Identification and organization of chloroplastic and cytosolic l-myo-inositol 1-phosphate synthase coding gene(s) in Oryza sativa: compari

详细信息    查看全文

• 作者：Sudipta Ray (1) (2)
  Barunava Patra (1) (3)
  Aparajita Das-Chatterjee (1) (4)
  Arnab Ganguli (1) (5)
  Arun Lahiri Majumder (1)
  
• 关键词：Chloroplastic l ; myo ; inositol ; 1 ; phosphate synthase ; MALDI ; TOF MS ; Transit peptide ; GFP fluorescence ; Genomewalking ; Porteresia coarctata
• 刊名：Planta
• 出版年：2010
• 出版时间：April 2010
• 年：2010
• 卷：231
• 期：5
• 页码：1211-1227
• 全文大小：1399KB
• 参考文献：1. Adhikari J, Majumder AL, Bhaduri TJ, DasGupta S, Majumder AL (1987) Chloroplast as a locale of l - / myo-inositol 1-phosphate synthase. Plant Physiol 85:611-14 CrossRef
  2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-10
  3. Armbruster U, Hertle A, Makarenko E, Zühlke J, Pribil M, Dietzmann A, Schliebner I, Aseeva E, Fenino E, Scharfenberg M, Voigt C, Leister D (2009) Chloroplast proteins without cleavable transit peptides: rare exceptions or a major constituent of the chloroplast proteome? Mol Plant 6:1325-335 CrossRef
  4. Bachhawat N, Mande SC (2000) Complex evolution of the inositol-1-phosphate synthase gene among archaea and eubacteria. Trends Genet 16:111-13 CrossRef
  5. Bannai H, Tamada Y, Maruyama O, Nakai K, Miyano S (2002) Extensive feature detection of N-terminal protein sorting signals. Bioinformatics 18:298-05 CrossRef
  6. Barcisewski J, Barciszewska M, Suter B, Kubli E (1985) Plant tRNA suppressors: in vivo readthrough properties and nucleotide sequence of yellow lupin seeds tRNATyr. Plant Sci 4:193-96 CrossRef
  7. Beier H, Barciszewska M, Krupp G, Mitnacht R, Gross HJ (1984) UAG readthrough during TMV RNA translation: isolation and sequence of two tRNAs Tyr with suppressor activity from tobacco plants. EMBO J 3:351-56
  8. Birney E, Clamp M, Durbin R (2004) Genewise and genomewise. Genome Res 14:988-95 CrossRef
  9. Bradford MM (1976) Quantitation of microgram quantities of protein utilizing the principle of protein–dye binding. Anal Biochem 72:248-54 CrossRef
  10. Brown CM, Stockwell PA, Trotman CNA, Tate WP (1990) Sequence analysis suggests that tetra-nucleotides signal the termination of protein synthesis in eukaryotes. Nucleic Acids Res 18:6339-345 CrossRef
  11. Chatterjee A, Majee M, Ghosh S, Majumder AL (2004) sll1722, an unassigned open reading frame of / Synechocystis PCC 6803, codes for l - / myo-inositol-1-phosphate synthase. Planta 218:989-98 CrossRef
  12. Chatterjee A, Dastidar KG, Maitra S, Majumder AL (2006) sll1981, an acetolactate synthase homologue of / Synechocystis sp. PCC6803, functions as l - / myo-inositol-1-phosphate synthase. Planta 224:367-79 CrossRef
  13. Clauser KR, Baker PR, Burlingame AL (1999) Role of accurate mass measurement (±10?ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal Chem 71:2871-882 CrossRef
  14. Dellaporta S, Wood J, Hicks JB (1983) A plant DNA minipreparation: version II. Plant Mol Biol Rep 1:19-1 CrossRef
  15. Dihazi H, Kessler R, Eschrich K (2001) One-step purification of recombinant yeast 6-phosphofructo-2-kinase after the identification of contaminants by MALDI-TOF MS. Protein Exp Purif 21:201-09 CrossRef
  16. Emanuelsson O, Nielsen H, Brunak S, von Heijne G (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 300:1005-016 CrossRef
  17. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-91 CrossRef
  18. GhoshDastidar K, Maitra S, Goswami L, Roy D, Das KP, Majumder AL (2006) An insight into the molecular basis of salt tolerance of l - / myo-inositol 1-P synthase (PcINO1) from / Porteresia coarctata (Roxb.) Tateoka, a halophytic wild rice. Plant Physiol 140:1279-296 CrossRef
  19. Guillot-Salomon T, Farineau N, Oursel A, Tuquet C (1987) Isolation and characterization of developing chloroplasts from light grown barley leaves. Physiol Plant 69:113-22 CrossRef
  20. Hait NC, Ray Chaudhuri A, Das A, Bhattacharyya S, Majumder AL (2002) Processing and activation of chloroplast l - / myo-inositol 1-phosphate synthase from / Oryza sativa requires signals from both light and salt. Plant Sci 162:559-68 CrossRef
  21. Herr AJ, Atkins JF, Gesteland RF (2000) Coupling of open reading frames by translational bypassing. Annu Rev Biochem 69:343-72 CrossRef
  22. Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999) Plant / cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 27:297-00 CrossRef
  23. Imhoff V, Bourdu R (1973) Formation, d’inositol par les chloroplasts isoles de pois. Phytochemistry 12:331-36 CrossRef
  24. Jarvis P, Soll J (2001) Toc, tic, and chloroplast protein import. Biochim Biophys Acta 1541:64-9 CrossRef
  25. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic Press, New York, pp 21-32
