Finding approximate gene clusters with GECKO 3
Winter S, Jahn K, Wehner S, Kuchenbecker L, Marz M, Stoye J, Böcker S (2016)
Nucleic Acids Research 44(20): 9600-9610.
Zeitschriftenaufsatz
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Autor*in
Winter, Sascha;
Jahn, Katharina;
Wehner, Stefanie;
Kuchenbecker, Leon;
Marz, Manja;
Stoye, JensUniBi ;
Böcker, Sebastian
Einrichtung
Abstract / Bemerkung
Gene-order-based comparison of multiple genomes provides signals for functional analysis of genes and the evolutionary process of genome organization. Gene clusters are regions of co-localized genes on genomes of different species. The rapid increase in sequenced genomes necessitates bioinformatics tools for finding gene clusters in hundreds of genomes. Existing tools are often restricted to few (in many cases, only two) genomes, and often make restrictive assumptions such as short perfect conservation, conserved gene order or monophyletic gene clusters. We present Gecko 3, an open-source software for finding gene clusters in hundreds of bacterial genomes, that comes with an easy-to-use graphical user interface. The underlying gene cluster model is intuitive, can cope with low degrees of conservation as well as misannotations and is complemented by a sound statistical evaluation. To evaluate the biological benefit of Gecko 3 and to exemplify our method, we search for gene clusters in a dataset of 678 bacterial genomes using Synechocystis sp. PCC 6803 as a reference. We confirm detected gene clusters reviewing the literature and comparing them to a database of operons; we detect two novel clusters, which were confirmed by publicly available experimental RNA-Seq data. The computational analysis is carried out on a laptop computer in <40 min.
Erscheinungsjahr
2016
Zeitschriftentitel
Nucleic Acids Research
Band
44
Ausgabe
20
Seite(n)
9600-9610
Urheberrecht / Lizenzen
ISSN
0305-1048
eISSN
1362-4962
Page URI
https://pub.uni-bielefeld.de/record/2905930
Zitieren
Winter S, Jahn K, Wehner S, et al. Finding approximate gene clusters with GECKO 3. Nucleic Acids Research. 2016;44(20):9600-9610.
Winter, S., Jahn, K., Wehner, S., Kuchenbecker, L., Marz, M., Stoye, J., & Böcker, S. (2016). Finding approximate gene clusters with GECKO 3. Nucleic Acids Research, 44(20), 9600-9610. doi:10.1093/nar/gkw843
Winter, Sascha, Jahn, Katharina, Wehner, Stefanie, Kuchenbecker, Leon, Marz, Manja, Stoye, Jens, and Böcker, Sebastian. 2016. “Finding approximate gene clusters with GECKO 3”. Nucleic Acids Research 44 (20): 9600-9610.
Winter, S., Jahn, K., Wehner, S., Kuchenbecker, L., Marz, M., Stoye, J., and Böcker, S. (2016). Finding approximate gene clusters with GECKO 3. Nucleic Acids Research 44, 9600-9610.
Winter, S., et al., 2016. Finding approximate gene clusters with GECKO 3. Nucleic Acids Research, 44(20), p 9600-9610.
S. Winter, et al., “Finding approximate gene clusters with GECKO 3”, Nucleic Acids Research, vol. 44, 2016, pp. 9600-9610.
Winter, S., Jahn, K., Wehner, S., Kuchenbecker, L., Marz, M., Stoye, J., Böcker, S.: Finding approximate gene clusters with GECKO 3. Nucleic Acids Research. 44, 9600-9610 (2016).
Winter, Sascha, Jahn, Katharina, Wehner, Stefanie, Kuchenbecker, Leon, Marz, Manja, Stoye, Jens, and Böcker, Sebastian. “Finding approximate gene clusters with GECKO 3”. Nucleic Acids Research 44.20 (2016): 9600-9610.
Daten bereitgestellt von European Bioinformatics Institute (EBI)
2 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
Modules of co-occurrence in the cyanobacterial pan-genome reveal functional associations between groups of ortholog genes.
Beck C, Knoop H, Steuer R., PLoS Genet 14(3), 2018
PMID: 29522508
Beck C, Knoop H, Steuer R., PLoS Genet 14(3), 2018
PMID: 29522508
GraphTeams: a method for discovering spatial gene clusters in Hi-C sequencing data.
