodopsin distribution pattern in marine Flavobacteriia.
Kumagai Y, Yoshizawa S, Nakajima Y, Watanabe M, Fukunaga T, Ogura Y, Hayashi T, Oshima K, Hattori M, Ikeuchi M, Kogure K, DeLong EF, Iwasaki W., ISME J 12(5), 2018
PMID: 29410487
Single-cell genomics based on Raman sorting reveals novel carotenoid-containing bacteria in the Red Sea.
Song Y, Kaster AK, Vollmers J, Song Y, Davison PA, Frentrup M, Preston GM, Thompson IP, Murrell JC, Yin H, Hunter CN, Huang WE., Microb Biotechnol 10(1), 2017
PMID: 27748032
Complete genome sequence of Lutibacter profundi LP1T isolated from an Arctic deep-sea hydrothermal vent system.
Wissuwa J, Bauer SL, Steen IH, Stokke R., Stand Genomic Sci 12(), 2017
PMID: 28078050
Microbial players and processes involved in phytoplankton bloom utilization in the water column of a fast-flowing, river-dominated estuary.
Smith MW, Herfort L, Fortunato CS, Crump BC, Simon HM., Microbiologyopen 6(4), 2017
PMID: 28318115
Comparative proteomics reveals signature metabolisms of exponentially growing and stationary phase marine bacteria.
Muthusamy S, Lundin D, Mamede Branca RM, Baltar F, González JM, Lehtiö J, Pinhassi J., Environ Microbiol 19(6), 2017
PMID: 28371138
Genome characteristics of the proteorhodopsin-containing marine flavobacterium Polaribacter dokdonensis DSW-5.
Yoon K, Song JY, Kwak MJ, Kwon SK, Kim JF., J Microbiol 55(7), 2017
PMID: 28432541
Evidence of microbial rhodopsins in Antarctic Dry Valley edaphic systems.
Guerrero LD, Vikram S, Makhalanyane TP, Cowan DA., Environ Microbiol 19(9), 2017
PMID: 28752953
Proteorhodopsin light-enhanced growth linked to vitamin-B1 acquisition in marine Flavobacteria.
Gómez-Consarnau L, González JM, Riedel T, Jaenicke S, Wagner-Döbler I, Sañudo-Wilhelmy SA, Fuhrman JA., ISME J 10(5), 2016
PMID: 26574687
Microbial Surface Colonization and Biofilm Development in Marine Environments.
Dang H, Lovell CR., Microbiol Mol Biol Rev 80(1), 2016
PMID: 26700108
Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology.
Pinhassi J, DeLong EF, Béjà O, González JM, Pedrós-Alió C., Microbiol Mol Biol Rev 80(4), 2016
PMID: 27630250
Prokaryotic Responses to Ammonium and Organic Carbon Reveal Alternative CO2 Fixation Pathways and Importance of Alkaline Phosphatase in the Mesopelagic North Atlantic.
Baltar F, Lundin D, Palovaara J, Lekunberri I, Reinthaler T, Herndl GJ, Pinhassi J., Front Microbiol 7(), 2016
PMID: 27818655
Niches of two polysaccharide-degrading Polaribacter isolates from the North Sea during a spring diatom bloom.
Xing P, Hahnke RL, Unfried F, Markert S, Huang S, Barbeyron T, Harder J, Becher D, Schweder T, Glöckner FO, Amann RI, Teeling H., ISME J 9(6), 2015
PMID: 25478683
Light-driven increase in carbon yield is linked to maintenance in the proteorhodopsin-containing Photobacterium angustum S14.
Courties A, Riedel T, Rapaport A, Lebaron P, Suzuki MT., Front Microbiol 6(), 2015
PMID: 26217320
The phylogenetic and ecological context of cultured and whole genome-sequenced planktonic bacteria from the coastal NW Mediterranean Sea.
Lekunberri I, Gasol JM, Acinas SG, Gómez-Consarnau L, Crespo BG, Casamayor EO, Massana R, Pedrós-Alió C, Pinhassi J., Syst Appl Microbiol 37(3), 2014
PMID: 24462268
Stimulation of growth by proteorhodopsin phototrophy involves regulation of central metabolic pathways in marine planktonic bacteria.