  26. Lackey KH, Pope PM, Johnson MD (2003) Expression of 1l - / myo-inositol-1-phosphate synthase in organelles. Plantphysiology 132:2240-247
  27. Laemmli VK (1970) Cleavages of structural proteins during assembly of the head of bacteriophage T₄. Nature 227:680-85 CrossRef
  28. Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouzé P, Rombauts S (2002) PlantCARE, a database of plant / cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res 30(1):325-27 CrossRef
  29. Loewus FA, Loewus MW (1983) / Myo-inositol: its biosynthesis and metabolism. Annu Rev Plant Physiol 34:132-61 CrossRef
  30. Majee M, Maitra S, Ghosh Dastidar K, Pattnaik S, Chatterjee A, Hait N, Das KP, Majumder AL (2004) A novel salt-tolerant l - / myo-inositol 1-phosphate synthase from / Porteresia coarctata Tateoka, a halophytic wild rice: molecular cloning, bacterial overexpression, characterization and functional introgression into tobacco conferring salt-tolerance phenotype. J Biol Chem 279(27):28539-8552 CrossRef
  31. Majumder AL, Johnson MD, Henry SA (1997) 1l - / myo-inositol-1-phosphate synthase. Biochim Biophys Acta 1348:245-56
  32. Majumder AL, Chatterjee A, Ghosh Dastidar K, Majee M (2003) Diversification and evolution of l - / myo-inositol 1-phosphate synthase. FEBS Letts 553:3-0 CrossRef
  33. Matsufuji S, Matsufuji T, Miyazaki Y, Murakami Y, Atkins J, Gesteland R, Hayashi S (1995) Autoregulatory frameshifting in decoding mammalian ornithine decarboxylase antizyme. Cell 80:51-0 CrossRef
  34. Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15:473-97 CrossRef
  35. Nakagawa H, Ohmiya K, Hattori T (1996) A rice bZIP protein, designated OSBZ8, is rapidly induced by abscisic acid. Plant J 9:217-27 CrossRef
  36. Nakai K, Horton P (1996) PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem Sci 24:34-5 CrossRef
  37. Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418-26
  38. Nielsen H, Engelbrecht J, Brunak S, von Heijne G (1997) Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng 10:1- CrossRef
  39. Nishiguchi R, Takanami M, Oka A (1987) Characterization and sequence determination of the replicator region in the hairy-root-inducing plasmid pRiA4b. Mol Gen Genet 206:1- CrossRef
  40. 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, Sasaki T (2006) The Rice Annotation Project Database (RAP-DB): hub for / Oryza sativa ssp. / japonica genome information. Nucleic Acids Res 34:D741–D744 CrossRef
  41. Rathnam CKM, Edwards GE (1976) Protoplasts as a tool for isolating functional chloroplast from leaves. Plant Cell Physiol 17:177-86
  42. Ratnam SS, Lakshmanan J, Casanova MF, Parthasarathy RN (2009) Identification of / myo-inositol-3-phosphate synthase isoforms: characterization, expression and putative role of a 16 kDa γc isoform. J Biol Chem 284:9443-457 CrossRef
  43. Ray Chaudhuri A, Majumder AL (1996) Salinity induced enhancement of l - / myo-inositol 1-phosphate synthase in rice ( / Oryza sativa L.). Plant Cell Environ 19:1337-342
  44. Ray Chaudhuri A, Hait NC, DasGupta S, Bhaduri TJ, Deb R, Majumder AL (1997) l - / myo-inositol 1-phosphate synthase from plant sources: characteristics of the chloroplastic and cytosolic enzymes. Plant Physiol 115:727-36
  45. Ribiero S, Golding GB (1998) The mosaic nature of the eukaryotic nucleus. Mol Biol Evol 15:779-88
  46. Roy Choudhury S, Roy S, Saha PP, Singh SK, Sengupta DN (2008) Characterization of differential ripening pattern in association with ethylene biosynthesis in the fruits of five naturally occurring banana cultivars and detection of a GCC-box-specific DNA-binding protein. Plant Cell Rep 27:1235-249 CrossRef
  47. Rozas J, Sánchez-DelBarrio JC, Messegyer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496-497 CrossRef
  48. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol and Evol 4:406-25
  49. Sherman WR, Stewart M, Zinbo M (1969) Mass spectrometric study on the mechanism of d -glucose 6 phosphate-span class="a-plus-plus emphasis type-small-caps">l- myo-inositol 1-phosphate cyclase. J Biol Chem 244:5703-708
  50. Siemering KR, Golbik R, Sever R, Haseloff J (1996) Mutations that suppress the thermosensitivity of green fluorescent protein. Curr Biol 6:1653-663 CrossRef
  51. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-599 CrossRef
  52. Villarejo A, Buren S, Larsson S, Dejardin A, Monne M, Rudhe C, Karlsson J, Jansson S, Lerouge P, Rolland N, von Heijne G, Grebe M, Bako L, Samuelsson G (2005) Evidence for a protein transported through the secretory pathway en route to the higher plant chloroplast. Nat Cell Biol 7:1224-231 CrossRef
  53. Yoshida KT, Wada T, Koyama H, Mizobuchi-Fukuoka R, Naito S (1999) Temporal and spatial patterns of accumulation of the transcript of / myo-inositol-1-phosphate synthase and phytin-containing particles during seed development in rice. Plant Physiol 119:65-2 CrossRef
  
