On an early gene for membrane-integral inorganic pyrophosphatase in the genome of an apparently pre-LUCA extremophile, the archaeon Candidatus Korarchaeum cryptofilum

Journal of Molecular Evolution

Volumn 78, Issue 2, 2014, Pages 140-147

  Baltscheffsky, Herrick ^a   Persson, Bengt ^b,c  

^a STOCKHOLM UNIVERSITY   (Sweden)

^b UPPSALA UNIVERSITY   (Sweden)

^c KAROLINSKA INSTITUTE   (Sweden)

Author keywords

Archaeon; Bioinformatics; Energy; Evolution; Extremophile; miPPase; Pyrophosphatase

Indexed keywords

INORGANIC PYROPHOSPHATASE;

AMINO ACID SEQUENCE; ARCHAEAL GENOME; ARCHAEON; ARTICLE; CHEMISTRY; CLASSIFICATION; EVOLUTION; GENETICS; MOLECULAR GENETICS; PHYLOGENY; PROTEIN MOTIF; SEQUENCE ALIGNMENT;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ARCHAEA; BIOLOGICAL EVOLUTION; GENOME, ARCHAEAL; INORGANIC PYROPHOSPHATASE; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT;

EID: 84894359431     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-014-9610-7     Document Type: Article

References (45)

