Molecular evolution of nitrate reductase genes

Journal of Molecular Evolution

Volumn 42, Issue 4, 1996, Pages 432-442

  Zhou, Jizhong ^a,b   Kleinhofs, Andris ^a  

^a WASHINGTON STATE UNIVERSITY   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

Angiosperms; Base composition; Dicots; Intron number and locations; Molecular clock; Monocots; Nitrate reductases; Relative rate test

Indexed keywords

AMINO ACID; DNA; NITRATE REDUCTASE; NUCLEOTIDE;

ALGA; AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; CHLAMYDOMONAS REINHARDTII; CODON; EVOLUTION; FUNGUS; GENE; HIGHER PLANT; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE HOMOLOGY;

ALGAE; ARABIDOPSIS; CHLAMYDOMONAS REINHARDTII; DICOTYLEDONEAE; EMBRYOPHYTA; FUNGI; LILIOPSIDA; MAGNOLIOPHYTA;

EID: 0029989811     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF02498637     Document Type: Article

References (62)

1. Amati BB, Goldschmidt-Clermont M, Wallace CJA, Rochaix J-D (1988) cDNA and deduced amino acid sequences of cytochrome c trom Chlamydomonas reinhardtii. Unexpected functional and phylogenetic implications. J Mol Evol 28:151-160
2. Blake CCF (1978) Do genes-in-pieces imply proteins-in-pieces? Nature 273:267-268
3. Boulter D (1972) Amino acid sequences of cylochrome c and plastocyanins in phylogenetic studies of higher plants. Syst Zool 22:549-553
4. Campbell H, Kinghorn JR (1990) Functional domains of assimilatory nitrate reductases and nitrite reductases. TIBS 15:315-319
5. Cavalier-Smith T (1985) Selfish DNA and the origin of introns. Nature 315:283-284
6. Chang C, Meyerowitz EM (1986) Molecular cloning and DNA sequence of the Arabidopsis thaliana alcohol dehydrogenase gene. Proc Natl Acad Sci USA 83:1408-1412
7. Cheng CL, Dewdney J, Nam HG, den Boer BGW, Goodman HM (1988) A new locus (NIA1) in Arabidopsis thaliana encoding nitrate reductases. EMBO J 7:3309-3314
8. Clegg MT, Zurawski G (1992) Chloroplast DNA and the study of plant phylogeny: present status and future aspects. In: Soltis PS, Soltis DE, Doyle JJ (eds) Molecular systematics of plants. Chapman and Hall. New York, pp 50-91
9. Clegg M (1990) Dating the monocot-dicot divergence. Trend Ecol Evol 5:1-2
10. Cooley RN, Tomsett AB (1985) Determination of the subunit size of NADPH-nitrate reductases from Aspergillus nidulans. Biochim Biophys Acta 831:89-93
11. Crawford NM, Smith M, Bellissimo D, Davis RW (1988) Sequence and nitrate regulation of the Arabidopsis thaliana mRNA encoding nitrate reductases, a metalloflavoprotein with three functional domains. Proc Natl Acad Sci USA 85:5006-5010
12. Cronquist A (1981) An integrated system of classification of flowering plants. Columbia University Press, New York
13. Dailey FA, Warner RL, Somers DA, Kleinhofs A (1982) Characteristics of a nitrate reductases in a barley mutant deficient in NADH nitrate reductases. Plant Physiol 69:1200-1204
14. Darnell JE, Doolittle WF (1986) Speculations on the early course of evolution. Proc Natl Acad Sci USA 83:1271-1275
15. Devereaux J, Haeberli P, Smithies O (1984) A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res 12: 387-395
16. Doebley J, Durbin M, Golenberg EM, Clegg MT, Ma DP (1990) Evolutionary analysis of the large subunit of carboxylase (rbcL) nucleotide sequence among the grasses (Gramineae). Evolution 44: 1097-1108
