Rao NN, Gomez-Garci MR, Kornberg A: Inorganic polyphosphate : essential for growth and survival. Ann Rev Biochem. 2009, 78: 605-647.
Article
PubMed
CAS
Google Scholar
Schwartz AW: Phosphorus in prebiotic chemistry. Philos Trans R Soc Lond B Biol Sci. 2006, 361: 1743-1749.
Article
PubMed
CAS
PubMed Central
Google Scholar
Jones ME, Lipmann F: Chemical and enzymatic synthesis of carbamyl phosphate. Proc Natl Acad Sci U S A. 1960, 46: 1194-1205.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kulaev IS, Vagabov VM: Polyphosphate metabolism in micro-organisms. Adv Microb Physiol. 1983, 24: 83-171.
Article
PubMed
CAS
Google Scholar
Zhang H, Ishige K, Kornberg A: A polyphosphate kinase (PPK2) widely conserved in bacteria. Proc Natl Acad Sci U S A. 2002, 99: 16678-16683.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kornberg A, Kumble AD: Inorganic polyphosphate in mammalian cells and tissues. J Biol Chem. 1995, 270: 5818-5822.
Article
PubMed
Google Scholar
Brown MRW, Kornberg A: The long and short of it – polyphosphate, PPK and bacterial survival. Trends Biochem Sci. 2008, 33: 284-290.
Article
PubMed
CAS
Google Scholar
Brown MRW, Kornberg A: Inorganic polyphosphate in the origin and survival of species. Proc Natl Acad Sci U S A. 2004, 101: 16085-16087.
Article
PubMed
CAS
PubMed Central
Google Scholar
Zhu Y, Huang W, Lee SSK, Xu W: Crystal structure of a polyphosphate kinase and its implications for polyphosphate synthesis. EMBO Rep. 2005, 6: 681-687.
Article
PubMed
CAS
PubMed Central
Google Scholar
Shiba T, Itoh H, Kameda A, Kobayashi K, Kawazoe Y, Noguchi T: Polyphosphate:AMP phosphotransferase as a polyphosphate-dependent nucleoside monophosphate kinase in Acinetobacter johnsonii 210A. J Bact. 2005, 187: 1859-1865.
Article
PubMed
CAS
PubMed Central
Google Scholar
Nocek B, Kochinyan S, Proudfoot M, Brown G, Evdokimova E, Osipiuk J, Edwards AM, Savchenko A, Joachimiak A, Yakunin AF: Polyphosphate-dependent synthesis of ATP and ADP by the family-2 polyphosphate kinases in bacteria. Proc Natl Acad Sci U S A. 2008, 105: 17730-17735.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kuroda A, Murphy H, Cashel M, Kornberg A: Guanosine tetra- and pentaphosphate promote accumulation of inorganic polyphosphate in Escherichia coli. J Biol Chem. 1997, 272: 21240-21243.
Article
PubMed
CAS
Google Scholar
Gomez-Garcia MR, Kornberg A: Formation of an actin like filament concurrent with the enzymatic synthesis of inorganic polyphosphate. Proc Natl Acad Sci U S A. 2004, 101: 15876-15880.
Article
PubMed
CAS
PubMed Central
Google Scholar
Hothorn M, Neumann H, Lenherr ED, Wehner M, Rybin V, Hassa PO, Uttenweiler A, Reinhardt M, Schmidt A, Seiler J, Ladurner AG, Herrmann C, Scheffzek K, Mayer A: Catalytic core of a membrane-associated eukaryotic polyphosphate polymerase. Science. 2009, 324: 513-516.
Article
PubMed
CAS
Google Scholar
Reusch RN, Huang R, Koch-Kosuka D: Novel components and enzymatic activities of the human erythrocyte plasma membrane pump. FEBS Letts. 1997, 412: 592-596.
Article
CAS
Google Scholar
Lonetti A, Szijgyarto Z, Bosch D, Loss O, Azevedo C, Saiardi A: Identification of an evolutionarily conserved family of inorganic polyphosphate endopolyphosphatases. J Biol Chem. 2011, 286 (37): 31966-31974.
Article
PubMed
CAS
PubMed Central
Google Scholar
Schaack S, Gilbert C, Fechotte C: Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends Ecol Evol. 2010, 25: 537-546.
Article
PubMed
PubMed Central
Google Scholar
Hooley P, Whitehead MP, Brown MRW: Eukaryote polyphosphate kinases – is the “Kornberg” complex ubiquitous?. Trends Biochem Sci. 2008, 33: 577-582.
Article
PubMed
CAS
Google Scholar
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25: 3389-3402.
Article
PubMed
CAS
PubMed Central
Google Scholar
Notre-Dame C, Higgins DG, Heringa J: T-Coffee: A novel method for multiple sequence alignments. J Mol Biol. 2000, 302: 205-217.
Article
CAS
Google Scholar
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG: The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 25: 4876-4882.
