link.springer.com

Sequence variation at the oxygen-evolving centre of photosystem II: a new class of ‘rogue’ cyanobacterial D1 proteins - Photosynthesis Research

  • ️Murray, James W.
  • ️Wed Dec 21 2011
  • Adachi J (1996) MOLPHY version 2.3: programs for molecular phylogenetics based on maximum likelihood. Comput Sci Monogr 28:1–150

    Google Scholar 

  • Adachi J, Hasegawa M (1992) MOLPHY: programs for molecular phylogenetics, I.—PROTML: maximum likelihood inference of protein phylogeny. Comput Sci Monogr 27:1–77

    Google Scholar 

  • Beitz E (2000) TeXshade: shading and labeling of multiple sequence alignments using LaTeX2e. Bioinformatics 16(2):135–139. doi:10.1093/bioinformatics/16.2.135

    Article  PubMed  CAS  Google Scholar 

  • Berman-Frank I, Lundgren P, Chen YB, Kupper H, Kolber Z, Bergman B, Falkowski P (2001) Segregation of nitrogen fixation and oxygenic photosynthesis in the marine cyanobacterium Trichodesmium. Science 294(5546):1534–1537. doi:10.1126/science

    Article  PubMed  CAS  Google Scholar 

  • Cardona T, Battchikova N, Zhang P, Stensjö K, Aro E-M, Lindblad P, Magnuson A (2009) Electron transfer protein complexes in the thylakoid membranes of heterocysts from the cyanobacterium Nostoc punctiforme. Biochim Biophys Acta Bioenerg 1787(4):252–263

    Article  CAS  Google Scholar 

  • Chu H-A, Nguyen AP, Debus RJ (1995) Amino acid residues that influence the binding of manganese or calcium to photosystem II. 1. The lumenal interhelical domains of the D1 polypeptide. Biochemistry 34(17):5839–5858. doi:10.1021/bi00017a016

    Article  PubMed  CAS  Google Scholar 

  • Clausen J, Winkler S, Hays A-MA, Hundelt M, Debus RJ, Junge W (2001) Photosynthetic water oxidation in Synechocystis sp. PCC6803: mutations D1–E189 K, R and Q are without influence on electron transfer at the donor side of photosystem II. Biochim Biophys Acta Bioenerg 1506(3):224–235

    Article  CAS  Google Scholar 

  • Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJL (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25(11):1422–1423. doi:10.1093/bioinformatics/btp163

    Article  PubMed  CAS  Google Scholar 

  • Debus RJ (2001) Amino acid residues that modulate the properties of tyrosine YZ and the manganese cluster in the water oxidizing complex of photosystem II. Biochim Biophys Acta Bioenerg 1503(1–2):164–186

    Article  CAS  Google Scholar 

  • Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D 60(12 Part 1):2126–2132. doi:10.1107/S0907444904019158

    Article  PubMed  Google Scholar 

  • Fay P (1992) Oxygen relations of nitrogen fixation in cyanobacteria. Microbiol Rev 56(2):340–373

    PubMed  CAS  Google Scholar 

  • Ferreira KN, Iverson TM, Maghlaoui K, Barber J, Iwata S (2004) Architecture of the photosynthetic oxygen-evolving center. Science 303(5665):1831–1838. doi:10.1126/science.1093087

    Article  PubMed  CAS  Google Scholar 

  • Guglielmi G, Cohen-Bazire G, Bryant DA (1981) The structure of Gloeobacter violaceus and its phycobilisomes. Arch Microbiol 129(3):181–189. doi:10.1007/bf00425248

    Article  CAS  Google Scholar 

  • Guskov A, Kern J, Gabdulkhakov A, Broser M, Zouni A, Saenger W (2009) Cyanobacterial photosystem II at 2.9-Å resolution and the role of quinones, lipids, channels and chloride. Nat Struct Mol Biol 16(3):334–342