Palovaara J, Akram N, Baltar F, Bunse C, Forsberg J, Pedrós-Alió C, González JM, Pinhassi J., Proc Natl Acad Sci U S A 111(35), 2014
PMID: 25136122
Master recyclers: features and functions of bacteria associated with phytoplankton blooms.
Buchan A, LeCleir GR, Gulvik CA, González JM., Nat Rev Microbiol 12(10), 2014
PMID: 25134618
Bio-entrapped membrane reactor and salt marsh sediment membrane bioreactor for the treatment of pharmaceutical wastewater: treatment performance and microbial communities.
Ng KK, Shi X, Yao Y, Ng HY., Bioresour Technol 171(), 2014
PMID: 25203236
Comparative genomics of planktonic Flavobacteriaceae from the Gulf of Maine using metagenomic data.
Tully BJ, Sachdeva R, Heidelberg KB, Heidelberg JF., Microbiome 2(), 2014
PMID: 25258679
Structure-to-function relationships of bacterial translocator protein (TSPO): a focus on Pseudomonas.
Leneveu-Jenvrin C, Connil N, Bouffartigues E, Papadopoulos V, Feuilloley MG, Chevalier S., Front Microbiol 5(), 2014
PMID: 25477872
Genomic makeup of the marine flavobacterium Nonlabens (Donghaeana) dokdonensis and identification of a novel class of rhodopsins.
Kwon SK, Kim BK, Song JY, Kwak MJ, Lee CH, Yoon JH, Oh TK, Kim JF., Genome Biol Evol 5(1), 2013
PMID: 23292138
Ecology of marine Bacteroidetes: a comparative genomics approach.
Fernández-Gómez B, Richter M, Schüler M, Pinhassi J, Acinas SG, González JM, Pedrós-Alió C., ISME J 7(5), 2013
PMID: 23303374
Regulation of proteorhodopsin gene expression by nutrient limitation in the marine bacterium Vibrio sp. AND4.
Akram N, Palovaara J, Forsberg J, Lindh MV, Milton DL, Luo H, González JM, Pinhassi J., Environ Microbiol 15(5), 2013
PMID: 23379752
Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein.
Riedel T, Gómez-Consarnau L, Tomasch J, Martin M, Jarek M, González JM, Spring S, Rohlfs M, Brinkhoff T, Cypionka H, Göker M, Fiebig A, Klein J, Goesmann A, Fuhrman JA, Wagner-Döbler I., PLoS One 8(3), 2013
PMID: 23526944
The genome of the alga-associated marine flavobacterium Formosa agariphila KMM 3901T reveals a broad potential for degradation of algal polysaccharides.
Mann AJ, Hahnke RL, Huang S, Werner J, Xing P, Barbeyron T, Huettel B, Stüber K, Reinhardt R, Harder J, Glöckner FO, Amann RI, Teeling H., Appl Environ Microbiol 79(21), 2013
PMID: 23995932
Comparative genomic analysis indicates that niche adaptation of terrestrial Flavobacteria is strongly linked to plant glycan metabolism.
Kolton M, Sela N, Elad Y, Cytryn E., PLoS One 8(9), 2013
PMID: 24086761
Patterns and architecture of genomic islands in marine bacteria.
Fernández-Gómez B, Fernàndez-Guerra A, Casamayor EO, González JM, Pedrós-Alió C, Acinas SG., BMC Genomics 13(), 2012
PMID: 22839777

82 References

Daten bereitgestellt von Europe PubMed Central.

Application of comparative genomics in the identification and analysis of novel families of membrane-associated receptors in bacteria.
Anantharaman V, Aravind L., BMC Genomics 4(1), 2003
PMID: 12914674
Biochemical evidence that starch breakdown by Bacteroides thetaiotaomicron involves outer membrane starch-binding sites and periplasmic starch-degrading enzymes.
Anderson KL, Salyers AA., J. Bacteriol. 171(6), 1989
PMID: 2722747
Genetic evidence that outer membrane binding of starch is required for starch utilization by Bacteroides thetaiotaomicron.
Anderson KL, Salyers AA., J. Bacteriol. 171(6), 1989
PMID: 2722748
Whole genome analysis of the marine Bacteroidetes'Gramella forsetii' reveals adaptations to degradation of polymeric organic matter.