Schulz T, Stoye J, Doerr D., BMC Genomics 19(suppl 5), 2018
PMID: 29745835
Schulz T, Stoye J, Doerr D., BMC Genomics 19(suppl 5), 2018
PMID: 29745835
87 References
Daten bereitgestellt von Europe PubMed Central.
Synteny and collinearity in plant genomes.
Tang H, Bowers JE, Wang X, Ming R, Alam M, Paterson AH., Science 320(5875), 2008
PMID: 18436778
Tang H, Bowers JE, Wang X, Ming R, Alam M, Paterson AH., Science 320(5875), 2008
PMID: 18436778
The use of gene clusters to infer functional coupling.
Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N., Proc. Natl. Acad. Sci. U.S.A. 96(6), 1999
PMID: 10077608
Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N., Proc. Natl. Acad. Sci. U.S.A. 96(6), 1999
PMID: 10077608
Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context.
Wolf YI, Rogozin IB, Kondrashov AS, Koonin EV., Genome Res. 11(3), 2001
PMID: 11230160
Wolf YI, Rogozin IB, Kondrashov AS, Koonin EV., Genome Res. 11(3), 2001
PMID: 11230160
Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs.
Korbel JO, Jensen LJ, von Mering C, Bork P., Nat. Biotechnol. 22(7), 2004
PMID: 15229555
Korbel JO, Jensen LJ, von Mering C, Bork P., Nat. Biotechnol. 22(7), 2004
PMID: 15229555
Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina).
Schwartze VU, Winter S, Shelest E, Marcet-Houben M, Horn F, Wehner S, Linde J, Valiante V, Sammeth M, Riege K, Nowrousian M, Kaerger K, Jacobsen ID, Marz M, Brakhage AA, Gabaldon T, Bocker S, Voigt K., PLoS Genet. 10(8), 2014
PMID: 25121733
Schwartze VU, Winter S, Shelest E, Marcet-Houben M, Horn F, Wehner S, Linde J, Valiante V, Sammeth M, Riege K, Nowrousian M, Kaerger K, Jacobsen ID, Marz M, Brakhage AA, Gabaldon T, Bocker S, Voigt K., PLoS Genet. 10(8), 2014
PMID: 25121733
Fast algorithms to enumerate all common intervals of two permutations
Uno T., Yagiura M.., 2000
Uno T., Yagiura M.., 2000
Algorithms for finding gene clusters
Heber S., Stoye J.., 2001
Heber S., Stoye J.., 2001
The algorithmic of gene teams
Bergeron A., Corteel S., Raffinot M.., 2002
Bergeron A., Corteel S., Raffinot M.., 2002
The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice.
Vandepoele K, Saeys Y, Simillion C, Raes J, Van De Peer Y., Genome Res. 12(11), 2002
PMID: 12421767
Vandepoele K, Saeys Y, Simillion C, Raes J, Van De Peer Y., Genome Res. 12(11), 2002
PMID: 12421767
Common intervals of two sequences
Didier G.., 2003
Didier G.., 2003
Fast identification and statistical evaluation of segmental homologies in comparative maps.
Calabrese PP, Chakravarty S, Vision TJ., Bioinformatics 19 Suppl 1(), 2003
PMID: 12855440
Calabrese PP, Chakravarty S, Vision TJ., Bioinformatics 19 Suppl 1(), 2003
PMID: 12855440
DAGchainer: a tool for mining segmental genome duplications and synteny.
Haas BJ, Delcher AL, Wortman JR, Salzberg SL., Bioinformatics 20(18), 2004
PMID: 15247098
Haas BJ, Delcher AL, Wortman JR, Salzberg SL., Bioinformatics 20(18), 2004
PMID: 15247098
Building genomic profiles for uncovering segmental homology in the twilight zone.
Simillion C, Vandepoele K, Saeys Y, Van de Peer Y., Genome Res. 14(6), 2004
PMID: 15173115
Simillion C, Vandepoele K, Saeys Y, Van de Peer Y., Genome Res. 14(6), 2004
PMID: 15173115
Identifying conserved gene clusters in the presence of homology families
He X., Goldwasser M.H.., 2005
He X., Goldwasser M.H.., 2005
Identification of genomic features using microsyntenies of domains: domain teams.
