Characterization of the orf1glnKamtB operon of Herbaspirillum seropedicae

Archives of Microbiology

Volumn 185, Issue 1, 2006, Pages 55-62

  Noindorf, Lilian ^a   Rego, Fabiane G M ^a   Baura, Valter A ^a   Monteiro, Rose A ^a   Wassem, Roseli ^a   Cruz, Leonardo M ^a   Rigo, Liu U ^a   Souza, Emanuel M ^a   Steffens, Maria B R ^a   Pedrosa, Fabio O ^a   Chubatsu, Leda S ^a  

^a FEDERAL UNIVERSITY OF PARANÁ   (Brazil)

Author keywords

Ammonium transporter; amtB; glnK; Herbaspirillum seropedicae; PII like protein

Indexed keywords

NITROGENASE; PROTEIN; PROTEIN AMTB; PROTEIN GLNK; PROTEIN ORF1; UNCLASSIFIED DRUG;

ARTICLE; GENE EXPRESSION; GENE ISOLATION; GENE SEQUENCE; GENETIC TRAIT; GENETIC TRANSCRIPTION; HERBASPIRILLUM; HERBASPIRILLUM SEROPEDICAE; MUTANT; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PRIORITY JOURNAL; PROTEIN FUNCTION;

BASE SEQUENCE; CATION TRANSPORT PROTEINS; GENES, BACTERIAL; HERBASPIRILLUM; OPEN READING FRAMES; OPERON; PII NITROGEN REGULATORY PROTEINS;

BACTERIA (MICROORGANISMS); HERBASPIRILLUM; HERBASPIRILLUM SEROPEDICAE; POACEAE;

EID: 33644545067     PISSN: 03028933     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00203-005-0066-4     Document Type: Article

References (41)

