TY - JOUR AU - Appleby, J. L. AU - Parkinson, J. S. AU - Bourret, R. B. PY - 1996 DA - 1996// TI - Signal transduction via the multi-step phosphorelay: Not necessarily a road less traveled JO - Cell VL - 86 UR - https://doi.org/10.1016/S0092-8674(00)80158-0 DO - 10.1016/S0092-8674(00)80158-0 ID - Appleby1996 ER - TY - JOUR AU - Thomason, P. AU - Kay, R. PY - 2000 DA - 2000// TI - Eukaryotic signal transduction via histidine-aspartate phosphorelay JO - J Cell Sci VL - 113 ID - Thomason2000 ER - TY - JOUR AU - Bourret, R. B. AU - Borkovich, K. A. AU - Simon, M. I. PY - 1991 DA - 1991// TI - Signal transduction pathways involving protein-phosphorylation in prokaryotes JO - Annu Rev Biochem VL - 60 UR - https://doi.org/10.1146/annurev.bi.60.070191.002153 DO - 10.1146/annurev.bi.60.070191.002153 ID - Bourret1991 ER - TY - JOUR AU - Paget, M. S. B. AU - Helmann, J. D. PY - 2003 DA - 2003// TI - The sigma 70 family of sigma factors JO - Genome Biol VL - 4 UR - https://doi.org/10.1186/gb-2003-4-1-203 DO - 10.1186/gb-2003-4-1-203 ID - Paget2003 ER - TY - JOUR AU - Dove, S. L. AU - Darst, S. A. AU - Hochschild, A. PY - 2003 DA - 2003// TI - Region 4 of sigma as a target for transcription regulation JO - Mol Microbiol VL - 48 UR - https://doi.org/10.1046/j.1365-2958.2003.03467.x DO - 10.1046/j.1365-2958.2003.03467.x ID - Dove2003 ER - TY - JOUR AU - Makino, K. AU - Shinagawa, H. AU - Amemura, M. AU - Nakata, A. PY - 1986 DA - 1986// TI - Nucleotide-sequence of the phoB gene, the positive regulatory gene for the phosphate regulon of Escherichia coli K-12 JO - J Mol Biol VL - 190 UR - https://doi.org/10.1016/0022-2836(86)90073-2 DO - 10.1016/0022-2836(86)90073-2 ID - Makino1986 ER - TY - JOUR AU - Ninfa, A. J. AU - Magasanik, B. PY - 1986 DA - 1986// TI - Covalent modification of the glnG product, NRI, by the glnL product, NRII, regulates the transcription of the glnALG operon in Escherichia coli JO - Proc Natl Acad Sci U S A VL - 83 UR - https://doi.org/10.1073/pnas.83.16.5909 DO - 10.1073/pnas.83.16.5909 ID - Ninfa1986 ER - TY - JOUR AU - Wurtzel, E. T. AU - Chou, M. Y. AU - Inouye, M. PY - 1982 DA - 1982// TI - Osmoregulation of gene-expression 1. DNA sequence of the ompR gene of the OmpB operon of Escherichia coli and characterization of its gene-product JO - J Biol Chem VL - 257 ID - Wurtzel1982 ER - TY - JOUR AU - Stock, A. M. AU - Robinson, V. L. AU - Goudreau, P. N. PY - 2000 DA - 2000// TI - Two-component signal transduction JO - Annu Rev Biochem VL - 69 UR - https://doi.org/10.1146/annurev.biochem.69.1.183 DO - 10.1146/annurev.biochem.69.1.183 ID - Stock2000 ER - TY - JOUR AU - Galperin, M. Y. PY - 2004 DA - 2004// TI - Bacterial signal transduction network in a genomic perspective JO - Environ Microbiol VL - 6 UR - https://doi.org/10.1111/j.1462-2920.2004.00633.x DO - 10.1111/j.1462-2920.2004.00633.x ID - Galperin2004 ER - TY - JOUR AU - Stover, C. K. AU - Pham, X. Q. AU - Erwin, A. L. AU - Mizoguchi, S. D. AU - Warrener, P. AU - Hickey, M. J. AU - Brinkman, F. S. L. AU - Hufnagle, W. O. AU - Kowalik, D. J. AU - Lagrou, M. AU - Garber, R. L. AU - Goltry, L. AU - Tolentino, E. AU - Westbrock-Wadman, S. AU - Yuan, Y. AU - Brody, L. L. AU - Coulter, S. N. AU - Folger, K. R. AU - Kas, A. AU - Larbig, K. AU - Lim, R. AU - Smith, K. AU - Spencer, D. AU - Wong, G. K. S. AU - Wu, Z. AU - Paulsen, I. T. AU - Reizer, J. AU - Saier, M. H. AU - Hancock, R. E. W. AU - Lory, S. AU - Olson, M. V. PY - 2000 DA - 2000// TI - Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen JO - Nature VL - 406 UR - https://doi.org/10.1038/35023079 DO - 10.1038/35023079 ID - Stover2000 ER - TY - JOUR AU - Mizuno, T. AU - Kaneko, T. AU - Tabata, S. PY - 1996 DA - 1996// TI - Compilation of all genes encoding bacterial two-component signal transducers in the genome of the cyanobacterium, Synechocystis sp. strain PCC 6803 JO - DNA Res VL - 3 UR - https://doi.org/10.1093/dnares/3.6.407 DO - 10.1093/dnares/3.6.407 ID - Mizuno1996 ER - TY - JOUR AU - Wang, L. AU - Sun, Y. P. AU - Chen, W. L. AU - Li, J. H. AU - Zhang, C. C. PY - 2002 DA - 2002// TI - Genomic analysis of protein kinases, protein phosphatases and two-component regulatory systems of the cyanobacterium Anabaena sp. strain PCC 7120 JO - FEMS Microbiol Lett VL - 217 UR - https://doi.org/10.1111/j.1574-6968.2002.tb11469.x DO - 10.1111/j.1574-6968.2002.tb11469.x ID - Wang2002 ER - TY - STD TI - Gibbs SP: Edited by: Fredrick JF. 1981, New York Academy of Sciences, 361 (FEB): 193-208.The Chloroplasts of Some Algal Groups May Have Evolved from Endosymbiotic Eukaryotic Algae: ; New York, N. Y..Annals of the New York Academy of Sciences, ID - ref14 ER - TY - CHAP AU - Margulis, L. PY - 1981 DA - 1981// BT - Symbiosis in Cell Evolution: Life and Its Environment on the Early Earth PB - Freeman CY - San Francisco ID - Margulis1981 ER - TY - JOUR AU - Cattolico, R. A. AU - Boothroyd, J. C. AU - Gibbs, S. P. PY - 1976 DA - 1976// TI - Synchronous growth and plastid replication in naturally wall-less alga Olisthodiscus luteus JO - Plant Physiol VL - 57 UR - https://doi.org/10.1104/pp.57.4.497 DO - 10.1104/pp.57.4.497 ID - Cattolico1976 ER - TY - JOUR AU - Stiller, J. W. AU - Reel, D. C. AU - Johnson, J. C. PY - 2003 DA - 2003// TI - A single origin of plastids revisited: convergent evolution in organellar genome content JO - J Phycol VL - 39 UR - https://doi.org/10.1046/j.1529-8817.2003.02070.x DO - 10.1046/j.1529-8817.2003.02070.x ID - Stiller2003 ER - TY - JOUR AU - Doran, E. AU - Cattolico, R. A. PY - 1997 DA - 1997// TI - Photoregulation of chloroplast gene transcription in the chromophytic alga Heterosigma carterae JO - Plant Physiol VL - 115 ID - Doran1997 ER - TY - JOUR AU - Reynolds, A. E. AU - McConaughy, B. L. AU - Cattolico, R. A. PY - 1993 DA - 1993// TI - Chloroplast genes of the marine alga Heterosigma carterae are transcriptionally regulated during a light/dark cycle JO - Mol Mar Biol Biotechnol VL - 2 ID - Reynolds1993 ER - TY - JOUR AU - Jacobs, M. A. AU - Connell, L. AU - Cattolico, R. A. PY - 1999 DA - 1999// TI - A conserved His-Asp signal response regulator-like gene in Heterosigma akashiwo chloroplasts JO - Plant Mol Biol VL - 41 UR - https://doi.org/10.1023/A:1006394925182 DO - 10.1023/A:1006394925182 ID - Jacobs1999 ER - TY - STD TI - The Stramenopile Chloroplast Genome Project. [http://chloroplast.ocean.washington.edu/forum/website_bug] UR - http://chloroplast.ocean.washington.edu/forum/website_bug ID - ref21 ER - TY - JOUR AU - Galperin, M. Y. AU - Nikolskaya, A. N. AU - Koonin, E. V. PY - 2001 DA - 2001// TI - Novel domains of the prokaryotic two-component signal transduction systems JO - FEMS Microbiol Lett VL - 203 UR - https://doi.org/10.1111/j.1574-6968.2001.tb10814.x DO - 10.1111/j.1574-6968.2001.tb10814.x ID - Galperin2001 ER - TY - JOUR AU - Schultz, J. AU - Milpetz, F. AU - Bork, P. AU - Ponting, C. P. PY - 1998 DA - 1998// TI - SMART, a simple modular architecture research tool: Identification of signaling domains JO - Proc Natl Acad Sci U S A VL - 95 UR - https://doi.org/10.1073/pnas.95.11.5857 DO - 10.1073/pnas.95.11.5857 ID - Schultz1998 ER - TY - STD TI - SMART: Simple Modular Architecture Research Tool. [http://smart.embl-heidelberg.de/] UR - http://smart.embl-heidelberg.de/ ID - ref24 ER - TY - JOUR AU - Kim, D. J. AU - Forst, S. PY - 2001 DA - 2001// TI - Genomic analysis of the histidine kinase family in bacteria and archaea JO - Microbiology VL - 147 UR - https://doi.org/10.1099/00221287-147-5-1197 DO - 10.1099/00221287-147-5-1197 ID - Kim2001 ER - TY - JOUR AU - Parkinson, J. S. AU - Kofoid, E. C. PY - 1992 DA - 1992// TI - Communication modules in bacterial signaling proteins JO - Annu Rev Genet VL - 26 UR - https://doi.org/10.1146/annurev.ge.26.120192.000443 DO - 10.1146/annurev.ge.26.120192.000443 ID - Parkinson1992 ER - TY - JOUR AU - Mikami, K. AU - Kanesaki, Y. AU - Suzuki, I. AU - Murata, N. PY - 2002 DA - 2002// TI - The histidine kinase Hik33 perceives osmotic stress and cold stress in