Article
PubMed
CAS
PubMed Central
Google Scholar
Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32: 1792-1797.
Article
PubMed
CAS
PubMed Central
Google Scholar
Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, Claverie JM, Gascuel O: Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 2008, 36: W465-W469.
Article
PubMed
CAS
PubMed Central
Google Scholar
Page RMD: Treeview. An application to display phylogenetic trees on personal computers. Comp Appl Biosci. 1996, 12: 357-358.
PubMed
CAS
Google Scholar
Eichinger LL, Noegel AA: Crawling into a new era – the Dictyostelium genome project. EMBO J. 2003, 22: 1941-1946.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kornberg A: Abundant microbial inorganic polyphosphate, Poly P kinases are underappreciated. Microbe. 2008, 3: 119-123.
Google Scholar
Lang D, Zimmer AD, Rensing SA, Resk R: Exploring plant biodiversity : the Physcomitrella genome and beyond. Trends Plant Sci. 2008, 13: 542-549.
Article
PubMed
CAS
Google Scholar
Poptsova MS, Gogarten JP: Using comparative genome analysis to identify problems in annotated microbial genomes. Microbiology. 2010, 156: 1909-1917.
Article
PubMed
CAS
Google Scholar
Dunning Hotopp JC, Clark ME, Oliveira DC, Foster JM, Fischer P, Muñoz Torres MC, Giebel JD, Kumar N, Ishmael N, Wang S, Ingram J, Nene RV, Shepard J, Tomkins J, Richards S, Spiro DJ, Ghedin E, Slatko BE, Tettelin H, Werren JH: Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science. 2007, 317: 1753-1756.
Article
PubMed
CAS
Google Scholar
Nikoh N, Tanaka K, Shibata F, Kondo N, Hizume M, Shimada M, Fukatsu T: Wolbachia genome integrated in an insect chromosome: evolution and fate of laterally transferred endosymbiont genes. Genome Res. 2008, 18: 272-280.
Article
PubMed
CAS
PubMed Central
Google Scholar
Klasson L, Kambris Z, Cook PE, Walker T, Sinkins SP: Horizontal gene transfer between Wolbachia and the mosquito Aedes aegypti. BMC Genomics. 2009, 10: 33-10.1186/1471-2164-10-33.
Article
PubMed
PubMed Central
Google Scholar
Finazzi G, Moreau H, Bowler C: Genomic insights into photosynthesis in eukaryotic phytoplankton. Trends Plant Sci. 2010, 15: 565-572.
Article
PubMed
CAS
Google Scholar
Huang J, Gogarten JP: Concerted gene recruitment in early plant evolution. Genome Biol. 2008, 9: R109-http://genomebiology.com/2008/9/7/R109,
Article
PubMed
PubMed Central
Google Scholar
Derelle E, Ferraz C, Escande ML, Eychenié S, Cooke R, Piganeau G, Desdevises Y, Bellec L, Moreau H, Grimsley N: Life cycle and genome of OtV5, a large DNA virus of the pelagic marine unicellular green alga Ostreococcus tauri. PLoS One. 2008, 3: e2250-10.1371/journal.pone.0002250.
Article
PubMed
PubMed Central
Google Scholar
Raymond J, Blankenship RE: Horizontal gene transfer in eukaryotic algal evolution. Proc Natl Acad Sci U S A. 2003, 100: 7419-7420.
Article
PubMed
CAS
PubMed Central
Google Scholar
Rohwer F, Thurber RV: Viruses manipulate the marine environment. Nature. 2009, 459: 207-212.
Article
PubMed
CAS
Google Scholar
Richards TA: Genome evolution:horizontal movement in the fungi. Curr Biol. 2011, 21: R166-
Article
PubMed
CAS
Google Scholar
Roy SW, Irimia M: Mystery of intron gain: new data and new models. Trends Genet. 2009, 25 (2): 67-73.
Article
PubMed
CAS
Google Scholar
Jeffares DC, Mourier T, Penny D: The biology of intron gain and loss. Trends Genet. 2006, 22: 16-22.
Article
PubMed
CAS
Google Scholar
Gladyshev EA, Meselson M, Arkhipova IR: Massive horizontal gene transfer in bdelloid rotifers. Science. 2008, 320: 1210-1213.
Article
PubMed
CAS
Google Scholar
Roy SW, Irimia M, Penny D: Very little intron gain in Entamoeba histolytica genes laterally transferred from prokaryotes. Mol Biol Evol. 2006, 23: 1824-1827.
Article
PubMed
CAS
Google Scholar
Roy SW, Penny D: Patterns of intron loss and gain in plants: intron-loss dominated evolution and genome-wide comparison of O. sativa and A.thaliana. Mol Biol Evol. 2007, 24: 171-181.
Article
PubMed
CAS
Google Scholar
Csuros M, Rogozin IB, Koonin EV: A detailed history of intron-rich eukaryotic ancestors inferred from a global survey of 100 complete genomes. PLoS Comp. Biol. 2011, 7: e1002150-10.1371/journal.pcbi.1002150.