Bauer M, Kube M, Teeling H, Richter M, Lombardot T, Allers E, Wurdemann CA, Quast C, Kuhl H, Knaust F, Woebken D, Bischof K, Mussmann M, Choudhuri JV, Meyer F, Reinhardt R, Amann RI, Glockner FO., Environ. Microbiol. 8(12), 2006
PMID: 17107561
The marine Gram-negative eubacteria: genera , , , , and
Baumann P., Baumann L.., 1981
Bacterial rhodopsin: evidence for a new type of phototrophy in the sea.
Beja O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP, Jovanovich SB, Gates CM, Feldman RA, Spudich JL, Spudich EN, DeLong EF., Science 289(5486), 2000
PMID: 10988064
Plant carbohydrate scavenging through tonB-dependent receptors: a feature shared by phytopathogenic and aquatic bacteria.
Blanvillain S, Meyer D, Boulanger A, Lautier M, Guynet C, Denance N, Vasse J, Lauber E, Arlat M., PLoS ONE 2(2), 2007
PMID: 17311090
Relationship between operon preference and functional properties of persistent genes in bacterial genomes.
Bratlie MS, Johansen J, Drablos F., BMC Genomics 11(), 2010
PMID: 20109203
Flavobacterium johnsoniae gliding motility genes identified by mariner mutagenesis.
Braun TF, Khubbar MK, Saffarini DA, McBride MJ., J. Bacteriol. 187(20), 2005
PMID: 16199564
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics.
Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18838391
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.
Castresana J., Mol. Biol. Evol. 17(4), 2000
PMID: 10742046
Isolation and characterization of nonspreading mutants of the gliding bacterium Cytophaga johnsonae.
Chang LE, Pate JL, Betzig RJ., J. Bacteriol. 159(1), 1984
PMID: 6735983
Mutational analysis of the ompA promoter from Flavobacterium johnsoniae.
Chen S, Bagdasarian M, Kaufman MG, Bates AK, Walker ED., J. Bacteriol. 189(14), 2007
PMID: 17483221
Phylogenetic diversity of aggregate-attached versus free-living marine bacterial assemblages
DeLong E., Franks D., Alldredge A.., 1993
Trans-translation: the tmRNA-mediated surveillance mechanism for ribosome rescue, directed protein degradation, and nonstop mRNA decay.
Dulebohn D, Choy J, Sundermeier T, Okan N, Karzai AW., Biochemistry 46(16), 2007
PMID: 17397189
A probabilistic model of local sequence alignment that simplifies statistical significance estimation.
Eddy SR., PLoS Comput. Biol. 4(5), 2008
PMID: 18516236
Identification of an UP element consensus sequence for bacterial promoters.
Estrem ST, Gaal T, Ross W, Gourse RL., Proc. Natl. Acad. Sci. U.S.A. 95(17), 1998
PMID: 9707549
Proteorhodopsins: an array of physiological roles?
Fuhrman JA, Schwalbach MS, Stingl U., Nat. Rev. Microbiol. 6(6), 2008
PMID: 18475306
The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage.
Ganesan H, Rakitianskaia AS, Davenport CF, Tummler B, Reva ON., BMC Bioinformatics 9(), 2008
PMID: 18687122
GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences.
Gao F, Zhang CT., Nucleic Acids Res. 34(Web Server issue), 2006
PMID: 16845098
Proteorhodopsin in the ubiquitous marine bacterium SAR11.
Giovannoni SJ, Bibbs L, Cho JC, Stapels MD, Desiderio R, Vergin KL, Rappe MS, Laney S, Wilhelm LJ, Tripp HJ, Mathur EJ, Barofsky DF., Nature 438(7064), 2005
PMID: 16267553
A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes.
Goldberg SM, Johnson J, Busam D, Feldblyum T, Ferriera S, Friedman R, Halpern A, Khouri H, Kravitz SA, Lauro FM, Li K, Rogers YH, Strausberg R, Sutton G, Tallon L, Thomas T, Venter E, Frazier M, Venter JC., Proc. Natl. Acad. Sci. U.S.A. 103(30), 2006
PMID: 16840556
Light stimulates growth of proteorhodopsin-containing marine Flavobacteria.
