Microbial relatives of seed storage proteins: Conservation of motifs in a functionally diverse superfamily of enzymes

Journal of Molecular Evolution

Volumn 46, Issue 2, 1998, Pages 147-154

  Dunwell, Jim M ^a   Gane, Paul J ^b,c  

^a UNIVERSITY OF READING   (United Kingdom)

^b INSTITUTE OF FOOD RESEARCH   (United Kingdom)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Enzyme superfamily; Germin; Histidine cluster; Mannose metabolism; Oxalate oxidase; Protein domain; Seed storage proteins

Indexed keywords

BACTERIAL PROTEIN; DIOXYGENASE; DNA; EPIMERASE; MANNOSE PHOSPHATE ISOMERASE; OXALATE DECARBOXYLASE; POLYKETIDE SYNTHASE; UNCLASSIFIED DRUG; VEGETABLE PROTEIN;

ARTICLE; DEHYDRATION; ENZYME ANALYSIS; EXTRACELLULAR MATRIX; MULTIGENE FAMILY; PHYTOCHEMISTRY; PROTEIN DNA INTERACTION; SEQUENCE ANALYSIS;

BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 0031888149     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00006289     Document Type: Article

References (43)

1. Babbitt PC, Mrachko GT, Hasson MS, Huisman GW, Kolter R, Ringe D, Petsko GA, Kenyon GL, Gerlt JA (1995) A functionally diverse enzyme superfamily that abstracts the a protons of carboxylic acids. Science 267:1159-1161
2. Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc 2nd Int Conf Intell Systems for Mol Biol. AAAI Press, Menlo Park, California, pp 28-36
3. Bäumlein H, Braun H, Kakhovskaya IA, Shutov AD (1995) Seed storage proteins of spermatophytes share a common ancestor with desiccation proteins of fungi. J Mol Evol 41:1070-1075
4. Bergh S, Uhlen M (1992) Analysis of a polyketide synthesis-encoding gene cluster of Streptomyces curacoi. Gene 117:131-136
5. Berna A, Bernier F (1997) Regulated expression of a wheat germin gene in tobacco: oxalate oxidase activity and apoplastic localization of the heterologous protein. Plant Mol Biol 33:417-429
6. Bernier F, Lemieux G, Pallotta D (1987) Gene families encode the major encystment-specific proteins of Physarum polycephalum plasmodia. Gene 59:265-277
7. Blanco G, Brian P, Pereda A, Méndez C, Salas JA, Chater KF (1993) Hybridization and DNA sequence analyses suggest an early evolutionary divergence of related biosynthetic gene sets encoding polyketide antibiotics and spore pigments in Streptomyces spp. Gene 130:107-116
8. Braun H, Czihal A, Shotov AD, Baumlein H (1996) A vicilin-like seed protein of cycads: similarity to sucrose-binding proteins. Plant Mol Biol 31:35-44
9. Brown JC, Jones AM (1994) Mapping the auxin-binding site of auxin-binding protein 1. J Biol Chem 269:21136-21140
10. Bult CJ et al. (1996) Complete genome sequence of the methanogenic archaeon Methanococcus jannaschii. Science 273:1058-1073
11. Bustos SA, Schleif RF (1993) Functional domains of the AraC protein. Proc Natl Acad Sci 90:5638-5642
12. Domon J-M, Dumas B, Lainé E, Meyer Y, David A, David H (1995) Three glycosylated polypeptides secreted by several embryogenic cell lines of pine show highly specific serological affinity to antibodies directed against the wheat germin apoprotein monomer. Plant Physiol 108:141-148
13. Gane PJ, Dunwell JM, Warwicker J (1997) Modelling based on the structure of vicilins predicts a histidine cluster in the active site of oxalate oxidase. J Mol Evol (in press)
14. Heim R, Strehler EE (1991) Cloning an Escherichia coli gene encoding a protein remarkably similar to mammalian aldehyde dehydrogenases. Gene 99:15-23
15. Heintzen C, Fischer R, Melzer S, Kappeler S, Apel K, Staiger D (1994) Orcadian oscillations of a transcript encoding a germin-like protein that is associated with cell walls in young leaves of the long-day plant Sinapis alba L. Plant Physiol 106:905-915
16. Henikoff S, Henikoff JG (1991) Automated assembly of protein blocks for database searching. Nucleic Acids Res 19:6565-6572
17. Hoog C, Schalling M, Grunder-Brundell E, Daneholt B (1991) Analysis of a murine germ cell-specific transcript encodes a putative zinc finger protein. Mol Reprod Dev 30:173-181
18. Hosokawa Y, Matsumoto A, Oka J, Itakura H, Yamaguchi K (1990) Isolation and characterization of a cDNA for rat liver cysteine dioxygenase. Biochem Biophys Res Commun 168:473-478
19. Kaneko T et al. (1996) Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res 3:109-136
20. Labedan B, Riley M (1995) Gene products of Escherichia coli: sequence comparisons and common ancestries. Mol Biol Evol 12: 980-9878