    Article  PubMed  CAS  Google Scholar 

  • Ishikita H, Saenger W, Loll B, Biesiadka J, Knapp E-W (2006) Energetics of a possible proton exit pathway for water oxidation in photosystem II. Biochemistry 45(7):2063–2071. doi:10.1021/bi051615h

    Article  PubMed  CAS  Google Scholar 

  • Kawakami K, Umena Y, Kamiya N, Shen J-R (2009) Location of chloride and its possible functions in oxygen-evolving photosystem II revealed by X-ray crystallography. Proc Natl Acad Sci 106(21):8567–8572. doi:10.1073/pnas.0812797106

    Article  PubMed  CAS  Google Scholar 

  • Kós PB, Deák Z, Cheregi O, Vass I (2008) Differential regulation of psbA and psbD gene expression, and the role of the different D1 protein copies in the cyanobacterium Thermosynechococcus elongatus BP-1. Biochim Biophys Acta Bioenerg 1777(1):74–83

    Article  Google Scholar 

  • Lovell SC, Word JM, Richardson JS, Richardson DC (2000) The penultimate rotamer library. Proteins 40(3):389–408. doi:10.1002/1097-0134(20000815)40:3<389:aid-prot50>3.0.co;2-2

    Article  PubMed  CAS  Google Scholar 

  • Madden TL, Tatusov RL, Zhang J, Russell FD (1996) Applications of network BLAST server. In: Methods in enzymology, vol 266. Academic Press, New York, pp 131–141

  • Mattoo AK, Hoffman-Falk H, Marder JB, Edelman M (1984) Regulation of protein metabolism: coupling of photosynthetic electron transport to in vivo degradation of the rapidly metabolized 32-kilodalton protein of the chloroplast membranes. Proc Natl Acad Sci 81(5):1380–1384

    Article  PubMed  CAS  Google Scholar 

  • Mohr R, Vosz B, Schliep M, Kurz T, Maldener I, Adams DG, Larkum ADW, Chen M, Hess WR (2010) A new chlorophyll d-containing cyanobacterium: evidence for niche adaptation in the genus Acaryochloris. ISME J 4(11):1456–1469

    Article  PubMed  CAS  Google Scholar 

  • Mulo P, Tyystjärvi T, Tyystjärvi E, Govindjee Mäenpää P, Aro E-M (1997) Mutagenesis of the D-E loop of photosystem II reaction centre protein D1. Function and assembly of photosystem II. Plant Mol Biol 33(6):1059–1071. doi:10.1023/a:1005765305956

  • Murray JW, Maghlaoui K, Kargul J, Ishida N, Lai T-L, Rutherford AW, Sugiura M, Boussac A, Barber J (2008) X-ray crystallography identifies two chloride binding sites in the oxygen evolving centre of photosystem II. Energy & Environmental Science 1(1):161–166

    Article  CAS  Google Scholar 

  • Nixon PJ, Rogner M, Diner BA (1991) Expression of a higher plant psbA gene in Synechocystis 6803 yields a functional hybrid photosystem II reaction center complex. Plant Cell 3(4):383–395. doi:10.1105/tpc.3.4.3833/4/383

    Article  PubMed  CAS  Google Scholar 

  • Nixon PJ, Komenda J, Barber J, Deak Z, Vass I, Diner BA (1995) Deletion of the PEST-like region of photosystem two modifies the Q-binding pocket but does not prevent rapid turnover of D1. J Biol Chem 270(25):14919–14927. doi:10.1074/jbc.270.25.14919

    Article  PubMed  CAS  Google Scholar 

  • Nixon PJ, Michoux F, Yu J, Boehm M, Komenda J (2010) Recent advances in understanding the assembly and repair of photosystem II. Ann Bot 106(1):1–16. doi:10.1093/aob/mcq059

    Article  PubMed  CAS  Google Scholar 

  • Pils B, Schultz J (2004) Inactive enzyme-homologues find new function in regulatory processes. J Mol Biol 340(3):399–404

    Article  PubMed  CAS  Google Scholar 

  • Rechsteiner M, Rogers SW (1996) PEST sequences and regulation by proteolysis. Trends Biochem Sci 21(7):267–271