17. Felsenstein J (1989) PHYLIP - Phylogeny inference package (version 3.2). Cladistics 5:164-166
18. Gaut BS, Clegg MT (1991) Molecular evolution of alcohol dehydrogenase 1 in members of the grass family. Proc Natl Acad Sci USA 88:2060-2064
19. Gilbert W (1978) Why genes in pieces? Nature 271:501
20. Gilbert W, Marchionni M, McKnight G (1986) On the antiquity of introns. Cell 46:151-154
21. Guerrero MG, Vega JM, Losada M (1981) The assimilatory nitrate-reducing system and its regulation. Annu Rev Plant Physiol 32: 169-204
22. Hamat HB, Kleinhofs A, Warner RL (1989) Nitrate reductases induction and molecular characterization in rice (Oryza sativa L.). Mol Gen Genet 218:93-98
23. Hamby RK, Zimmer EA (1992) Ribosomal RNA as a phylogenetic tool in plant systematics. In: Soltis PS, Soltis DE, Doyle JJ (eds) Molecular systematics of plants. Chapman and Hall, New York, pp 50-91
24. Hamby RK, Zimmer EA (1987) Ribosomal RNA sequences for inferring phylogeny within the grass family (Poaceae). Plant Syst Evol 160:29-37
25. Hoff T, Stummann BM, Henningsen KW (1992) Structure, function and regulation of nitrate reductases in higher plants. Physiol Plant 84:616-624
26. Horner RD (1983) Purification and comparison of nil-1 and wild-type NADH: nitrate reductases of Neurospora crassa. Biochim Biophys Acta 744:7-15
27. Johnstone IL, McCabe PC, Greaves P, Gurr SJ, Cole GE, Brow MAD, Unkles SE, Clutterbuck AJ, Kinghorn JR, Innis MA (1990) Isolation and characterization of the crnA-niiA-niaD gene cluster for nitrate assimilation in Aspergillus nidulans. Gene 90:181-192
28. Kleinhofs A, Chao S, Sharp PJ (1988) Mapping of the nitrate reductases genes in barley and wheat. In: Miller TE, Koebner RMD (eds) Proceedings seventh international wheat genetics symposium, vol 1. Institute of Plant Science Research, Cambridge, pp 541-546
29. Kleinhofs A, Warner RL, Melzer (1989) Genetics and molecular biology of higher plant nitrate reductases. In: Poulton JE, Romeo JT, Conn EE (eds) Recent advances in phytochemistry, vol 23, Plant Nitrogen Metabolism. Plenum, New York, pp 117-155
30. Kleinhofs A, Warner RL (1990) Advances in nitrate assimilation. In: Miller BJ, Lea PJ (eds). Intermediary nitrogen metabolism, vol 16, Stumpf PK, Conn EE (eds). The biochemistry of plants. Academic Press, New York, pp 89-120
31. Kubo Y, Oguara N, Nakagawa H (1988) Limited proteolysis of the nitrate reductases from spinach leaves. J Biol Chem 263:19684-19689
32. Li WH, Graur D (1991) Fundamentals of molecular evolution. Sinauer, MA
33. Li W-H, Tanimura M (1987) The molecular clock runs more slowly in man than in apes and monkeys. Nature 326:93-96
34. Liaud MF, Zhang DX, Cerff R (1990) Differential intron loss and endosymbiotic transfer of chloroplast glyceraldehyde-3-phosphate genes to the nucleus. Proc Natl Acad Sci USA 87:8918-8922
35. Liaud MF, Brinkmann H, Cerff R (1992) The α-tubulin gene family of pea: primary structures, genomic organization and intron-dependent evolution of genes. Plant Mol Biol 18:639-651
36. Losada M (1976) Metalloenzymes of the nitrate-reducing system. J Mol Catalysis 1:245-264
37. Martin W, Lydiate D, Brinkmann H, Forkmann G, Saedler H, Cerff R (1993) Molecular phylogenies in angiosperm evolution. Mol Biol Evol 10:140-162
38. Martin W, Gierl A, Saedler H (1989) Molecular evidence for pre-Cretaceous angiosperm origins. Nature 339:46-48