Pasek S, Bergeron A, Risler JL, Louis A, Ollivier E, Raffinot M., Genome Res. 15(6), 2005
PMID: 15899966
Pasek S, Bergeron A, Risler JL, Louis A, Ollivier E, Raffinot M., Genome Res. 15(6), 2005
PMID: 15899966
Gene teams with relaxed proximity constraint
Kim S., Choi J.-H., Yang J.., 2005
Kim S., Choi J.-H., Yang J.., 2005
Syntons, metabolons and interactons: an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data.
Boyer F, Morgat A, Labarre L, Pothier J, Viari A., Bioinformatics 21(23), 2005
PMID: 16216829
Boyer F, Morgat A, Labarre L, Pothier J, Viari A., Bioinformatics 21(23), 2005
PMID: 16216829
Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice.
Wang X, Shi X, Li Z, Zhu Q, Kong L, Tang W, Ge S, Luo J., BMC Bioinformatics 7(), 2006
PMID: 17038171
Wang X, Shi X, Li Z, Zhu Q, Kong L, Tang W, Ge S, Luo J., BMC Bioinformatics 7(), 2006
PMID: 17038171
Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms.
Sinha AU, Meller J., BMC Bioinformatics 8(), 2007
PMID: 17343765
Sinha AU, Meller J., BMC Bioinformatics 8(), 2007
PMID: 17343765
Gecko and GhostFam—rigorous and efficient gene cluster detection in prokaryotic genomes
Schmidt T., Stoye J.., 2007
Schmidt T., Stoye J.., 2007
Efficiently identifying max-gap clusters in pairwise genome comparison.
Ling X, He X, Xin D, Han J, Han J., J. Comput. Biol. 15(6), 2008
PMID: 18631023
Ling X, He X, Xin D, Han J, Han J., J. Comput. Biol. 15(6), 2008
PMID: 18631023
Detecting gene clusters under evolutionary constraint in a large number of genomes.
Ling X, He X, Xin D., Bioinformatics 25(5), 2009
PMID: 19158161
Ling X, He X, Xin D., Bioinformatics 25(5), 2009
PMID: 19158161
Syntenator: multiple gene order alignments with a gene-specific scoring function.
Rodelsperger C, Dieterich C., Algorithms Mol Biol 3(), 2008
PMID: 18990215
Rodelsperger C, Dieterich C., Algorithms Mol Biol 3(), 2008
PMID: 18990215
CYNTENATOR: progressive gene order alignment of 17 vertebrate genomes.
Rodelsperger C, Dieterich C., PLoS ONE 5(1), 2010
PMID: 20126624
Rodelsperger C, Dieterich C., PLoS ONE 5(1), 2010
PMID: 20126624
Bacterial syntenies: an exact approach with gene quorum.
Denielou YP, Sagot MF, Boyer F, Viari A., BMC Bioinformatics 12(), 2011
PMID: 21605461
Denielou YP, Sagot MF, Boyer F, Viari A., BMC Bioinformatics 12(), 2011
PMID: 21605461
i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets.
Proost S, Fostier J, De Witte D, Dhoedt B, Demeester P, Van de Peer Y, Vandepoele K., Nucleic Acids Res. 40(2), 2011
PMID: 22102584
Proost S, Fostier J, De Witte D, Dhoedt B, Demeester P, Van de Peer Y, Vandepoele K., Nucleic Acids Res. 40(2), 2011
PMID: 22102584
Identifying gene clusters by discovering common intervals in indeterminate strings
Doerr D., Stoye J., Böcker S., Jahn K.., 2014
Doerr D., Stoye J., Böcker S., Jahn K.., 2014
Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
Partitioning biological data with transitivity clustering.
Wittkop T, Emig D, Lange S, Rahmann S, Albrecht M, Morris JH, Bocker S, Stoye J, Baumbach J., Nat. Methods 7(6), 2010
PMID: 20508635
Wittkop T, Emig D, Lange S, Rahmann S, Albrecht M, Morris JH, Bocker S, Stoye J, Baumbach J., Nat. Methods 7(6), 2010
PMID: 20508635
Computation of median gene clusters.