Synechocystis sp. PCC 6803 JO - Mol Microbiol VL - 46 UR - https://doi.org/10.1046/j.1365-2958.2002.03202.x DO - 10.1046/j.1365-2958.2002.03202.x ID - Mikami2002 ER - TY - JOUR AU - van Waasbergen, L. G. AU - Dolganov, N. AU - Grossman, A. R. PY - 2002 DA - 2002// TI - nblS, a gene involved in controlling photosynthesis-related gene expression during high light and nutrient stress in Synechococcus elongatus PCC 7942 JO - J Bacteriol VL - 184 UR - https://doi.org/10.1128/JB.184.9.2481-2490.2002 DO - 10.1128/JB.184.9.2481-2490.2002 ID - van Waasbergen2002 ER - TY - JOUR AU - Martinez-Hackert, E. AU - Stock, A. M. PY - 1997 DA - 1997// TI - Structural relationships in the OmpR family of winged-helix transcription factors JO - J Mol Biol VL - 269 UR - https://doi.org/10.1006/jmbi.1997.1065 DO - 10.1006/jmbi.1997.1065 ID - Martinez-Hackert1997 ER - TY - JOUR AU - Okamura, H. AU - Hanaoka, S. AU - Nagadoi, A. AU - Makino, K. AU - Nishimura, Y. PY - 2000 DA - 2000// TI - Structural comparison of the PhoB and OmpR DNA-binding/transactivation domains and the arrangement of PhoB molecules on the phosphate box JO - J Mol Biol VL - 295 UR - https://doi.org/10.1006/jmbi.1999.3379 DO - 10.1006/jmbi.1999.3379 ID - Okamura2000 ER - TY - JOUR AU - Itou, H. AU - Tanaka, I. PY - 2001 DA - 2001// TI - The OmpR-family of proteins: insight into the tertiary structure and functions of two-component regulator proteins JO - J Biochem (Tokyo) VL - 129 UR - https://doi.org/10.1093/oxfordjournals.jbchem.a002863 DO - 10.1093/oxfordjournals.jbchem.a002863 ID - Itou2001 ER - TY - JOUR AU - Martinez-Hackert, E. AU - Stock, A. M. PY - 1997 DA - 1997// TI - The DNA-binding domain of OmpR: crystal structure of a winged helix transcription factor JO - Structure VL - 5 UR - https://doi.org/10.1016/S0969-2126(97)00170-6 DO - 10.1016/S0969-2126(97)00170-6 ID - Martinez-Hackert1997 ER - TY - JOUR AU - Buckler, D. R. AU - Zhou, Y. C. AU - Stock, A. M. PY - 2002 DA - 2002// TI - Evidence of intradomain and interdomain flexibility in an OmpR/PhoB homolog from Thermotoga maritima JO - Structure VL - 10 UR - https://doi.org/10.1016/S0969-2126(01)00706-7 DO - 10.1016/S0969-2126(01)00706-7 ID - Buckler2002 ER - TY - JOUR AU - Gruber, T. M. AU - Gross, C. A. PY - 2003 DA - 2003// TI - Multiple sigma subunits and the partitioning of bacterial transcription space JO - Annu Rev Microbiol VL - 57 UR - https://doi.org/10.1146/annurev.micro.57.030502.090913 DO - 10.1146/annurev.micro.57.030502.090913 ID - Gruber2003 ER - TY - JOUR AU - Helmann, J. D. AU - Chamberlin, M. J. PY - 1988 DA - 1988// TI - Structure and function of bacterial sigma factors JO - Annu Rev Biochem VL - 57 UR - https://doi.org/10.1146/annurev.bi.57.070188.004203 DO - 10.1146/annurev.bi.57.070188.004203 ID - Helmann1988 ER - TY - JOUR AU - Dove, S. L. AU - Hochschild, A. PY - 2001 DA - 2001// TI - Bacterial two-hybrid analysis of interactions between region 4 of the sigma(70) subunit of RNA polymerase and the transcriptional regulators Rsd from Escherichia coli and AlgQ from Pseudomonas aeruginosa JO - J Bacteriol VL - 183 UR - https://doi.org/10.1128/JB.183.21.6413-6421.2001 DO - 10.1128/JB.183.21.6413-6421.2001 ID - Dove2001 ER - TY - JOUR AU - Gruber, T. M. AU - Bryant, D. A. PY - 1997 DA - 1997// TI - Molecular systematic studies of eubacteria, using sigma(70)-type sigma factors of group 1 and group 2 JO - J Bacteriol VL - 179 ID - Gruber1997 ER - TY - JOUR AU - Huckauf, J. AU - Nomura, C. AU - Forchhammer, K. AU - Hagemann, M. PY - 2000 DA - 2000// TI - Stress responses of Synechocystis sp. strain PCC 6803 mutants impaired in genes encoding putative alternative sigma factors JO - Microbiol VL - 146 UR - https://doi.org/10.1099/00221287-146-11-2877 DO - 10.1099/00221287-146-11-2877 ID - Huckauf2000 ER - TY - JOUR AU - Imamura, S. AU - Yoshihara, S. AU - Nakano, S. AU - Shiozaki, N. AU - Yamada, A. AU - Tanaka, K. AU - Takahashi, H. AU - Asayama, M. AU - Shirai, M. PY - 2003 DA - 2003// TI - Purification, characterization, and