39. Martin PG, Dowd JM, Stone SJL (1983) The study of plant phytogeny using amino acid sequences of ribulose-1,5-bisphosphate carboxylase. II The analysis of small subunit data to form phylogenetic trees. Aust J Bot 31:411-419
40. Martinez P, Martin W, Cerff R (1989) Structure, evolution and anaerobic regulation of a nuclear gene encoding cytosolic glyceraldehyde-3-phosphate dehydrogenase from maize. J Mol Biol 208:551-565
41. Meagher RB, Berry-Iowe S, Rice K (1989) Molecular evolution of the small subunit of ribulose bisphosphate carboxylase: nucleotide substitution and gene conversion. Genetics 123:845-863
42. Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:290-300
43. Pesole G, Bozzetti MP, Preparata G, Saccone C (1991) Glutamine synthetase gene evolution: a good molecular clock. Proc Natl Acad Sci USA 88:522-526
44. Redinbaugh MG, Campbell WH (1981) Purification and characterization of NAD(P)H:nitrate reductases and NADH:nitrate reductases from corn roots. Plant Physiol 68:115-120
45. Renosto F, Schmidt ND, Segel IH (1982) Nitrate reductases from Penicillium chrysogenum: the reduced flavin-adenine dinucleotide-dependent reaction. Arch Biochem Biophys 219:12-20
46. Ritland K, Clegg MT (1987) Evolutionary analysis of plant DNA sequences. Am Nat 130:S74-S100
47. Rothschild LJ, Ragan MA, Coleman AW, Heywood P, Gerbi SA (1986) Are rRNA sequence comparisons the Rosetta stone of phylogenetics? Cell 47:640
48. Sarich VM, Wilson AC (1967) Rates of albumin evolution in primates. Proc Natl Acad Sci USA 58:142-148
49. Scogin R (1981) Amino acid sequence studies and plant phytogeny. In: Yong DA, Sieger DS (eds) Phytochemistry and angiosperm phylogeny. Praeger, New York, pp 19-42
50. Shen TC, Funkhouser EA, Guerrero MG (1976) NADH- and NAD(P)H-nitrate reductases in rice seedlings. Plant Physiol 58: 292-294
51. Stebbins GL (1981) Coevolution of grasses and herbivores. Ann Mo Bot Gard 68:75-86
52. Streit L, Nelson RS, Harper JE (1985) Nitrate reductases from wild-type and nrl-mutant soybean (Glycine max[L]Merr) leaves. I Purification, kinetics, and physical properties. Plant Physiol 78:80-84
53. Sueoka N (1992) Directional mutation pressure, selective constraints, and genetic equilibria. J Mol Evol 34:95-114
54. Sueoka N (1988) Directional mutation pressure and neutral molecular evolution. Proc Natl Acad Sci USA 85:2653-2657
55. Sueoka N (1962) On the genetic basis of variation and heterogeneity of DNA base composition. Proc Natl Acad Sci USA 48:582-592
56. Warner RL, Narayanan KR, Kleinhofs A (1987) Inheritance and expression of NAD( P)H nitrate reductase in barley. Theor Appl Genet 74:714-717
57. Warner RL, Kleinhofs A (1992) Genetics and molecular biology of nitrate metabolism in higher plants. Physiol Plant 85:245-252
58. Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221-271
59. Wolfe KH, Gouy M, Yang YW, Sharp PM, Li WH (1989) Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc Natl Acad Sci USA 86:6201-6205
60. Wolfe KH, Li WH, Sharp PM (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci USA 84:9054-9058
61. Zhou JZ (1993) Molecular evolution of nitrate reductases. PhD dissertation, Washington State University, Pullman, WA 99164
62. Zuckerkandl E, Pauling L (1965) Evolutionary divergence and convergence in proteins. In: Bryson V, Vogel H (eds) Evolving genes and proteins. Academic Press, New York, pp 97-166