The PII superfamily revised: A novel group and evolutionary insights

Journal of Molecular Evolution

Volumn 68, Issue 4, 2009, Pages 322-336

  Sant'Anna, Fernando Hayashi ^a   Trentini, Débora Broch ^a   De Souto Weber, Shana ^a   Cecagno, Ricardo ^a   Da Silva, Sérgio Ceroni ^a   Schrank, Irene Silveira ^a  

^a FEDERAL UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

Author keywords

AmtB; Cellular signaling; GlnB; GlnK; Horizontal gene transfer; Metal efflux pump; Nif; Nitrogen metabolism; PII

Indexed keywords

BACTERIAL PROTEIN; PII PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; EVOLUTIONARY HOMOLOGY; GENE SEQUENCE; GENE TRANSFER; GENETIC ANALYSIS; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; UNINDEXED SEQUENCE;

AMINO ACID SEQUENCE; AZOSPIRILLUM BRASILENSE; BACTERIA; BACTERIAL PROTEINS; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; PII NITROGEN REGULATORY PROTEINS; RNA, RIBOSOMAL, 16S; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

PROKARYOTA;

EID: 64949176032     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-009-9209-6     Document Type: Article

References (44)

1. SF Altschul TL Madden AA Schaffer J Zhang Z Zhang W Miller DJ Lipman 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res 25 3389 3402
2. T Arcondéguy R Jack M Merrick 2001 P(II) signal transduction proteins, pivotal players in microbial nitrogen control Microbiol Mol Biol Rev 65 80 105
3. F Arnesano L Banci M Benvenuti I Bertini V Calderone S Mangani MS Viezzoli 2003 The evolutionarily conserved trimeric structure of CutA1 proteins suggests a role in signal transduction J Biol Chem 278 46 45999 46006
4. J Brown 2003 Ancient horizontal gene transfer Nat Rev Genet 4 121 132
5. N Brown J Stoyanov S Kidd J Hobman 2003 The MerR family of transcriptional regulators FEMS Microbiol Rev 27 145 163
6. MJ Conroy A Durand D Lupo XD Li PA Bullough FK Winkler M Merrick 2007 The crystal structure of the Escherichia coli AmtB-GlnK complex reveals how GlnK regulates the ammonia channel Proc Natl Acad Sci USA 104 1213 1218
7. JA Dodsworth JA Leigh 2007 NifI inhibits nitrogenase by competing with Fe protein for binding to the MoFe protein Biochem Biophys Res Commun 364 378 382
8. RC Edgar 2004 MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res 32 1792 1797
9. J Felsenstein 1985 Confidence intervals on phylogenies: an approach using the bootstrap Evolution 39 783 791
10. ST Fong J Camakaris BT Lee 1995 Molecular genetics of a chromosomal locus involved in copper tolerance in Escherichia coli K-12 Mol Microbiol 15 6 1127 1137
11. K Forchhammer 2008 PII signal transducers: novel functional and structural insights Trends Microbiol 16 65 72
12. K Forchhammer 2004 Global carbon/nitrogen control by PII signal transduction in cyanobacteria: from signals to targets FEMS Microbiol Rev 28 319 333
13. S Guindon F Lethiec P Duroux O Gascuel 2005 PHYML Online-a web server for fast maximum likelihood-based phylogenetic inference Nucleic Acids Res 33 W557 W559
14. Hanada S, Pierson BK (2006) The family Chloroflexaceae. In: Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes: a handbook on the biology of bacteria. Springer, New York, pp 815-842
15. A Hesketh D Fink B Gust HU Rexer B Scheel K Chater W Wohlleben A Engels 2002 The GlnD and GlnK homologues of Streptomyces coelicolor A3(2) are functionally dissimilar to their nitrogen regulatory system counterparts from enteric bacteria Mol Microbiol 46 2 319 330
16. Huber R, Eder W (2006) Aquificales. In: Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes. Springer, New York, pp 925-938
17. L Huergo L Chubatsu E Souza FO Pedrosa M Steffens M Merrick 2006 Interactions between PII proteins and the nitrogenase regulatory enzymes DraT and DraG in Azospirillum brasilense FEBS Lett 580 5232 5236
18. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic Press, New York, pp 21-132
19. JA Leigh JA Dodsworth 2007 Nitrogen regulation in bacteria and archaea Annu Rev Microbiol 61 349 377