gene expression of all sigma factors of RNA polymerase in a cyanobacterium JO - J Mol Biol VL - 325 UR - https://doi.org/10.1016/S0022-2836(02)01242-1 DO - 10.1016/S0022-2836(02)01242-1 ID - Imamura2003 ER - TY - JOUR AU - Iyer, L. M. AU - Koonin, E. V. AU - Aravind, L. PY - 2004 DA - 2004// TI - Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer JO - Gene VL - 335 UR - https://doi.org/10.1016/j.gene.2004.03.017 DO - 10.1016/j.gene.2004.03.017 ID - Iyer2004 ER - TY - JOUR AU - Hara, K. AU - Morita, M. AU - Takahashi, R. AU - Sugita, M. AU - Kato, S. AU - Aoki, S. PY - 2001 DA - 2001// TI - Characterization of two genes, sig1 and sig2, encoding distinct plastid sigma factors(1) in the moss Physcomitrella patens: phylogenetic relationships to plastid sigma factors in higher plants JO - FEBS Lett VL - 499 UR - https://doi.org/10.1016/S0014-5793(01)02530-3 DO - 10.1016/S0014-5793(01)02530-3 ID - Hara2001 ER - TY - JOUR AU - Ichikawa, K. AU - Sugita, M. AU - Imaizumi, T. AU - Wada, M. AU - Aoki, S. PY - 2004 DA - 2004// TI - Differential expression on a daily basis of plastid sigma factor genes from the moss Physcomitrella patens. Regulatory interactions among PpSig5, the circadian clock, and blue light signaling mediated by cryptochromes JO - Plant Physiol VL - 136 UR - https://doi.org/10.1104/pp.104.053033 DO - 10.1104/pp.104.053033 ID - Ichikawa2004 ER - TY - STD TI - The Joint Genome Institute Eukaryotic Genomics. [http://genome.jgi-psf.org/] UR - http://genome.jgi-psf.org/ ID - ref43 ER - TY - JOUR AU - Doyle, J. J. PY - 1992 DA - 1992// TI - Gene trees and species trees - molecular systematics as one-character taxonomy JO - Syst Bot VL - 17 UR - https://doi.org/10.2307/2419070 DO - 10.2307/2419070 ID - Doyle1992 ER - TY - JOUR AU - Maddison, W. P. PY - 1997 DA - 1997// TI - Gene trees in species trees JO - Syst Biol VL - 46 UR - https://doi.org/10.1093/sysbio/46.3.523 DO - 10.1093/sysbio/46.3.523 ID - Maddison1997 ER - TY - JOUR AU - Felsenstein, J. PY - 1978 DA - 1978// TI - Cases in which parsimony or compatibility methods will be positively misleading JO - Syst Zool VL - 27 UR - https://doi.org/10.2307/2412923 DO - 10.2307/2412923 ID - Felsenstein1978 ER - TY - JOUR AU - Foster, P. G. PY - 2004 DA - 2004// TI - Modeling compositional heterogeneity JO - Syst Biol VL - 53 UR - https://doi.org/10.1080/10635150490445779 DO - 10.1080/10635150490445779 ID - Foster2004 ER - TY - STD TI - Whatley JM: Edited by: Fredrick JF. 1981, New York Academy of Sciences, 361 (FEB): 154-165. Chloroplast evolution - ancient and modern: ; New York, N. Y.. Annals of the New York Academy of Sciences, ID - ref48 ER - TY - JOUR AU - Mizuno, T. PY - 1997 DA - 1997// TI - Compilation of all genes encoding two-component phosphotransfer signal transducers in the genome of Escherichia coli JO - DNA Res VL - 4 UR - https://doi.org/10.1093/dnares/4.2.161 DO - 10.1093/dnares/4.2.161 ID - Mizuno1997 ER - TY - JOUR AU - Koretke, K. K. AU - Lupas, A. N. AU - Warren, P. V. AU - Rosenberg, M. AU - Brown, J. R. PY - 2000 DA - 2000// TI - Evolution of two-component signal transduction JO - Mol Biol Evol VL - 17 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026297 DO - 10.1093/oxfordjournals.molbev.a026297 ID - Koretke2000 ER - TY - JOUR AU - Kessler, U. AU - Maid, U. AU - Zetsche, K. PY - 1992 DA - 1992// TI - An equivalent to bacterial ompR genes is encoded on the plastid genome of red algae JO - Plant Mol Biol VL - 18 UR - https://doi.org/10.1007/BF00020019 DO - 10.1007/BF00020019 ID - Kessler1992 ER - TY - JOUR AU - Bernard, C. AU - de Marsac, N. T. AU - Thomas, J. C. PY - 1994 DA - 1994// TI - A ompR gene in the plastid genome of Rhodella violacea JO - Plant Physiol VL - 106 UR - https://doi.org/10.1104/pp.106.2.795 DO - 10.1104/pp.106.2.795 ID - Bernard1994 ER - TY - JOUR AU - Reith, M. AU - Munholland, J. PY - 1995 DA - 1995// TI - Complete nucleotide sequence of the Porphyra purpurea chloroplast genome JO - Plant Mol Biol Rep VL - 