Gomez-Consarnau L, Gonzalez JM, Coll-Llado M, Gourdon P, Pascher T, Neutze R, Pedros-Alio C, Pinhassi J., Nature 445(7124), 2007
PMID: 17215843
Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation.
Gomez-Consarnau L, Akram N, Lindell K, Pedersen A, Neutze R, Milton DL, Gonzalez JM, Pinhassi J., PLoS Biol. 8(4), 2010
PMID: 20436956
Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria).
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., Proc. Natl. Acad. Sci. U.S.A. 105(25), 2008
PMID: 18552178
Sodium ion cycle in bacterial pathogens: evidence from cross-genome comparisons.
Hase CC, Fedorova ND, Galperin MY, Dibrov PA., Microbiol. Mol. Biol. Rev. 65(3), 2001
PMID: 11528000
Heme uptake by Microscilla marina and evidence for heme uptake systems in the genomes of diverse marine bacteria.
Hopkinson BM, Roe KL, Barbeau KA., Appl. Environ. Microbiol. 74(20), 2008
PMID: 18757577
Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy.
Hou S, Saw JH, Lee KS, Freitas TA, Belisle C, Kawarabayasi Y, Donachie SP, Pikina A, Galperin MY, Koonin EV, Makarova KS, Omelchenko MV, Sorokin A, Wolf YI, Li QX, Keum YS, Campbell S, Denery J, Aizawa S, Shibata S, Malahoff A, Alam M., Proc. Natl. Acad. Sci. U.S.A. 101(52), 2004
PMID: 15596722
Enhancement of survival and electricity production in an engineered bacterium by light-driven proton pumping.
Johnson ET, Baron DB, Naranjo B, Bond DR, Schmidt-Dannert C, Gralnick JA., Appl. Environ. Microbiol. 76(13), 2010
PMID: 20453141
Prediction of lipoprotein signal peptides in Gram-negative bacteria.
Juncker AS, Willenbrock H, Von Heijne G, Brunak S, Nielsen H, Krogh A., Protein Sci. 12(8), 2003
PMID: 12876315
Predicted highly expressed genes of diverse prokaryotic genomes.
Karlin S, Mrazek J., J. Bacteriol. 182(18), 2000
PMID: 10960111
Characterizations of highly expressed genes of four fast-growing bacteria.
Karlin S, Mrazek J, Campbell A, Kaiser D., J. Bacteriol. 183(17), 2001
PMID: 11489855
Genomic and proteomic comparisons between bacterial and archaeal genomes and related comparisons with the yeast and fly genomes.
Karlin S, Brocchieri L, Campbell A, Cyert M, Mrazek J., Proc. Natl. Acad. Sci. U.S.A. 102(20), 2005
PMID: 15883367
Light-induced transcriptional responses associated with proteorhodopsin-enhanced growth in a marine flavobacterium
Kimura H., Young C., Martinez A., DeLong E.., 2011
Complete genome sequences of Krokinobacter sp. strain 4H-3-7-5 and Lacinutrix sp. strain 5H-3-7-4, polysaccharide-degrading members of the family Flavobacteriaceae.
Klippel B, Lochner A, Bruce DC, Davenport KW, Detter C, Goodwin LA, Han J, Han S, Hauser L, Land ML, Nolan M, Ovchinnikova G, Pennacchio L, Pitluck S, Tapia R, Woyke T, Wiebusch S, Basner A, Abe F, Horikoshi K, Keller M, Antranikian G., J. Bacteriol. 193(17), 2011
PMID: 21725025
Bioenergetics of marine bacteria.
Kogure K., Curr. Opin. Biotechnol. 9(3), 1998
PMID: 9650273
Versatile and open software for comparing large genomes.
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL., Genome Biol. 5(2), 2004
PMID: 14759262
Light-dependent growth and proteorhodopsin expression by Flavobacteria and SAR11 in experiments with Delaware coastal waters.
Lami R, Cottrell MT, Campbell BJ, Kirchman DL., Environ. Microbiol. 11(12), 2009
PMID: 19691506
Salt-dependent properties of proteins from extremely halophilic bacteria.
Lanyi JK., Bacteriol Rev 38(3), 1974
PMID: 4607500
Clustal W and Clustal X version 2.0.
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG., Bioinformatics 23(21), 2007
PMID: 17846036
Gene context conservation of a higher order than operons.