1. Baldani JI, Baldani VLD, Seldin L, Dobereiner J (1986) Characterization of Herbaspirilium seropedicae gen. nov. sp nov., a new root-associated nitrogen-fixing bacterium. Int J Syst Bacteriol 36:86-93
2. Baldani VLD, Baldani JI, Olivares F, Dobereiner J (1991) Identication and ecology of Herbaspirillum seropedicae and the closely related Pseudomonas rubrisubalbicans. Symbiosis 13:65-73
3. Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340:783-795, DOI: 10.1016/j.jmb.2004.05.028
4. Benelli EM, Souza EM, Funayama S, Rigo LU, Pedrosa FO (1997) Evidence for two possible glnB-type genes in Herbaspirillum seropedicae. J Bacteriol 179:4623-4626
5. Blakey D, Leech A, Thomas GH, Coutts G, Findlay K, Merrick M (2002) Purification of the Escherichia coli ammonium transporter AmtB reveals a trimeric stoichiometry. Biochem J 364:527-535
6. Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248-254
7. Carr PD, Cheah E, Suffolk PM, Vasudevan SG, Dixon NE, Ollis DL (1996) X-ray structure of the signal transduction protein from Escherichia cou at 1.9Å. Acta Crystallogr Sect D: Biol Crystallogr 52:93-104, DOI: 10.1107/S0907444995007293
8. Chaney AL, Marbach EP (1962) Modified reagents for determination of urea and ammonia. Clin Chem 8:130-132
9. Coutts G, Thomas G, Blakey D, Merrick M (2002) Membrane sequestration of the signal transduction protein GlnK by the ammonium transporter AmtB. EMBO J 21:536-545
10. de Zamaroczy M (1998) Structural homologues P(II) and P(Z) of Azospirillum brasilense provide intracellular signalling for selective regulation of various nitrogen-dependent functions. Mol Microbiol 29:449-463, DOI: 10.1046/j.1365-2958.1998.00938.x
11. Fu H, Burris RH (1989) Ammonium inhibition of nitrogenase activity in Herbaspirillum seropedicae. J Bacteriol 171:3168-3175
12. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95-98
13. Henikoff S (1984) Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing. Gene 28:351-359
14. Huergo LF, Noindorf L, Sousa EM, Steffens MBR, Yates GM, Pedrosa FO, Chubatsu LS (1999) Partial cloning of the ammonium transporter genes of Azospirillum brasilense and Herbaspirillum seropedicae. In: Pedrosa FO, Hungria M, Yates MG, Newton WE (eds) Nitrogen fixation: from molecules to crop productivy. Kluwer Academic Publishers, Netherlands
15. Khademi S, O'Connell J III, Remis J, Robles-Colmenares Y, Miercke LJ, Stroud RM (2004) Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 Å. Science 305:1587-1594, DOI: 10.1126/science.1101952
16. Kahsay RY, Gao G, Liao L (2005) An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes. Bioinformatics 21:1853-1858
17. Klassen G, Pedrosa FO, Souza EM, Funayama S, Rigo LU (1997) Effect of nitrogen compounds on nitrogenase activity in Herbaspirillum seropedicae SMR1. Can J Microbiol 43:887-891
18. Kokotek W, Lotz W (1989) Construction of a lacZ-kanamycin-resistance cassette, useful for site-directed mutagenesis and as a promoter probe. Gene 84:467-471
19. Machado HB, Funayama S, Rigo LU, Pedrosa FO (1991) Excretion of ammonium by Azospirillum brasilense mutants resistant to ethylenediamine. Can J Microbiol 37:549-553
20. Machado IM, Yates MG, Machado HB, Souza EM, Pedrosa FO (1996) Cloning and sequencing of the nitrogenase structural genes nifHDK of Herbaspirillum seropedicae. Braz J Med Biol Res 29:1599-1602
21. MacPherson KH, Xu Y, Cheah E, Carr PD, van Heeswijk WC, Westerhoff HV, Luque E, Vasudevan SG, Ollis DL (1998) Crystallization and preliminary X-ray analysis of Escherichia coli GlnK. Acta Crystallogr Sect D: Biol Crystallogr 54:996-998, DOI: 10.1107/S0907444998001887
22. Marini AM, Matassi G, Raynal V, Andre B, Cartron JP, Cherif-Zahar B (2000) The human Rhesus-associated RhAG protein and a kidney homologue promote ammonium transport in yeast. Nat Genet 3:341-344, DOI: 10.1038/81656
23. Martin DE, Hurek T, Reinhold-Hurek B (2000) Occurrence of three PII-like signal transmitter proteins in the diazotrophic proteobacterium Azoarcus sp. BH72. Mol Microbiol 38:276-288
24. Martin DE, Reinhold-Hurek B (2002) Distinct roles of PII-like signal transmitter proteins and amtB in Regulation of nif gene expression, nitrogenase activity, and posttranslational modification of NifH in Azoarcus sp. Strain BH72 184:2251-2259, DOI: 10.1128/JB.184.8.2251-2259.2002
25. Mead DA, Szczesna-Skorupa E, Kemper B (1986) Single-stranded DNA 'blue' T7 promoter plasmids: a versatile tandem promoter system for cloning and protein engineering. Protein Eng 1:67-74
26. Miller JH (1972) Experiments in molecular genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor
27. Nakai K, Kanehisa M (1991) Expert system for predicting protein localization sites in Gram-negative bacteria. Proteins 11:95-110
28. Pedrosa FO, Benelli EM, Yates MG, Wassem R, Monteiro RA, Klassen G, Steffens MB, Souza EM, Chubatsu LS, Rigo LU (2001) Recent developments in the structural organization and regulation of nitrogen fixation genes in Herbaspirillum seropedicae. J Biotechnol 91:189-195, DOI: 10.1016/S0168-1656(01) 00343-1
29. Persuhn DC, Souza EM, Steffens MBR, Pedrosa FO, Yates MG, Rigo LU (2000) The transcriptional activator NtrC controls the expression and activity of glutamine synthetase in Herbaspirillum seropedicae. FEMS Microbiol Lett 192:217-221, DOI: 10.1016/S0378-1097(00)00435-3
30. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
31. Simon R, Prieffer U, Puhler A (1983) A broad host range mobilization system for in vitro genetic engineering: transposon mutagenesis in Gram-negative bacteria. BioTechnology 1:784-791
32. Souza EM, Pedrosa FP, Rigo LU, Machado HB, Yates MG (2000) Expression of the nif A gene of Herbaspirillum seropedicae: role of the NtrC and NifA binding sites and of the -24/-12 promoter element. Microbiology 146:1407-1418
33. Spaink HP, Okker RJH, Wijffelman CA, Pees E, Lugtenberg BJJ (1987) Promoters in the nodulation region of the Rhizobium leguminosarum sym plasmid pRL1JI. Plant Mol Biol 9:27-39
34. Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28:33-36
35. Thomas G, Coutts G, Merrick M (2000a) The glnKamtB operon. A conserved gene pair in prokaryotes. Mol Microbiol 37:331-344, DOI: 10.1016/S0168-9525(99) 01887-9
36. Thomas GH, Mullins JG, Merrick M (2000b) Membrane topology of the Mep/Amt family of ammonium transporters. Mol Microbiol 2:331-344, DOI: 10.1046/j.1365-2958.2000.01994.x
37. Xu Y, Cheah E, Carr PD, van Heeswijk WC, Westerhoff HV, Vasudevan SG, Ollis DL (1998) GlnK, a PH-homologue: structure reveals ATP binding site and indicates how the T-loops may be involved in molecular recognition. J Mol Biol 2821:149k-165k, DOI: 10.1006/jmbi.1998.1979
38. Yakunin AF, Hallenbeck PC (2002) AmtB is necessary for NH4+-induced nitrogenase switch-off and ADP-ribosylation in Rhodobacter capsulatus. J Bacteriol 184:4081-4088, DOI:10.1128/JB.184.15.4081-4088.2002
39. Young JPW (1992) Phylogenetic classification of nitrogen-fixing organisms. In: Stacey G, Burris RH, Evans HJ (eds) Biological nitrogen fixation. Chapman and Hall, New York
40. Zhang Y, Burris RH, Ludden PW, Roberts GP (1997) Regulation of nitrogen fixation in Azospirillum brasilense. FEMS Microbiol Lett 152:195-204, DOI: 10.1016/S0378-1097(97)00187-0
41. Zheng L, Kostrewa D, Bernèche S, Winkler FK, Li XD (2004) The mechanism of ammonia transport based on the crystal structure of AmtB of Escherichia coli. Proc Natl Acad Sci USA 101:17090-17095, DOI: 10.1073/pnas.0406475101