13 UR - https://doi.org/10.1007/BF02669187 DO - 10.1007/BF02669187 ID - Reith1995 ER - TY - JOUR AU - Glöckner, G. AU - Rosenthal, A. AU - Valentin, K. PY - 2000 DA - 2000// TI - The structure and gene repertoire of an ancient red algal plastid genome JO - J Mol Evol VL - 51 ID - Glöckner2000 ER - TY - JOUR AU - Ohta, N. AU - Matsuzaki, M. AU - Misumi, O. AU - Miyagishima, S. AU - Nozaki, H. AU - Tanaka, K. AU - Shin-I, T. AU - Kohara, Y. AU - Kuroiwa, T. PY - 2003 DA - 2003// TI - Complete sequence and analysis of the plastid genome of the unicellular red alga Cyanidioschyzon merolae JO - DNA Res VL - 10 UR - https://doi.org/10.1093/dnares/10.2.67 DO - 10.1093/dnares/10.2.67 ID - Ohta2003 ER - TY - JOUR AU - Hagopian, J. C. AU - Reis, M. AU - Kitajima, J. P. AU - Bhattacharya, D. AU - de Oliveira, M. C. PY - 2004 DA - 2004// TI - Comparative analysis of the complete plastid genome sequence of the red alga Gracilaria tenuistipitata var. liui provides insights into the evolution of rhodoplasts and their relationship to other plastids JO - J Mol Evol VL - 59 UR - https://doi.org/10.1007/s00239-004-2638-3 DO - 10.1007/s00239-004-2638-3 ID - Hagopian2004 ER - TY - JOUR AU - Stirewalt, V. L. AU - Michalowski, C. B. AU - Loffelhardt, W. AU - Bohnert, H. J. AU - Bryant, D. A. PY - 1995 DA - 1995// TI - Nucleotide sequence of the cyanelle genome from Cyanophora paradoxa JO - Plant Mol Biol Rep VL - 13 UR - https://doi.org/10.1007/BF02669186 DO - 10.1007/BF02669186 ID - Stirewalt1995 ER - TY - JOUR AU - Puerta, M. V. S. AU - Bachvaroff, T. R. AU - Delwiche, C. F. PY - 2005 DA - 2005// TI - The complete plastid genome sequence of the haptophyte Emiliania huxleyi: a comparison to other plastid genomes JO - DNA Res VL - 12 UR - https://doi.org/10.1093/dnares/12.2.151 DO - 10.1093/dnares/12.2.151 ID - Puerta2005 ER - TY - JOUR AU - Douglas, S. E. AU - Penny, S. L. PY - 1999 DA - 1999// TI - The plastid genome of the cryptophyte alga, Guillardia theta: Complete sequence and conserved synteny groups confirm its common ancestry with red algae JO - J Mol Evol VL - 48 UR - https://doi.org/10.1007/PL00006462 DO - 10.1007/PL00006462 ID - Douglas1999 ER - TY - CHAP AU - Lemieux, C. AU - Otis, C. AU - Turmel, M. PY - 2007 DA - 2007// TI - A clade uniting the green algae Mesostigma viride and Chlorokybus atmophyticus represents the deepest branch of the Streptophyta in chloroplast genome-based phylogenies BT - BMC Biology ID - Lemieux2007 ER - TY - JOUR AU - Kowallik, K. V. AU - Stoebe, B. AU - Schaffran, I. AU - KrothPancic, P. AU - Freier, U. PY - 1995 DA - 1995// TI - The chloroplast genome of a chlorophyll a+c-containing alga, Odontella sinensis JO - Plant Mol Biol Rep VL - 13 UR - https://doi.org/10.1007/BF02669188 DO - 10.1007/BF02669188 ID - Kowallik1995 ER - TY - JOUR AU - Armbrust, E. V. AU - Berges, J. A. AU - Bowler, C. AU - Green, B. R. AU - Martinez, D. AU - Putnam, N. H. AU - Zhou, S. G. AU - Allen, A. E. AU - Apt, K. E. AU - Bechner, M. AU - Brzezinski, M. A. AU - Chaal, B. K. AU - Chiovitti, A. AU - Davis, A. K. AU - Demarest, M. S. AU - Detter, J. C. AU - Glavina, T. AU - Goodstein, D. AU - Hadi, M. Z. AU - Hellsten, U. AU - Hildebrand, M. AU - Jenkins, B. D. AU - Jurka, J. AU - Kapitonov, V. V. AU - Kroger, N. AU - Lau, W. W. Y. AU - Lane, T. W. AU - Larimer, F. W. AU - Lippmeier, J. C. AU - Lucas, S. AU - Medina, M. AU - Montsant, A. AU - Obornik, M. AU - Parker, M. S. AU - Palenik, B. AU - Pazour, G. J. AU - Richardson, P. M. AU - Rynearson, T. A. AU - Saito, M. A. AU - Schwartz, D. C. AU - Thamatrakoln, K. AU - Valentin, K. AU - Vardi, A. AU - Wilkerson, F. P. AU - Rokhsar, D. S. PY - 2004 DA - 2004// TI - The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism JO - Science VL - 306 UR - https://doi.org/10.1126/science.1101156 DO - 10.1126/science.1101156 ID - Armbrust2004 ER - TY - JOUR AU - Urao, T. AU - Yamaguchi-Shinozaki, K. AU - Shinozaki, K. PY - 2000 DA - 2000// TI - Two-component systems in plant signal transduction JO - Trends Plant Sci VL - 5 UR - https://doi.org/10.1016/S1360-1385(99)01542-3 DO - 10.1016/S1360-1385(99)01542-3 ID - Urao2000 ER - TY - JOUR AU - Kiba, T. AU - Taniguchi, M. AU - Imamura, A. AU - Ueguchi, C. AU - Mizuno, T. AU - Sugiyama, T. PY - 1999 DA - 1999// TI - Differential expression of genes for response regulators in response to cytokinins and nitrate in Arabidopsis thaliana JO - Plant Cell Physiol VL - 40 UR - https://doi.org/10.1093/oxfordjournals.pcp.a029604 DO - 10.1093/oxfordjournals.pcp.a029604 ID - Kiba1999 ER - TY - JOUR AU - Brandstatter, I. AU - Kieber, J. J. PY - 1998 DA - 1998// TI - Two genes with similarity to bacterial response regulators are rapidly and specifically induced by cytokinin in Arabidopsis JO - Plant Cell VL - 10 UR - https://doi.org/10.1105/tpc.10.6.1009 DO - 10.1105/tpc.10.6.1009 ID - Brandstatter1998 ER - TY - JOUR AU - Wilkinson, J. Q. AU - Lanahan, M. B. AU - Yen, H. C. AU - Giovannoni, J. J. AU - Klee, H. J. PY - 1995 DA - 1995// TI - An ethylene-inducible component of signal-transduction encoded by never-ripe JO - Science VL - 270 UR - https://doi.org/10.1126/science.270.5243.1807 DO - 10.1126/science.270.5243.1807 ID - Wilkinson1995 ER - TY - JOUR AU - Wurgler-Murphy, S. M. AU - Saito, H. PY - 1997 DA - 1997// TI - Two-component signal transducers and MAPK cascades JO - Trends Biochem Sci VL - 22 UR - https://doi.org/10.1016/S0968-0004(97)01036-0 DO - 10.1016/S0968-0004(97)01036-0 ID - Wurgler-Murphy1997 ER - TY - JOUR AU - Marin, K. AU - Suzuki, L. AU - Yamaguchi, K. AU - Ribbeck, K. AU - Yamamoto, H. AU - Kanesaki, Y. AU - Hagemann, M. AU - Murata, N. PY - 2003 DA - 2003// TI - Identification of histidine kinases that act as sensors in the perception of salt stress in Synechocystis sp. PCC 6803 JO - Proc Natl Acad Sci U S A VL - 100 UR - https://doi.org/10.1073/pnas.1532302100 DO - 10.1073/pnas.1532302100 ID - Marin2003 ER - TY - JOUR AU - Suzuki, I. AU - Kanesaki, Y. AU - Mikami, K. AU - Kanehisa, M. AU - Murata, N. PY - 2001 DA - 2001// TI - Cold-regulated genes under control of the cold sensor Hik33 in Synechocystis JO - Mol Microbiol VL - 40 UR - https://doi.org/10.1046/j.1365-2958.2001.02379.x DO - 10.1046/j.1365-2958.2001.02379.x ID - Suzuki2001 ER - TY - JOUR AU - Taylor, B. L. AU - Zhulin, I. B. PY - 1999 DA - 1999// TI - PAS domains: internal sensors of oxygen, redox potential, and light JO - Microbiol Mol Biol Rev VL - 63 ID - Taylor1999 ER - TY - JOUR AU - Allen, J. F. PY - 2003 DA - 2003// TI - The function of genomes in bioenergetic organelles JO - Philos Trans R Soc Lond Ser B-Biol Sci VL - 358 UR - https://doi.org/10.1098/rstb.2002.1191 DO - 10.1098/rstb.2002.1191 ID - Allen2003 ER - TY - JOUR AU - Allen, J. F. AU - Nilsson, A. PY - 1997 DA - 1997// TI - Redox signalling and the structural basis of regulation of photosynthesis by protein phosphorylation JO - Physiol Plant VL - 100 UR - https://doi.org/10.1111/j.1399-3054.1997.tb00012.x DO - 10.1111/j.1399-3054.1997.tb00012.x ID - Allen1997 ER - TY - JOUR AU - Hefti, M. H. AU - Francoijs, K. J. AU - de Vries, S. C. AU - Dixon, R. AU - Vervoort, J. PY - 2004 DA - 2004// TI - The PAS fold - A redefinition of the PAS domain based upon structural prediction JO - Eur J Biochem VL - 271 UR - https://doi.org/10.1111/j.1432-1033.2004.04023.x DO - 10.1111/j.1432-1033.2004.04023.x ID - Hefti2004 ER - TY - JOUR AU - Schobert, M. AU - Gorisch, H. PY - 2001 DA - 2001// TI - A soluble two-component regulatory system controls expression of quinoprotein ethanol dehydrogenase (QEDH) but not expression of cytochrome c(550) of the ethanol-oxidation system in Pseudomonas aeruginosa JO - Microbiol VL - 147 UR - https://doi.org/10.1099/00221287-147-2-363 DO - 10.1099/00221287-147-2-363 ID - Schobert2001 ER - TY - JOUR AU - Hutchings, M. I. AU - Hoskisson, P. A. AU - Chandra, G. AU - Buttner, M. J. PY - 2004 DA - 2004// TI - Sensing and responding to diverse extracellular signals? Analysis of the sensor kinases and response regulators of