Bocker S, Jahn K, Mixtacki J, Stoye J., J. Comput. Biol. 16(8), 2009
PMID: 19689215
Bocker S, Jahn K, Mixtacki J, Stoye J., J. Comput. Biol. 16(8), 2009
PMID: 19689215
Efficient computation of approximate gene clusters based on reference occurrences.
Jahn K., J. Comput. Biol. 18(9), 2011
PMID: 21899430
Jahn K., J. Comput. Biol. 18(9), 2011
PMID: 21899430
Jahn K.., 2010
Statistics for approximate gene clusters
Jahn K., Winter S., Stoye J., Böcker S.., 2013
Jahn K., Winter S., Stoye J., Böcker S.., 2013
Controlling the false discovery rate: a practical and powerful approach to multiple testing
Benjamini Y., Hochberg Y.., 1995
Benjamini Y., Hochberg Y.., 1995
STRING v9.1: protein-protein interaction networks, with increased coverage and integration.
Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ., Nucleic Acids Res. 41(Database issue), 2012
PMID: 23203871
Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ., Nucleic Acids Res. 41(Database issue), 2012
PMID: 23203871
The COG database: an updated version includes eukaryotes.
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA., BMC Bioinformatics 4(), 2003
PMID: 12969510
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA., BMC Bioinformatics 4(), 2003
PMID: 12969510
RefSeq: an update on mammalian reference sequences.
Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM, Murphy MR, O'Leary NA, Pujar S, Rajput B, Rangwala SH, Riddick LD, Shkeda A, Sun H, Tamez P, Tully RE, Wallin C, Webb D, Weber J, Wu W, DiCuccio M, Kitts P, Maglott DR, Murphy TD, Ostell JM., Nucleic Acids Res. 42(Database issue), 2013
PMID: 24259432
Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM, Murphy MR, O'Leary NA, Pujar S, Rajput B, Rangwala SH, Riddick LD, Shkeda A, Sun H, Tamez P, Tully RE, Wallin C, Webb D, Weber J, Wu W, DiCuccio M, Kitts P, Maglott DR, Murphy TD, Ostell JM., Nucleic Acids Res. 42(Database issue), 2013
PMID: 24259432
Comparative analysis of the primary transcriptome of Synechocystis sp. PCC 6803.
Kopf M, Klahn S, Scholz I, Matthiessen JK, Hess WR, Voß B., DNA Res. 21(5), 2014
PMID: 24935866
Kopf M, Klahn S, Scholz I, Matthiessen JK, Hess WR, Voß B., DNA Res. 21(5), 2014
PMID: 24935866
The metabolic network of Synechocystis sp. PCC 6803: systemic properties of autotrophic growth.
Knoop H, Zilliges Y, Lockau W, Steuer R., Plant Physiol. 154(1), 2010
PMID: 20616194
Knoop H, Zilliges Y, Lockau W, Steuer R., Plant Physiol. 154(1), 2010
PMID: 20616194
Flux balance analysis of cyanobacterial metabolism: the metabolic network of Synechocystis sp. PCC 6803.
Knoop H, Grundel M, Zilliges Y, Lehmann R, Hoffmann S, Lockau W, Steuer R., PLoS Comput. Biol. 9(6), 2013
PMID: 23843751
Knoop H, Grundel M, Zilliges Y, Lehmann R, Hoffmann S, Lockau W, Steuer R., PLoS Comput. Biol. 9(6), 2013
PMID: 23843751
Stress sensors and signal transducers in cyanobacteria.
Los DA, Zorina A, Sinetova M, Kryazhov S, Mironov K, Zinchenko VV., Sensors (Basel) 10(3), 2010
PMID: 22294932
Los DA, Zorina A, Sinetova M, Kryazhov S, Mironov K, Zinchenko VV., Sensors (Basel) 10(3), 2010
PMID: 22294932
Transformation in the cyanobacterium Synechocystis sp. 6803
Grigorieva G., Shestakov S.., 1982
Grigorieva G., Shestakov S.., 1982
Optimum conditions for transformation of Synechocystis sp. PCC 6803.
Zang X, Liu B, Liu S, Arunakumara KK, Zhang X., J. Microbiol. 45(3), 2007
PMID: 17618230
Zang X, Liu B, Liu S, Arunakumara KK, Zhang X., J. Microbiol. 45(3), 2007
PMID: 17618230
DOOR 2.0: presenting operons and their functions through dynamic and integrated views.