• 作者单位：Sudipta Ray (1) (2)
  Barunava Patra (1) (3)
  Aparajita Das-Chatterjee (1) (4)
  Arnab Ganguli (1) (5)
  Arun Lahiri Majumder (1)
  
  1. Plant Molecular and Cellular Genetics, Bose Institute (Centenary Campus), P1/12 CIT Scheme VII M, Kolkata, 700054, India
  2. Department of Botany, Centre of Advanced Studies, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
  3. Kentucky Tobacco Research and Development Centre, University of Kentucky, Lexington, KY, USA
  4. Molecular and Cell Biology Department, Goldman School of Dental Medicine, Boston University Medical Center, Boston, MA, 02118, USA
  5. Chembiotek, Block BN, Plot 7, Sector V, Salt lake Electronic Complex, Kolkata, 700091, India
  

文摘

The gene coding for rice chloroplastic l-myo-inositol-1-phosphate synthase (MIPS; EC 5.5.1.4) has been identified by matrix-assisted laser desorption time-of-flight mass spectrometry analysis of the purified and immunologically cross-reactive ~60?kDa chloroplastic protein following two-dimensional polyacrylamide gel electrophoresis, which exhibited sequence identity with the cytosolic MIPS coded by OsINO1-1 gene. A possible chloroplastic transit peptide sequence was identified upstream of the OsINO1-1 gene upon analysis of rice genome. RT-PCR and confocal microscope studies confirmed transcription, effective translation and its functioning as a chloroplast transit peptide. Bioinformatic analysis mapped the chloroplastic MIPS (OsINO1-1) gene on chromosome 3, and a second MIPS gene (OsINO1-2) on chromosome 10 which lacks conventional chloroplast transit peptide sequence as in OsINO1-1. Two new PcINO1 genes, with characteristic promoter activity and upstream cis-elements were identified and cloned, but whether these proteins can be translocated to the chloroplast or not is yet to be ascertained. Electrophoretic mobility shift assay carried out with nuclear extract of Porteresia coarctata leaves grown under both control and stressed condition shows binding of nuclear proteins with the upstream elements. Nucleotide divergence among the different Oryza and Porteresia INO1 genes were calculated and compared.