1. +-translocating pyrophosphatases. Microbiology 152:1243-1247
2. Baltscheffsky M (1967) Inorganic pyrophosphate and ATP as energy donors in chromatophores from Rhodospirillum rubrum. Nature 216:241-243
3. Baltscheffsky H (1997) Major "anastrophes" in the origin and early evolution of biological energy conversion. J Theor Biol 187:495-501
4. Baltscheffsky H, von Stedingk L-V, Heldt H-W, Klingenberg M (1966) Inorganic pyrophsphate: formation in bacterial photophosphorylation. Science 153:1120-1122
5. Baltscheffsky M, Nadanaciva S, Schultz A (1998) A pyrophosphate synthase gene: molecular cloning and sequencing of the cDNA encoding the inorganic pyrophosphate synthase from Rhodospirillum rubrum. Biochim Biophys Acta 1364:301-306
6. +-PPases: a tightly membrane bound family. FEBS Lett 457:527-533
7. Baltscheffsky H, Schultz A, Persson B, Baltscheffsky M (2001) Tetra- and nonapeptidyl motifs in the origin and evolution of photosynthetic bioenergy conversion. Possible implications for the molecular origin of phosphate metabolism. In: Chela-Flores J, Owen T, Raulin F (eds) First steps in the origin of life in the universe. Kluwer, Dordrecht, pp 173-178
8. Baltscheffsky H, Schultz A, Baltscheffsky M (2002) Fundamental characteristics of life and of the molecular origin and evolution of biological energy conversion. In: Palyi G, Zucchi C, Caglioti L (eds) Fundamentals of life. Elsevier, New York, pp 87-94
9. Baltscheffsky H, Persson B, Schultz A, Peréz-Castineira JR, Baltscheffsky M (2004) Origin and evolution of very early sequence motifs in enzymes. In: Seckbach J, Chela-Flores J, Owen T, Raulin F (eds) Life in the universe. Kluwer, Dordrecht, pp 107-110
10. + transport in prokaryotes. Microbiol Mol Biol Rev 77:267-276
11. Baymann F, Lebrun E, Brugna M, Schoepp-Cothenet B, Giudici-Orticoni MT, Nitschke W (2003) The redox protein construction kit: pre-last universal common ancestor evolution of energy-conserving enzymes. Phil Trans R Soc Lond B 358:267-274
12. Beskow A, Baltscheffsky H (2012) Här kommer anastrofen! Forskning Framsteg 10:30-31 (in Swedish)
13. Bielen AM, Willquist K, Engman J, van der Oost J, van Niel Ed WJ, Kengen SWM (2010) Pyrophosphate as a central energy carrier in the hydrogen-producing extremely thermophilic Caldicellulosiruptor saccharolyticus. FEMS Microbiol Lett 307:48-54
14. Branscomb E, Russell MJ (2013) Turnstiles and bifurcators: the disequilibrium converting engines that put metabolism on the road. Biochim Biophys Acta 1827:62-78
15. Elkins JG, Podar M, Graham DE, Makarova KS, Wolf Y, Randau L, Hedlund BP, Brochier-Armanet C, Kunin V, Anderson I, Lapidus A, Goltsman E, Barry K, Koonin EV, Hugenholtz P, Kyrpides N, Wanner G, Richardson P, Keller M, Stetter KO (2008) A korarchaeal genome reveals insights into the evolution of the archaea. Proc Natl Acad Sci USA 105:8102-8107
16. Farid TA, Kodali G, Solomon LA, Lichtenstein BR, Sheehan MM, Fry BA, Bialas C, Ennist NM, Siedlecki JA, Zhao Z, Stetz MA, Valentine KG, Anderson JLR, Wand AJ, Discher BM, Moser CC, Dutton PL (2013) Elementary tetrahelical protein design for diverse oxidoreductase functions. Nat Chem Biol 9:826-833
17. Giger L, Caner S, Obexer R, Kast P, Baker D, Ban N, Hilvert D (2013) Evolution of a designed retro-aldolase leads to complete active site remodeling. Nat Chem Biol 9:494-498
18. +-PPase family. FEBS J 273:5183-5193
19. +, and early evolution. Orig Life Evol Biosph 41:483-493
20. Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772-780
21. Kellosalo J, Kajander T, Kogan K, Pokharel K, Goldman A (2012) The structure and catalytic cycle of a sodium-pumping pyrophosphatase. Science 337:473-476
22. Kyrpides N, Overbeek R, Ouzounis C (1999) Universal protein families and the functional content of the last universal common ancestor. J Mol Evol 49:413-423
23. Lane N, Martin WF (2010) The origin of membrane bioenergetics. Cell 151:1406-1416
24. Lane N, Allen JF, Martin W (2010) How did LUCA make a living? Chemiosmosis in the origin of life. BioEssays 32:271-280
25. Lazcano A, Miller SL (1999) On the origin of metabolic pathways. J Mol Evol 49:424-431
26. +-translocating pyrophosphatase. Nature 484:399-403
27. Lipmann F (1941) Metabolic generation and utilization of phosphate bond energy. Adv Enzymol 1:99-162
28. Lipmann F (1965) Projecting backward from the present stage of evolution of biosynthesis. In: Fox SW (ed) The origins of prebiological systems and of their molecular matrices. Academic Press, New York, pp 212-216
29. López-Marqués RL, Péres-Castineira JR, Losada M, Serrano A (2004) Differential regulation of soluble and membrane-bound inorganic pyrophosphatases in the photosynthetic bacterium Rhodospirillum rubrum provides insights into pyrophosphate-based stress bioenergetics. J Bacteriol 186:5418-5426
30. +-translocating pyrophosphatases. J Biol Chem 286:21633-21642
31. +-pyrophosphatases can transport protons at low sodium concentrations. J Biol Chem 288(49):35489-35499. doi: 10.1074/jbc.M113.510909
32. +. Proc Natl Acad Sci USA 110:1255-1260
33. +-pyrophosphatase: a novel primary sodium pump. Biochemistry 46:8872-8878
34. Milner-White EJ, Russell MJ (2011) Functional capabilities of the earliest peptides and the emergence of life. Genes 2:671-688
35. Moyle J, Mitchell R, Mitchell P (1972) Proton-translocating pyrophosphatase of Rhodospirillum rubrum. FEBS Lett 23:233-236
36. Mulkidjanian AY, Galperin MY, Makarova KS, Wolf YI, Koonin EV (2008) Evolutionary primacy of sodium bioenergetics. Biol Direct 3:13
37. Nitschke W, Russell MJ (2009) Hydrothermal focusing of chemical and chemiosmotic energy, supported by delivery of catalytic Fe, Ni, Mo/W Co, S and Se, forced life to emerge. J Mol Evol 69:481-496
38. Perrière G, Gouy M (1996) WWW-query: an on-line retrieval system for biological sequence banks. Biochimie 78:364-369
39. Russell MJ, Hall AJ (1997) The emergence of life from iron monosulphide bubbles at a submarine hydrothermal redox and pH front. J Geol Soc Lond 154:377-402
40. Russell MJ, Daniel RM, Hall AJ, Sherringham J (1994) A hydrothermally precipitated catalytic iron sulphide membrane as a first step toward life. J Mol Evol 39:231-243
41. Schoepp-Cothenet B, van Lis R, Atteia A, Baymann F, Capowiez L, Ducluzeau AL, Duval S, ten Brink F, Russell MJ, Nitschke W (2013) On the universal core of bioenergetics. Biochim Biophys Acta 1827:79-93
42. +-PPases: yesterday, today and tomorrow. IUBMB Life 59:76-83
43. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539
44. UniProt Consortium (2011) Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res 39:D214-D219
45. Yamagata Y, Watanabe H, Saitoh M, Namba T (1991) Volcanic production of polyphosphates and its relevance to prebiotic evolution. Nature 352:516-519