Mao X, Ma Q, Zhou C, Chen X, Zhang H, Yang J, Mao F, Lai W, Xu Y., Nucleic Acids Res. 42(Database issue), 2013
PMID: 24214966
Mao X, Ma Q, Zhou C, Chen X, Zhang H, Yang J, Mao F, Lai W, Xu Y., Nucleic Acids Res. 42(Database issue), 2013
PMID: 24214966
Transcript mapping based on dRNA-seq data.
Bischler T, Kopf M, Voß B., BMC Bioinformatics 15(), 2014
PMID: 24780064
Bischler T, Kopf M, Voß B., BMC Bioinformatics 15(), 2014
PMID: 24780064
Transcription regulation of plastid genes involved in sulfate transport in Viridiplantae.
Lyubetsky VA, Seliverstov AV, Zverkov OA., Biomed Res Int 2013(), 2013
PMID: 24073405
Lyubetsky VA, Seliverstov AV, Zverkov OA., Biomed Res Int 2013(), 2013
PMID: 24073405
pilG Gene cluster and split pilL genes involved in pilus biogenesis, motility and genetic transformation in the cyanobacterium Synechocystis sp. PCC 6803.
Yoshihara S, Geng X, Ikeuchi M., Plant Cell Physiol. 43(5), 2002
PMID: 12040098
Yoshihara S, Geng X, Ikeuchi M., Plant Cell Physiol. 43(5), 2002
PMID: 12040098
Organization of a large gene cluster encoding ribosomal proteins in the cyanobacterium Synechococcus sp. strain PCC 6301: comparison of gene clusters among cyanobacteria, eubacteria and chloroplast genomes.
Sugita M, Sugishita H, Fujishiro T, Tsuboi M, Sugita C, Endo T, Sugiura M., Gene 195(1), 1997
PMID: 9300823
Sugita M, Sugishita H, Fujishiro T, Tsuboi M, Sugita C, Endo T, Sugiura M., Gene 195(1), 1997
PMID: 9300823
The tufB-secE-nusG-rplKAJL-rpoB gene cluster of the liberibacters: sequence comparisons, phylogeny and speciation.
Teixeira DC, Eveillard S, Sirand-Pugnet P, Wulff A, Saillard C, Ayres AJ, Bove JM., Int. J. Syst. Evol. Microbiol. 58(Pt 6), 2008
PMID: 18523188
Teixeira DC, Eveillard S, Sirand-Pugnet P, Wulff A, Saillard C, Ayres AJ, Bove JM., Int. J. Syst. Evol. Microbiol. 58(Pt 6), 2008
PMID: 18523188
Prokaryotic genomes: the emerging paradigm of genome-based microbiology.
Koonin EV, Galperin MY., Curr. Opin. Genet. Dev. 7(6), 1997
PMID: 9468784
Koonin EV, Galperin MY., Curr. Opin. Genet. Dev. 7(6), 1997
PMID: 9468784
Phylogenomic analysis of the Chlamydomonas genome unmasks proteins potentially involved in photosynthetic function and regulation.
Grossman AR, Karpowicz SJ, Heinnickel M, Dewez D, Hamel B, Dent R, Niyogi KK, Johnson X, Alric J, Wollman FA, Li H, Merchant SS., Photosyn. Res. 106(1-2), 2010
PMID: 20490922
Grossman AR, Karpowicz SJ, Heinnickel M, Dewez D, Hamel B, Dent R, Niyogi KK, Johnson X, Alric J, Wollman FA, Li H, Merchant SS., Photosyn. Res. 106(1-2), 2010
PMID: 20490922
Functional characterization of Synechocystis sp. strain PCC 6803 pst1 and pst2 gene clusters reveals a novel strategy for phosphate uptake in a freshwater cyanobacterium.
Pitt FD, Mazard S, Humphreys L, Scanlan DJ., J. Bacteriol. 192(13), 2010
PMID: 20435726
Pitt FD, Mazard S, Humphreys L, Scanlan DJ., J. Bacteriol. 192(13), 2010
PMID: 20435726
Cloning and transcription analysis of the ndh(A-I-G-E) gene cluster and the ndhD gene of the cyanobacterium Synechocystis sp. PCC6803.