Streptomyces coelicolor A3(2) JO - Microbiol VL - 150 UR - https://doi.org/10.1099/mic.0.27181-0 DO - 10.1099/mic.0.27181-0 ID - Hutchings2004 ER - TY - JOUR AU - Ashby, M. K. AU - Houmard, J. AU - Mullineaux, C. W. PY - 2002 DA - 2002// TI - The ycf27 genes from cyanobacteria and eukaryotic algae: distribution and implications for chloroplast evolution JO - FEMS Microbiol Lett VL - 214 ID - Ashby2002 ER - TY - JOUR AU - Ashby, M. K. AU - Mullineaux, C. W. PY - 1999 DA - 1999// TI - Cyanobacterial ycf27 gene products regulate energy transfer from phycobilisomes to photosystems I and II JO - FEMS Microbiol Lett VL - 181 UR - https://doi.org/10.1111/j.1574-6968.1999.tb08852.x DO - 10.1111/j.1574-6968.1999.tb08852.x ID - Ashby1999 ER - TY - JOUR AU - Makino, K. AU - Amemura, M. AU - Kim, S. K. AU - Nakata, A. AU - Shinagawa, H. PY - 1993 DA - 1993// TI - Role of the sigma-70 subunit of RNA polymerase in transcriptional activation by activator protein Phob in Escherichia coli JO - Genes and Development VL - 7 UR - https://doi.org/10.1101/gad.7.1.149 DO - 10.1101/gad.7.1.149 ID - Makino1993 ER - TY - JOUR AU - Kondo, H. AU - Nakagawa, A. AU - Nishihira, J. AU - Nishimura, Y. AU - Mizuno, T. AU - Tanaka, I. PY - 1997 DA - 1997// TI - Escherichia coli positive regulator OmpR has a large loop structure at the putative RNA polymerase interaction site JO - Nat Struct Biol VL - 4 UR - https://doi.org/10.1038/nsb0197-28 DO - 10.1038/nsb0197-28 ID - Kondo1997 ER - TY - JOUR AU - Douglas, S. AU - Zauner, S. AU - Fraunholz, M. AU - Beaton, M. AU - Penny, S. AU - Deng, L. T. AU - Wu, X. N. AU - Reith, M. AU - Cavalier-Smith, T. AU - Maier, U. G. PY - 2001 DA - 2001// TI - The highly reduced genome of an enslaved algal nucleus JO - Nature VL - 410 UR - https://doi.org/10.1038/35074092 DO - 10.1038/35074092 ID - Douglas2001 ER - TY - JOUR AU - Troxler, R. F. AU - Zhang, F. AU - Hu, J. AU - Bogorad, L. PY - 1994 DA - 1994// TI - Evidence that sigma-factors are components of chloroplast RNA-Polymerase JO - Plant Physiol VL - 104 UR - https://doi.org/10.1104/pp.104.2.753 DO - 10.1104/pp.104.2.753 ID - Troxler1994 ER - TY - JOUR AU - Liu, B. AU - Troxler, R. F. PY - 1996 DA - 1996// TI - Molecular characterization of a positively photoregulated nuclear gene for a chloroplast RNA polymerase sigma factor in Cyanidium caldarium JO - Proc Natl Acad Sci U S A VL - 93 UR - https://doi.org/10.1073/pnas.93.8.3313 DO - 10.1073/pnas.93.8.3313 ID - Liu1996 ER - TY - JOUR AU - Tanaka, K. AU - Oikawa, K. AU - Ohta, N. AU - Kuroiwa, H. AU - Kuroiwa, T. AU - Takahashi, H. PY - 1996 DA - 1996// TI - Nuclear encoding of a chloroplast RNA polymerase sigma subunit in a red alga JO - Science VL - 272 UR - https://doi.org/10.1126/science.272.5270.1932 DO - 10.1126/science.272.5270.1932 ID - Tanaka1996 ER - TY - JOUR AU - Hajdukiewicz, P. T. J. AU - Allison, L. A. AU - Maliga, P. PY - 1997 DA - 1997// TI - The two RNA polymerases encoded by the nuclear and the plastid compartments transcribe distinct groups of genes in tobacco plastids JO - EMBO J VL - 16 UR - https://doi.org/10.1093/emboj/16.13.4041 DO - 10.1093/emboj/16.13.4041 ID - Hajdukiewicz1997 ER - TY - JOUR AU - Link, G. PY - 1996 DA - 1996// TI - Green life: control of chloroplast gene transcription JO - BioEssays VL - 18 UR - https://doi.org/10.1002/bies.950180608 DO - 10.1002/bies.950180608 ID - Link1996 ER - TY - JOUR AU - Rajasekhar, V. K. AU - Sun, E. AU - Meeker, R. AU - Wu, B. W. AU - Tewari, K. K. PY - 1991 DA - 1991// TI - Highly purified pea chloroplast RNA-polymerase transcribes both ribosomal-RNA and messenger-RNA genes JO - Eur J Biochem VL - 195 UR - https://doi.org/10.1111/j.1432-1033.1991.tb15697.x DO - 10.1111/j.1432-1033.1991.tb15697.x ID - Rajasekhar1991 ER - TY - JOUR AU - Hess, W. R. AU - Prombona, A. AU - Fieder, B. AU - Subramanian, A. R. AU - Börner, T. PY - 1993 DA - 1993// TI - Chloroplast rps15 and the rpoB/C1/C2 gene-cluster are strongly transcribed in ribosome-deficient plastids: evidence