Article
CAS
Google Scholar
Gustavsson S, Lebrun A-S, Nordén K, Chaumont F, Johanson U: A novel plant major intrinsic protein in Physcomitrella patens most similar to bacterial glycerol channels. Plant Physiol. 2003, 139: 287-295.
Article
Google Scholar
Stenoien HK: Compact genes are highly expressed in the moss Physcomitrella patens. J Evol Biol. 2007, 20: 1223-1229.
Article
PubMed
CAS
Google Scholar
Markmann-Mulisch U, Hadi MZ, Koepchen K, Alonso JC, Russo VE, Schell J, Reiss B: The organization of Physcomitrella patens RAD51 genes is unique among eukaryotic organisms. Proc Natl Acad Sci U S A. 2002, 99: 2959-2964.
Article
PubMed
CAS
PubMed Central
Google Scholar
Sucgang R, Kuo A, Tian X, Salerno W, Parikh A, Feasley CL, Dalin E, Tu H, Huang E, Barry K, Lindquist E, Shapiro H, Bruce D, Schmutz J, Salamov A, Fey P, Gaudet P, Anjard C, Babu MM, Basu S, Bushmanova Y, van der Wel H, Katoh-Kurasawa M, Dinh C, Coutinho PM, Saito T, Elias M, Schaap P, Kay RR, Henrissat B, Eichinger L, Rivero F, Putnam NH, West CM, Loomis WF, Chisholm RL, Shaulsky G, Strassmann JE, Queller DC, Kuspa A, Grigoriev IV: Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum. Genome Biol. 2011, 12: R20-
Article
PubMed
CAS
PubMed Central
Google Scholar
Hirano K, Nakajima M, Asano K, Nishiyama T, Sakakibara H, Kojima M, Katoh E, Xiang H, Tanahashi T, Hasebe M, Banks JA, Ashikari M, Kitano H, Ueguchi-Tanaka M, Matsuoka M: The GID-1 mediated gibberellin perception mechanism is conserved in the lycophyte Selaginella meoellendorffii but not in the bryophyte Physcomitrella patens. Plant Cell. 2007, 19: 3058-3079.
Article
PubMed
CAS
PubMed Central
Google Scholar
Yasigawa F, Nishida K, Yoshida M, Ohnuma M, Shimada T, Fujiwara T, Yoshida Y, Misumi O, Kuroiwa H, Kuroiwa T: Identification of novel proteins in isolated polyphosphate vacuoles in the primitive red alga Cyanidioschyzon merolae. Plant J. 2009, 60: 882-893.
Article
Google Scholar
Mitsuhashi N, Ohnishi M, Sekiguchi Y, Kwon YU, Chang YT, Chung SK, Inoue Y, Reid RJ, Yagisawa H, Mimura T: Phytic acid synthesis and vacuolar accumulation in suspension-cultured cells of Catharanthus roseus induced by high concentration of inorganic phosphate and cations. Plant Physiol. 2005, 138: 1607-1614.
Article
PubMed
CAS
PubMed Central
Google Scholar
Le Bihan T, Martin SF, Chirnside ES, Van Ooijen G, Barrios-Llerena ME, O’Neill JS, Shliaha PV, Kerr LE, Millar AJ: Shotgun proteomic analysis of the unicellular alga Ostreococcus tauri. J Proteomics. 2011, 74: 2060-2070.
Article
PubMed
CAS
Google Scholar
Nishiyama T, Fujita T, Shin-I T, Seki M, Nishide H, Uchiyama I, Kamiya A, Carninci P, Hayashizaki Y, Shinozaki K, Kohara Y, Hasebe M: Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana; implication for land plant evolution. Proc Natl Acad Sci U S A. 2003, 100: 8007-8012.
Article
PubMed
CAS
PubMed Central
Google Scholar
Emanuelsson O, Brunak S, Von Heijne G, Nielson H: Locating proteins in the cell using TargetP, SignalP and related tools. Nature Protoc. 2007, 2: 953-971.
Article
CAS
Google Scholar
Zhao J, Zhao J, Niu W, Yao J, Mohr S, Marcotte EM, Lambowitz AM: Group II intron protein localisation insertion sites are affected by polyphosphate. PLoS Biol. 2008, 6: e150-http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0060150,
Article
PubMed
PubMed Central
Google Scholar
Zhang H, Gomez-Garcia MR, Brown MRW, Kornberg A: Inorganic polyphosphate in Dictyostelium: influence on development, sporulation and predation. Proc Natl Acad Sci U S A. 2005, 102: 2731-2735.
Article
PubMed
CAS
PubMed Central
Google Scholar
Lenton TM, Crouch M, Johnson M, Pires N, Dolan L: First plants cooled the Ordovician. Nature Geosci. 2012, 5: 86-89.
Article
CAS
Google Scholar