20. Margulis L (1993) Symbiosis in cell evolution, 2nd edn. WH Freeman, New York
21. DS Navaratnam FS Fernando JD Priddle K Giles SM Clegg DJ Pappin I Craig AD Smith 2000 Hydrophobic protein that copurifies with human brain acetylcholinesterase: amino acid sequence, genomic organization, and chromosomal localization J Neurochem 74 5 2146 2153
22. KB Nicholas HB Nicholas DW Deerfield 1997 GeneDoc: analysis and visualization of genetic variation EMBNEW NEWS 4 14
23. CE Nichols S Sainsbury NS Berrow D Alderton NJ Saunders DK Stammers RJ Owens 2006 Structure of the PII signal transduction protein of Neisseria meningitidis at 1.85 A resolution Acta Crystallogr Sect F Struct Biol Cryst Commun 62 494 497
24. A Ninfa M Atkinson 2000 PII signal transduction proteins Trends Microbiol 8 172 179
25. A Ninfa P Jiang 2005 PII signal transduction proteins: sensors of [alpha]-ketoglutarate that regulate nitrogen metabolism Curr Opin Microbiol 8 168 173
26. T Osanai K Tanaka 2007 Keeping in touch with PII: PII-interacting proteins in unicellular cyanobacteria Plant Cell Physiol 48 908 914
27. EJ Patriarca R Tatè M Iaccarino 2002 Key role of bacterial NH(4)(+) metabolism in Rhizobium-plant symbiosis Microbiol Mol Biol Rev 66 203 222
28. 3 gas channels Transfus Clin Biol 13 85 94
29. AL Perrier X Cousin N Boschetti R Haas JM Chatel S Bon WL Roberts SR Pickett J Massoulié TL Rosenberry E Krejci 2000 Two distinct proteins are associated with tetrameric acetylcholinesterase on the cell surface J Biol Chem 275 44 34260 34265
30. JA Raven JF Allen 2003 Genomics and chloroplast evolution: what did cyanobacteria do for plants? Genome Biol 4 209
31. J Raymond J Siefert C Staples R Blankenship 2004 The natural history of nitrogen fixation Mol Biol Evol 21 541 554
32. L Reitzer 2003 Nitrogen assimilation and global regulation in Escherichia coli Annu Rev Microbiol 57 155 176
33. P Rice I Longden A Bleasby 2000 EMBOSS: the European Molecular Biology Open Software Suite Trends Genet 16 276 277
34. N Saitou 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees Mol Biol Evol 4 406 425
35. H Sakai H Wang C Takemoto-Hori T Kaminishi H Yamaguchi Y Kamewari T Terada S Kuramitsu M Shirouzu S Yokoyama 2005 Crystal structures of the signal transducing protein GlnK from Thermus thermophilus HB8 J Struct Biol 149 99 110
36. J Strösser A Lüdke S Schaffer R Krämer A Burkovski 2004 Regulation of GlnK activity: modification, membrane sequestration and proteolysis as regulatory principles in the network of nitrogen control in Corynebacterium glutamicum Mol Microbiol 54 1 132 147
37. K Tamura J Dudley M Nei S Kumar 2007 MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software, version 4.0 Mol Biol Evol 24 1596 1599
38. G Thomas G Coutts M Merrick 2000 The glnKamtB operon: a conserved gene pair in prokaryotes Trends Genet 16 11 14
39. H Wang CC Franke S Nordlund A Norén 2005 Reversible membrane association of dinitrogenase reductase activating glycohydrolase in the regulation of nitrogenase activity in Rhodospirillum rubrum; dependence on GlnJ and AmtB1 FEMS Microbiol Lett 253 273 279
40. CR Woese 1987 Bacterial evolution Microbiol Rev 51 221 271
41. Y Xu PD Carr P Clancy M Garcia-Dominguez K Forchhammer F Florencio SG Vasudevan MN de Tandeau DL Ollis 2003 The structures of the PII proteins from the cyanobacteria Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803 Acta Crystallogr D Biol Crystallogr 59 2183 2190
42. Y Xu E Cheah PD Carr WC van Heeswijk HV Westerhoff SG Vasudevan DL Ollis 1998 GlnK, a PII-homologue: structure reveals ATP binding site and indicates how the T-loops may be involved in molecular recognition J Mol Biol 282 149 165
43. O Yildiz C Kalthoff S Raunser W Kuhlbrandt 2007 Structure of GlnK1 with bound effectors indicates regulatory mechanism for ammonia uptake EMBO J 26 589 599
44. Zuckerkandl E, Pauling L (1965) Evolutionary divergence and convergence in proteins. In: Bryson V, Vogel HJ (eds) Evolving genes and proteins. Academic Press, New York, pp 97-166