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Characterization of a Gene Encoding Diaminopimelate Decarboxylase from Rice  

Kim, Jung-Sup (Faculty of Biotechnology, Cheju National University)
Lee, Soon-Dong (Department of Science Education, Cheju National University)
Publication Information
Animal cells and systems / v.10, no.4, 2006 , pp. 197-201 More about this Journal
Abstract
Diaminopimelate decarboxylase (DAPDC, EC 4.1.1.20) catalyzes the conversion of diaminopimelate into lysine (Lys), which is the last step in Lys biosynthetic pathway. The genes for DAPDC have been reported in many bacteria, and more recently in Arabidopsis. Here we report characterization of a gene for DAPDC from rice (OsDAPDC). Sequence analysis of a cDNA clone revealed a full-length open reading frame for OsDAPDC that encoded 490 amino acids, approximately 53.2 kDa protein. The OsDAPDC protein contains a consensus binding site for pyridoxal-5'-phosphate as a cofactor and has a sequence at the amino terminus that resembles a transit peptide for localization to plastids, similar to that of Arabidopsis. Single gene encoding DAPDC was found in chromosome II in rice. The predicted amino acid sequence of OsDAPDC is highly homologous to that of the enzymes for DAPDC encoded by lysA of many bacteria. Expression of OsDAPDC in lysA mutants of Escherichia coli shows that the gene is able to functionally complement the mutants. These results suggest that OsDAPDC encodes a protein for diaminopimelate decarboxylase in rice.
Keywords
Rice; diaminopimelate decarboxylase; complementation; lysA; pyridoxal-5'-phosphate;
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1 Yamamoto J, Shimizu M, and Yamane K (1991) Molecular cloning and analysis of nucleotide sequence of the Bacillus subtilis lysA gene region using B. subtilis phage vectors and a multi-copy plasmid, pUB110. Agric Bioi Chem 55: 1615-1626   DOI   ScienceOn
2 Thompson JD, Higgins DO; and Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680   DOI
3 Wheeler DL, Church DM, Federhen S, Lash AE, Madden TL, Pontius JU, Schuler GD, Schriml LM, Sequeira E, Tatusova TA, and Wagner L (2003) Database resources ofthe National Center for Biotechnology. Nucleic Acids Res 31: 28-33   DOI   ScienceOn
4 Osato N, Itoh M, Konno H, Kondo S, Shibata K, Carninci P, Shiraki T, Shinagawa A, Arakawa T, Kikuchi S, Sato K, Kawai J, and Hayashizaki Y (2002) A computer-based method of selecting clones for a full-length cDNA project: simultaneous collection of negligibly redundant and variant cDNAs. Genome Res 12: 1127-1134   DOI   ScienceOn
5 Sambrook J, and Russell DW (2001) Molecular Cloning: a Laboratory Manual, Cold Spring Harbor Laboratory Press. Cold Spring Harbor
6 Sandmeier E, Hale TI, and Christen P (1994) Multiple evolutionary origin of pyridoxal-5'-phosphate-dependent amino acid decarboxylases. Eur J Biochem 221: 997-1002   DOI   ScienceOn
7 Mills DA and Flickinger MC (1993) Cloning and sequence analysis of the meso-diaminopimelate decarboxylase gene from Bacillus methanolicus MGA3 and comparison to other decarboxylase genes. Appl Environ Microbiol 59: 2927-2937
8 Nakai K and Kanehisa M (1992) A knowledge base for predicting protein localization sites in eukaryotic cells. Genomics 14: 897-911   DOI
9 Ohyanagi H, Tanaka T, Sakai H, Shigemoto Y, Yamaguchi K, Habara T, Fujii Y, Antonio BA, Nagamura Y, Imanishi T, Ikeo K, Itoh T, Gojobori T, and Sasaki T (2006) The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information. Nucleic Acids Res 34: D741-744   DOI   ScienceOn
10 Kelland JG, Arnold LD, Palcic MM, Pickard MA, and Vederas JC (1986) Analogs of diaminopimelic acid as inhibitors of mesodiaminopimelate decarboxylase from Bacillus sphaericus and wheat germ. J Bioi Chem 261: 13216-13223
11 Kim J (2006) Diaminopimelate decarboxylase from Arabidopsis contains motifs for pyridoxal-5'-phosphate and substrate. Asian J Plant Sci 5: 260-265   DOI
12 Kim J and Leustek T (1996) Cloning and analysis of the gene for cystathionine g-synthase from Arabidopsis thaliana. Plant Mol Bioi 32: 1117-1124   DOI
13 Gokulan K, Rupp B, Pavelka MS Jr, Jacobs WR Jr, and Sacchettini JC (2003) Crystal structure of Mycobacterium tuberculosis diaminopimelate decarboxylase, an essential enzyme in bacterial lysine biosynthesis. J Bioi Chem 278: 18588-18596   DOI   ScienceOn
14 Martin C, Cami B, Yeh P, Stragier P, Parsot C, and Patte JC (1988) Pseudomonas aeruginosa diaminopimelate decarboxylase: evolutionary relationship with other amino acid decarboxylases. Mol Bioi Evol 5: 549-559
15 Galili G, Amir R, Hoefgen R, and Hesse H (2005) Improving the levels of essential amino acids and sulfur metabolites in plants. Bioi Chem 386: 817-831   DOI   ScienceOn
16 Girodeau JM, Agouridas C, Masson M, Pineau R, and Le Goffic F (1986) The lysine pathway as a target for a new genera of synthetic antibacterial antibiotics? J Med Chem 29: 1023-1030   DOI
17 Hofinann K, Bucher P, Falquet L, and Bairoch A (1999) The PROS1TE database, its status in 1999. Nucleic Acids Res 27: 215-219   DOI   ScienceOn
18 Hudson AO, Bless C, Macedo P, Chattetjee SP, Singh BK, Gilvarg C, and Leustek T (2005) Biosynthesis. of lysine in plants: evidence for a variant of the known bactenal pathways. Biochim Biophys Acta 1721: 27-36   DOI   ScienceOn
19 Azevedo RA, Arruda P, Turner WL, and Lea PJ (1997) The biosynthesis and metabolism of the aspartate derived amino acids in higher plants. Phytochemistry 46: 395-419   DOI   ScienceOn
20 Cremer J, Treptow C, Eggeling L, and Sahm H (1988) Regulation of enzymes of lysine biosynthesis in Corynebacterium glutamicum. J Gen Microbiol 134: 3221-3229