    PubMed  CAS  Google Scholar 

  • Seefeldt LC, Hoffman BM, Dean DR (2009) Mechanism of mo-dependent nitrogenase. Annu Rev Biochem 78(1):701–722. doi:10.1146/annurev.biochem.78.070907.103812

    Article  PubMed  CAS  Google Scholar 

  • Sicora CI, Brown CM, Cheregi O, Vass I, Campbell DA (2008) The psbA gene family responds differentially to light and UVB stress in Gloeobacter violaceus PCC 7421, a deeply divergent cyanobacterium. Biochim Biophys Acta Bioenerg 1777(2):130–139

    Article  CAS  Google Scholar 

  • Stöckel J, Welsh EA, Liberton M, Kunnvakkam R, Aurora R, Pakrasi HB (2008) Global transcriptomic analysis of Cyanothece 51142 reveals robust diurnal oscillation of central metabolic processes. Proc Natl Acad Sci 105(16):6156–6161. doi:10.1073/pnas.0711068105

    Article  PubMed  Google Scholar 

  • Summerfield TC, Toepel Jr, Sherman LA (2008) Low-oxygen induction of normally cryptic psbA genes in cyanobacteria. Biochemistry 47(49):12939–12941. doi:10.1021/bi8018916

    Article  PubMed  CAS  Google Scholar 

  • Swingley WD, Chen M, Cheung PC, Conrad AL, Dejesa LC, Hao J, Honchak BM, Karbach LE, Kurdoglu A, Lahiri S, Mastrian SD, Miyashita H, Page L, Ramakrishna P, Satoh S, Sattley WM, Shimada Y, Taylor HL, Tomo T, Tsuchiya T, Wang ZT, Raymond J, Mimuro M, Blankenship RE, Touchman JW (2008) Niche adaptation and genome expansion in the chlorophyll d-producing cyanobacterium Acaryochloris marina. Proc Natl Acad Sci 105(6):2005–2010. doi:10.1073/pnas.0709772105

    Article  PubMed  CAS  Google Scholar 

  • Takishita K, Uchida A (1999) Molecular cloning and nucleotide sequence analysis of psbA from the dinoflagellates: origin of the dinoflagellate plastid. Phycol Res 47(3):207–216. doi:10.1046/j.1440-1835.1999.00163.x

    Article  CAS  Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22(22):4673–4680. doi:10.1093/nar/22.22.4673

    Article  PubMed  CAS  Google Scholar 

  • Toepel J, Welsh E, Summerfield TC, Pakrasi HB, Sherman LA (2008) Differential transcriptional analysis of the cyanobacterium Cyanothece sp. strain ATCC 51142 during light-dark and continuous-light growth. J Bacteriol 190(11):3904–3913. doi:10.1128/jb.00206-08

    Article  PubMed  CAS  Google Scholar 

  • Tripp HJ, Bench SR, Turk KA, Foster RA, Desany BA, Niazi F, Affourtit JP, Zehr JP (2010) Metabolic streamlining in an open-ocean nitrogen-fixing cyanobacterium. Nature 464(7285):90–94

    Article  PubMed  CAS  Google Scholar 

  • Umena Y, Kawakami K, Shen JR, Kamiya N (2011) Crystal structure of oxygen-evolving photosystem II at a resolution of. Nature 473(7345):55–60. doi:10.1038/nature09913

    Article  PubMed  CAS  Google Scholar 

  • Yocum CF (2008) The calcium and chloride requirements of the O2 evolving complex. Coord Chem Rev 252(3–4):296–305

    Article  CAS  Google Scholar 

  • Zehr JP, Bench SR, Carter BJ, Hewson I, Niazi F, Shi T, Tripp HJ, Affourtit JP (2008) Globally distributed uncultivated oceanic N2-fixing cyanobacteria lack oxygenic photosystem II. Science 322(5904):1110–1112. doi:10.1126/science.1165340

    Article  PubMed  CAS  Google Scholar