Lathe WC 3rd, Snel B, Bork P., Trends Biochem. Sci. 25(10), 2000
PMID: 11050428
Gene organization: selection, selfishness, and serendipity.
Lawrence JG., Annu. Rev. Microbiol. 57(), 2003
PMID: 14527286
Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host.
Martinez A, Bradley AS, Waldbauer JR, Summons RE, DeLong EF., Proc. Natl. Acad. Sci. U.S.A. 104(13), 2007
PMID: 17372221
Bacterial gliding motility: multiple mechanisms for cell movement over surfaces.
McBride MJ., Annu. Rev. Microbiol. 55(), 2001
PMID: 11544349
Cytophaga-flavobacterium gliding motility.
McBride MJ., J. Mol. Microbiol. Biotechnol. 7(1-2), 2004
PMID: 15170404
Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis.
McBride MJ, Xie G, Martens EC, Lapidus A, Henrissat B, Rhodes RG, Goltsman E, Wang W, Xu J, Hunnicutt DW, Staroscik AM, Hoover TR, Cheng YQ, Stein JL., Appl. Environ. Microbiol. 75(21), 2009
PMID: 19717629
In a class of its own--the RNA polymerase sigma factor sigma 54 (sigma N).
Merrick MJ., Mol. Microbiol. 10(5), 1993
PMID: 7934866
GenDB--an open source genome annotation system for prokaryote genomes.
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A., Nucleic Acids Res. 31(8), 2003
PMID: 12682369
Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction.
Morris RM, Nunn BL, Frazar C, Goodlett DR, Ting YS, Rocap G., ISME J 4(5), 2010
PMID: 20164862
SprB is a cell surface component of the Flavobacterium johnsoniae gliding motility machinery.
Nelson SS, Bollampalli S, McBride MJ., J. Bacteriol. 190(8), 2008
PMID: 18281397
Use and misuse of correspondence analysis in codon usage studies.
Perriere G, Thioulouse J., Nucleic Acids Res. 30(20), 2002
PMID: 12384602
Changes in bacterioplankton composition under different phytoplankton regimens.
Pinhassi J, Sala MM, Havskum H, Peters F, Guadayol O, Malits A, Marrase C., Appl. Environ. Microbiol. 70(11), 2004
PMID: 15528542
Anoxic aggregates-an ephemeral phenomenon in the pelagic environment?
Ploug H., Kühl M., Buchholz-Cleven B., Jørgensen B.., 1997
Nucleotide sequence of the ribosomal protein gene cluster adjacent to the gene for RNA polymerase subunit beta in Escherichia coli.
Post LE, Strycharz GD, Nomura M, Lewis H, Dennis PP., Proc. Natl. Acad. Sci. U.S.A. 76(4), 1979
PMID: 377281
Genes for a microaerobically induced oxidase complex in Bradyrhizobium japonicum are essential for a nitrogen-fixing endosymbiosis.
Preisig O, Anthamatten D, Hennecke H., Proc. Natl. Acad. Sci. U.S.A. 90(8), 1993
PMID: 8386371
HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection.
Puigbo P, Romeu A, Garcia-Vallve S., Nucleic Acids Res. 36(Database issue), 2007
PMID: 17933767
OPTIMIZER: a web server for optimizing the codon usage of DNA sequences.
Puigbo P, Guzman E, Romeu A, Garcia-Vallve S., Nucleic Acids Res. 35(Web Server issue), 2007
PMID: 17439967
The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation.
Qin QL, Zhang XY, Wang XM, Liu GM, Chen XL, Xie BB, Dang HY, Zhou BC, Yu J, Zhang YZ., BMC Genomics 11(), 2010
PMID: 20398413
MEROPS: the peptidase database.
Rawlings ND, Barrett AJ, Bateman A., Nucleic Acids Res. 38(Database issue), 2009
PMID: 19892822
Constitutive expression of the proteorhodopsin gene by a flavobacterium strain representative of the proteorhodopsin-producing microbial community in the North Sea.
Riedel T, Tomasch J, Buchholz I, Jacobs J, Kollenberg M, Gerdts G, Wichels A, Brinkhoff T, Cypionka H, Wagner-Dobler I., Appl. Environ. Microbiol. 76(10), 2010
PMID: 20305030
Dynamics of bacterial community composition and activity during a mesocosm diatom bloom.