Ellersiek U, Steinmuller K., Plant Mol. Biol. 20(6), 1992
PMID: 1463844
Ellersiek U, Steinmuller K., Plant Mol. Biol. 20(6), 1992
PMID: 1463844
Cyanobacteria contain a mitochondrial complex I-homologous NADH-dehydrogenase.
Berger S, Ellersiek U, Steinmuller K., FEBS Lett. 286(1-2), 1991
PMID: 1907569
Berger S, Ellersiek U, Steinmuller K., FEBS Lett. 286(1-2), 1991
PMID: 1907569
Membrane topology of MntB, the transmembrane protein component of an ABC transporter system for manganese in the cyanobacterium Synechocystis sp. strain PCC 6803.
Bartsevich VV, Pakrasi HB., J. Bacteriol. 181(11), 1999
PMID: 10348875
Bartsevich VV, Pakrasi HB., J. Bacteriol. 181(11), 1999
PMID: 10348875
Identification and transcriptional control of the genes encoding the Caulobacter crescentus ClpXP protease.
Osteras M, Stotz A, Schmid Nuoffer S, Jenal U., J. Bacteriol. 181(10), 1999
PMID: 10322004
Osteras M, Stotz A, Schmid Nuoffer S, Jenal U., J. Bacteriol. 181(10), 1999
PMID: 10322004
Genes essential to iron transport in the cyanobacterium Synechocystis sp. strain PCC 6803.
Katoh H, Hagino N, Grossman AR, Ogawa T., J. Bacteriol. 183(9), 2001
PMID: 11292796
Katoh H, Hagino N, Grossman AR, Ogawa T., J. Bacteriol. 183(9), 2001
PMID: 11292796
Posttranslational regulation of nitrate assimilation in the cyanobacterium Synechocystis sp. strain PCC 6803.
Kobayashi M, Takatani N, Tanigawa M, Omata T., J. Bacteriol. 187(2), 2005
PMID: 15629921
Kobayashi M, Takatani N, Tanigawa M, Omata T., J. Bacteriol. 187(2), 2005
PMID: 15629921
Role of NtcB in activation of nitrate assimilation genes in the cyanobacterium Synechocystis sp. strain PCC 6803.
Aichi M, Takatani N, Omata T., J. Bacteriol. 183(20), 2001
PMID: 11566981
Aichi M, Takatani N, Omata T., J. Bacteriol. 183(20), 2001
PMID: 11566981
Comparative genome analysis of the closely related Synechocystis strains PCC 6714 and PCC 6803.
Kopf M, Klahn S, Pade N, Weingartner C, Hagemann M, Voß B, Hess WR., DNA Res. 21(3), 2014
PMID: 24408876
Kopf M, Klahn S, Pade N, Weingartner C, Hagemann M, Voß B, Hess WR., DNA Res. 21(3), 2014
PMID: 24408876
The Kdp-ATPase system and its regulation.
Ballal A, Basu B, Apte SK., J. Biosci. 32(3), 2007
PMID: 17536175
Ballal A, Basu B, Apte SK., J. Biosci. 32(3), 2007
PMID: 17536175
The sufR gene (sll0088 in Synechocystis sp. strain PCC 6803) functions as a repressor of the sufBCDS operon in iron-sulfur cluster biogenesis in cyanobacteria.
Wang T, Shen G, Balasubramanian R, McIntosh L, Bryant DA, Golbeck JH., J. Bacteriol. 186(4), 2004
PMID: 14761990
Wang T, Shen G, Balasubramanian R, McIntosh L, Bryant DA, Golbeck JH., J. Bacteriol. 186(4), 2004
PMID: 14761990
A novel Sinorhizobium meliloti operon encodes an alpha-glucosidase and a periplasmic-binding-protein-dependent transport system for alpha-glucosides.
Willis LB, Walker GC., J. Bacteriol. 181(14), 1999
PMID: 10400573
Willis LB, Walker GC., J. Bacteriol. 181(14), 1999
PMID: 10400573
Identification of cyanobacterial cell division genes by comparative and mutational analyses.