21. Lane BG, Bernier F, Dratewka-Kos E, Shafei R, Kennedy TD, Pyne C, Munro JR, Vaughan T, Walters D, Altomare F (1991) Homologies between members of the germin gene family in hexaploid wheat and similarities between these wheat germins and certain Physarum spherulins. J Biol Chem 266:10461-10468
22. Lane BG, Cuming AC, Fregeau J, Carpita NC, Hurkman WJ, Bernier F, Dratewka-Kos E, Kennedy TD (1992) Germin isoforms are discrete temporal markers of early plant development. Eur J Biochem 209:961-969
23. Lane BG, Dunwell JM, Ray JA, Schmitt MR, Cuming AC (1993) Germin, a protein marker of early plant development, is an oxalate oxidase. J Biol Chem 268:12239-12242
24. Lawrence MC, Izard T, Beuchat M, Blagrove RJ, Colman PM (1994) Structure of phaseolin at 2.2 Å resolution: Implications for a common vicilin/legumin structure and the genetic engineering of seed storage proteins. J Mol Biol 238:748-776
25. Li Y, Strohl WR (1996) Cloning, purification, and properties of a phosphotyrosine protein from Streptomyces coelicolor A3(2). J Bacteriol 178:136-142
26. Malherbe P, Kohler C, Da Prada M, Lang G, Kiefer V, Schwarcz R, Lahm HW, Cesura AM (1994) Molecular cloning and functional expression of human 3-hydroxyanthranilic-acid dioxygenase. J Biol Chem 269:13792-13797
27. May TB, Shinabarger D, Boyd A, Chakrabarty AM (1994) Identification of amino acid residues involved in the activity of phosphomannose isomerase-guanosine 5′-diphospho-D-mannose pyrophosphorylase. A bifunctional enzyme in the alginate biosynthetic pathway of Pseudomonas aeruginosa. J Biol Chem 269:4872-4877
28. Mehta A, Datta A (1991) Oxalate decarboxylase from Collybia velutipes. Purification, characterisation and cloning. J Biol Chem 266: 23548-23553
29. Murzin AG (1993) Can homologous proteins evolve different enzymatic activities? Trends Biochem Sci 18:403-405
30. Ono M, Sage-Ono K, Inoue M, Kamada H, Harada H (1996) Transient increase in the level of mRNA for a germin-like protein in leaves of the short-day plant Pharbitis nil during the photoperiodic induction of flowering. Plant Cell Physiol 37:855-861
31. Pang Q, Hays JB, Rajagopal I, Schaefer TS (1993) Selection of Arabidopsis cDNAs that partially correct phenotypes of Escherichia coli DNA-damage-sensitive mutants and analysis of two plant cDNAs that appear to express UV-specific dark repair activities. Plant Mol Biol 22:411-426
32. Parker LL, Hall BG (1990) Characterisation and nucleotide sequence of the cryptic cel operon of Excherichia coli K12. Genetics 124:455-471
33. Popham DL, Sengupta S, Setlow P (1995) Heat, hydrogen peroxide, and UV resistance of Bacillus subtilis spores with increased core water content and with or without major DNA-binding proteins. Appl Environ Microbiol 61:3633-3638
34. Proudfoot AEI, Turcatti G, Wells TNC, Payton MA, Smith DJ (1994) Purification, cDNA cloning and heterologous expression of human phosphomannose isomerase. Eur J Biochem 219:415-423
35. Sau S, Lee CY (1996) Cloning of type 8 capsule genes and analysis of gene clusters of different capsular polysaccharides in Staphylococcus aureus. J Bacteriol 178:2118-2126
36. Setlow P (1995) Mechanisms for the prevention of damage to DNA in spores of Bacillus species. Ann Rev Microbiol 49:29-54
37. Smith CA, Pinkney M, Guiney DG, Thomas CM (1993) The ancestral IncP replication system consisted of contiguous oriV and trfA segments as deduced from a comparison of the nucleotide sequences of diverse IncP plasmids. J Gen Microbiol 139:1761-1766
38. Stokkermans JPWG, Pierik AJ, Wolbert RBG, Hagen WR, Van Dongen WMAM, Veeger C (1992) The primary structure of a protein containing a putative [6Fe-6S] prismane cluster from Desulfovibrio vulgaris (Hildenborough). Eur J Biochem 208:435-442
39. Thorson JS, Lo SF, Ploux O, He X, Liu HW (1994) Studies on the biosynthesis of 3,6-dideoxyhexoses: molecular cloning and characterization of the asc (ascarylose) region from Yersinia pseudotuberculosis serogroup VA. J Bacteriol 176:5483-5493
40. Venis MA, Napier R (1995) Auxin receptors and auxin binding proteins. Crit Rev Plant Sci 14:27-47
41. Worley KC, Wiese BA, Smith RF (1990) BEAUTY: an enhanced BLAST-based search tool that integrates multiple biological information resources into sequence similarity search results. Genome Res 5:173-184
42. Yohda M, Endo I, Abe Y, Ohta T, Iida T, Maruyama T, Kagawa Y (1996) Gene for aspartate racemase from the sulfur-dependent hyperthermophilic archaeum, Desulfurococcus strain SY. J Biol Chem 271:22017-22021
43. Yoshida K, Seki S, Fujimura M, Miwa Y, Fujita Y (1995) Cloning and sequencing of a 36-kb region of the Bacillus subtilis genome between the gnt and iol operons. DNA Res 2:61-69