for a functioning non-chloroplast-encoded RNA-polymerase JO - EMBO J VL - 12 ID - Hess1993 ER - TY - JOUR AU - Choquet, Y. AU - Vallon, O. PY - 2000 DA - 2000// TI - Synthesis, assembly and degradation of thylakoid membrane proteins JO - Biochimie (Paris) VL - 82 UR - https://doi.org/10.1016/S0300-9084(00)00609-X DO - 10.1016/S0300-9084(00)00609-X ID - Choquet2000 ER - TY - JOUR AU - McIntosh, L. AU - Cattolico, R. A. PY - 1978 DA - 1978// TI - Preservation of algal and higher plant ribosomal-RNA integrity during extraction and electrophoretic quantitation JO - Anal Biochem VL - 91 UR - https://doi.org/10.1016/0003-2697(78)90546-8 DO - 10.1016/0003-2697(78)90546-8 ID - McIntosh1978 ER - TY - CHAP AU - Sambrook, J. AU - Fritsch, E. F. AU - Maniatis, T. PY - 1989 DA - 1989// BT - Molecular Cloning: a Laboratory Handbook PB - Cold Spring Harbor Laboratory Press CY - Cold Spring Harbor, New York ID - Sambrook1989 ER - TY - STD TI - User-Developed Protocol: Isolation of genomic DNA. [http://www1.qiagen.com/literature/protocols/pdf/QG08.pdf] UR - http://www1.qiagen.com/literature/protocols/pdf/QG08.pdf ID - ref91 ER - TY - JOUR AU - Altschul, S. F. AU - Madden, T. L. AU - Schäffer, A. A. AU - Zhang, J. AU - Zhang, Z. AU - Miller, W. AU - Lipman, D. J. PY - 1997 DA - 1997// TI - Gapped BLAST and PSI-BLAST: a new generation of protein database search programs JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.17.3389 DO - 10.1093/nar/25.17.3389 ID - Altschul1997 ER - TY - JOUR AU - Higgins, D. AU - Thompson, J. AU - Gibson, T. AU - Thompson, J. D. AU - Higgins, D. G. AU - Gibson, T. J. PY - 1994 DA - 1994// TI - CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. JO - Nucleic Acids Res VL - 22 UR - https://doi.org/10.1093/nar/22.22.4673 DO - 10.1093/nar/22.22.4673 ID - Higgins1994 ER - TY - STD TI - Multiple Sequence Alignment by CLUSTALW. [http://align.genome.jp/] UR - http://align.genome.jp/ ID - ref94 ER - TY - STD TI - SignalP 3.0 Server. [http://www.cbs.dtu.dk/services/SignalP/] UR - http://www.cbs.dtu.dk/services/SignalP/ ID - ref95 ER - TY - JOUR AU - Bendtsen, J. D. AU - Nielsen, H. AU - von Heijne, G. AU - Brunak, S. PY - 2004 DA - 2004// TI - Improved prediction of signal peptides: SignalP 3.0. JO - J Mol Biol VL - 340 UR - https://doi.org/10.1016/j.jmb.2004.05.028 DO - 10.1016/j.jmb.2004.05.028 ID - Bendtsen2004 ER - TY - JOUR AU - Apt, K. E. AU - Zaslavkaia, L. AU - Lippmeier, J. C. AU - Lang, M. AU - Kilian, O. AU - Wetherbee, R. AU - Grossman, A. R. AU - Kroth, P. G. PY - 2002 DA - 2002// TI - In vivo characterization of diatom multipartite plastid targeting signals JO - Cell Science VL - 115 UR - https://doi.org/10.1242/jcs.00092 DO - 10.1242/jcs.00092 ID - Apt2002 ER - TY - JOUR AU - Chaal, B. K. AU - Green, B. R. PY - 2005 DA - 2005// TI - Protein import pathways in 'complex' chloroplasts derived from secondary endosymbiosis involving a red algal ancestor JO - Plant Mol Biol VL - 57 UR - https://doi.org/10.1007/s11103-004-7848-y DO - 10.1007/s11103-004-7848-y ID - Chaal2005 ER - TY - JOUR AU - Berman, H. M. AU - Battistuz, T. AU - Bhat, T. N. AU - Bluhm, W. F. AU - Bourne, P. E. AU - Burkhardt, K. AU - Feng, Z. AU - Gilliland, G. L. AU - Iype, L. AU - Jain, S. AU - Fagan, P. AU - Marvin, J. AU - Padilla, D. AU - Ravichandran, V. AU - Schneider, B. AU - Thanki, N. AU - Weissig, H. AU - Westbrook, J. D. AU - Zardecki, C. PY - 2002 DA - 2002// TI - The Protein Data Bank JO - Acta Crystallogr Sect D Biol Crystallogr VL - D58 UR - https://doi.org/10.1107/S0907444902003451 DO - 10.1107/S0907444902003451 ID - Berman2002 ER - TY - STD TI - RCSB Protein Data Bank. [http://www.rcsb.org/pdb/home/home.do] UR - http://www.rcsb.org/pdb/home/home.do ID - ref100 ER - TY - STD TI - Chemical Computing Group. [http://www.chemcomp.com] UR - http://www.chemcomp.com ID - ref101 ER - TY - STD TI - Cyanidioschyzon merolae Genome Project. [http://merolae.biol.s.u-tokyo.ac.jp/] UR - http://merolae.biol.s.u-tokyo.ac.jp/ ID - ref102 ER -