Miyagishima SY, Wolk CP, Osteryoung KW., Mol. Microbiol. 56(1), 2005
PMID: 15773984
Miyagishima SY, Wolk CP, Osteryoung KW., Mol. Microbiol. 56(1), 2005
PMID: 15773984
Highly expressed and alien genes of the Synechocystis genome.
Mrazek J, Bhaya D, Grossman AR, Karlin S., Nucleic Acids Res. 29(7), 2001
PMID: 11266562
Mrazek J, Bhaya D, Grossman AR, Karlin S., Nucleic Acids Res. 29(7), 2001
PMID: 11266562
Gene expression patterns of sulfur starvation in Synechocystis sp. PCC 6803.
Zhang Z, Pendse ND, Phillips KN, Cotner JB, Khodursky A., BMC Genomics 9(), 2008
PMID: 18644144
Zhang Z, Pendse ND, Phillips KN, Cotner JB, Khodursky A., BMC Genomics 9(), 2008
PMID: 18644144
The narA locus of Synechococcus sp. strain PCC 7942 consists of a cluster of molybdopterin biosynthesis genes.
Rubio LM, Flores E, Herrero A., J. Bacteriol. 180(5), 1998
PMID: 9495759
Rubio LM, Flores E, Herrero A., J. Bacteriol. 180(5), 1998
PMID: 9495759
Requirement of the nitrogen starvation-induced protein Sll0783 for polyhydroxybutyrate accumulation in Synechocystis sp. strain PCC 6803.
Schlebusch M, Forchhammer K., Appl. Environ. Microbiol. 76(18), 2010
PMID: 20675451
Schlebusch M, Forchhammer K., Appl. Environ. Microbiol. 76(18), 2010
PMID: 20675451
Cloning, purification and characterization of the protein subunit of ribonuclease P from the cyanobacterium Synechocystis sp. PCC 6803.
Pascual A, Vioque A., Eur. J. Biochem. 241(1), 1996
PMID: 8898883
Pascual A, Vioque A., Eur. J. Biochem. 241(1), 1996
PMID: 8898883
Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization.
Zhang Y, Rodionov DA, Gelfand MS, Gladyshev VN., BMC Genomics 10(), 2009
PMID: 19208259
Zhang Y, Rodionov DA, Gelfand MS, Gladyshev VN., BMC Genomics 10(), 2009
PMID: 19208259
A conserved rubredoxin is necessary for photosystem II accumulation in diverse oxygenic photoautotrophs.
Calderon RH, Garcia-Cerdan JG, Malnoe A, Cook R, Russell JJ, Gaw C, Dent RM, de Vitry C, Niyogi KK., J. Biol. Chem. 288(37), 2013
PMID: 23900844
Calderon RH, Garcia-Cerdan JG, Malnoe A, Cook R, Russell JJ, Gaw C, Dent RM, de Vitry C, Niyogi KK., J. Biol. Chem. 288(37), 2013
PMID: 23900844
Peschek G., Löffelhardt W., Schmetterer G.., 1999
Carboxysome genomics: a status report
Cannon G.C., Heinhorst S., Bradburne C.E., Shively J.M.., 2002
Cannon G.C., Heinhorst S., Bradburne C.E., Shively J.M.., 2002
Export of extracellular polysaccharides modulates adherence of the Cyanobacterium synechocystis.
Fisher ML, Allen R, Luo Y, Curtiss R 3rd., PLoS ONE 8(9), 2013
PMID: 24040267
Fisher ML, Allen R, Luo Y, Curtiss R 3rd., PLoS ONE 8(9), 2013
PMID: 24040267
Distinct constitutive and low-CO2-induced CO2 uptake systems in cyanobacteria: genes involved and their phylogenetic relationship with homologous genes in other organisms.
Shibata M, Ohkawa H, Kaneko T, Fukuzawa H, Tabata S, Kaplan A, Ogawa T., Proc. Natl. Acad. Sci. U.S.A. 98(20), 2001
PMID: 11562454
Shibata M, Ohkawa H, Kaneko T, Fukuzawa H, Tabata S, Kaplan A, Ogawa T., Proc. Natl. Acad. Sci. U.S.A. 98(20), 2001
PMID: 11562454
The "anchor polypeptide" of cyanobacterial phycobilisomes. Molecular characterization of the Synechococcus sp. PCC 6301 apce gene.