Riemann L, Steward GF, Azam F., Appl. Environ. Microbiol. 66(2), 2000
PMID: 10653721
Connected gene neighborhoods in prokaryotic genomes.
Rogozin IB, Makarova KS, Murvai J, Czabarka E, Wolf YI, Tatusov RL, Szekely LA, Koonin EV., Nucleic Acids Res. 30(10), 2002
PMID: 12000841
Conjugative transposons: an unusual and diverse set of integrated gene transfer elements.
Salyers AA, Shoemaker NB, Stevens AM, Li LY., Microbiol. Rev. 59(4), 1995
PMID: 8531886
The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.
Sharp PM, Li WH., Nucleic Acids Res. 15(3), 1987
PMID: 3547335
Microbial ecology of organic aggregates in aquatic ecosystems
Simon M., Grossart H., Schweitzer B., Ploug H.., 2002
Discovering functional novelty in metagenomes: examples from light-mediated processes.
Singh AH, Doerks T, Letunic I, Raes J, Bork P., J. Bacteriol. 191(1), 2008
PMID: 18849420
Genetic elements of Bacteroides species: a moving story.
Smith CJ, Tribble GD, Bayley DP., Plasmid 40(1), 1998
PMID: 9657930
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.
Stamatakis A., Bioinformatics 22(21), 2006
PMID: 16928733
Energy starved Candidatus Pelagibacter ubique substitutes light-mediated ATP production for endogenous carbon respiration.
Steindler L, Schwalbach MS, Smith DP, Chan F, Giovannoni SJ., PLoS ONE 6(5), 2011
PMID: 21573025
Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time.
Stepanauskas R, Sieracki ME., Proc. Natl. Acad. Sci. U.S.A. 104(21), 2007
PMID: 17502618
The SAR92 clade: an abundant coastal clade of culturable marine bacteria possessing proteorhodopsin.
Stingl U, Desiderio RA, Cho JC, Vergin KL, Giovannoni SJ., Appl. Environ. Microbiol. 73(7), 2007
PMID: 17293499
Carbohydrate metabolism and carbon fixation in Roseobacter denitrificans OCh114.
Tang KH, Feng X, Tang YJ, Blankenship RE., PLoS ONE 4(10), 2009
PMID: 19794911
Photosensing in chemotrophic, non-phototrophic bacteria: let there be light sensing too.
van der Horst MA, Key J, Hellingwerf KJ., Trends Microbiol. 15(12), 2007
PMID: 18024131
Environmental genome shotgun sequencing of the Sargasso Sea.
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO., Science 304(5667), 2004
PMID: 15001713
Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models.
Waack S, Keller O, Asper R, Brodag T, Damm C, Fricke WF, Surovcik K, Meinicke P, Merkl R., BMC Bioinformatics 7(), 2006
PMID: 16542435
Utilization of iron/organic ligand complexes by marine bacterioplankton
Weaver R., Kirchman D., Hutchins D.., 2003
Assembling the marine metagenome, one cell at a time.
Woyke T, Xie G, Copeland A, Gonzalez JM, Han C, Kiss H, Saw JH, Senin P, Yang C, Chatterji S, Cheng JF, Eisen JA, Sieracki ME, Stepanauskas R., PLoS ONE 4(4), 2009
PMID: 19390573
Genome sequence of the cellulolytic gliding bacterium Cytophaga hutchinsonii.
Xie G, Bruce DC, Challacombe JF, Chertkov O, Detter JC, Gilna P, Han CS, Lucas S, Misra M, Myers GL, Richardson P, Tapia R, Thayer N, Thompson LS, Brettin TS, Henrissat B, Wilson DB, McBride MJ., Appl. Environ. Microbiol. 73(11), 2007
PMID: 17400776
Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont
Xu Q.., 2010
PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.
Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, Dao P, Sahinalp SC, Ester M, Foster LJ, Brinkman FS., Bioinformatics 26(13), 2010
PMID: 20472543
Segmentation algorithm for DNA sequences
Zhang C.-T., Gao F., Zhang R.., 2005
Photoheterotrophy in marine prokaryotes
Zubkov M.., 2009
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