Capuano V, Braux AS, Tandeau de Marsac N, Houmard J., J. Biol. Chem. 266(11), 1991
PMID: 1901865
Capuano V, Braux AS, Tandeau de Marsac N, Houmard J., J. Biol. Chem. 266(11), 1991
PMID: 1901865
Biochemical analysis of three putative KaiC clock proteins from Synechocystis sp. PCC 6803 suggests their functional divergence.
Wiegard A, Dorrich AK, Deinzer HT, Beck C, Wilde A, Holtzendorff J, Axmann IM., Microbiology (Reading, Engl.) 159(Pt 5), 2013
PMID: 23449916
Wiegard A, Dorrich AK, Deinzer HT, Beck C, Wilde A, Holtzendorff J, Axmann IM., Microbiology (Reading, Engl.) 159(Pt 5), 2013
PMID: 23449916
Hirt H., Shinozaki K.., 2004
Analysis and manipulation of aspartate pathway genes for L-lysine overproduction from methanol by Bacillus methanolicus.
Nærdal I, Netzer R, Ellingsen TE, Brautaset T., Appl. Environ. Microbiol. 77(17), 2011
PMID: 21724876
Nærdal I, Netzer R, Ellingsen TE, Brautaset T., Appl. Environ. Microbiol. 77(17), 2011
PMID: 21724876
Regulation of the cyanobacterial CO2-concentrating mechanism involves internal sensing of NADP+ and α-ketogutarate levels by transcription factor CcmR.
Daley SM, Kappell AD, Carrick MJ, Burnap RL., PLoS ONE 7(7), 2012
PMID: 22911771
Daley SM, Kappell AD, Carrick MJ, Burnap RL., PLoS ONE 7(7), 2012
PMID: 22911771
Characterization of a stress-responsive operon in the cyanobacterium Synechocystis sp. strain PCC 6803.
Singh AK, Sherman LA., Gene 297(1-2), 2002
PMID: 12384281
Singh AK, Sherman LA., Gene 297(1-2), 2002
PMID: 12384281
Mutational analysis of genes involved in pilus structure, motility and transformation competency in the unicellular motile cyanobacterium Synechocystis sp. PCC 6803.
Yoshihara S, Geng X, Okamoto S, Yura K, Murata T, Go M, Ohmori M, Ikeuchi M., Plant Cell Physiol. 42(1), 2001
PMID: 11158445
Yoshihara S, Geng X, Okamoto S, Yura K, Murata T, Go M, Ohmori M, Ikeuchi M., Plant Cell Physiol. 42(1), 2001
PMID: 11158445
An arsenate reductase from Synechocystis sp. strain PCC 6803 exhibits a novel combination of catalytic characteristics.
Li R, Haile JD, Kennelly PJ., J. Bacteriol. 185(23), 2003
PMID: 14617642
Li R, Haile JD, Kennelly PJ., J. Bacteriol. 185(23), 2003
PMID: 14617642
Near-UV cyanobacteriochrome signaling system elicits negative phototaxis in the cyanobacterium Synechocystis sp. PCC 6803.
Song JY, Cho HS, Cho JI, Jeon JS, Lagarias JC, Park YI., Proc. Natl. Acad. Sci. U.S.A. 108(26), 2011
PMID: 21670284
Song JY, Cho HS, Cho JI, Jeon JS, Lagarias JC, Park YI., Proc. Natl. Acad. Sci. U.S.A. 108(26), 2011
PMID: 21670284
Cold-regulated genes under control of the cold sensor Hik33 in Synechocystis.
Suzuki I, Kanesaki Y, Mikami K, Kanehisa M, Murata N., Mol. Microbiol. 40(1), 2001
PMID: 11298290
Suzuki I, Kanesaki Y, Mikami K, Kanehisa M, Murata N., Mol. Microbiol. 40(1), 2001
PMID: 11298290
The CopRS two-component system is responsible for resistance to copper in the cyanobacterium Synechocystis sp. PCC 6803.
Giner-Lamia J, Lopez-Maury L, Reyes JC, Florencio FJ., Plant Physiol. 159(4), 2012
PMID: 22715108
Giner-Lamia J, Lopez-Maury L, Reyes JC, Florencio FJ., Plant Physiol. 159(4), 2012
PMID: 22715108
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