Sorghum and sugarcane proteomics

Genomics of the Saccharinae

Volumn , Issue , 2013, Pages 141-168

  Ndimba, Bongani Kaiser ^a,b   Ngara, Rudo ^a  

^a UNIVERSITY OF THE WESTERN CAPE   (South Africa)

^b AGRICULTURAL RESEARCH COUNCIL   (South Africa)

Author keywords

2D SDS PAGE; AS6; Isoelectric focusing; Mass spectrometry; MN1618; Proteomics; Saccharinae; Sorghum bicolor

Indexed keywords

EID: 84888068109     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4419-5947-8_7     Document Type: Chapter

References (112)

1. Aebersold R, Goodlett DR (2001) Mass spectrometry in proteomics. Chem Rev 101:269-295
2. Albertin W, Langella O, Joets J, Negroni L, Zivy M, Damerval C, Thiellement H (2009) Comparative proteomics of leaf, stem, and root tissues of synthetic Brassica napus. Proteomics 9:793-799
3. Andersson I, Backlund A (2008) Structure and function of Rubisco. Plant Physiol Biochem 46:275-291
4. Arakaki AK, Ceccarelli EA, Carrillo N (1997) Plant-type ferredoxin-NADP+reductases: a basal structural framework and a multiplicity of functions. Fed Am Soc Exp Biol J 11:133-140
5. Bannai H, Tamada Y, Maruyama O, Nakai K, Miyano S (2002) Extensive feature detection of N-terminal protein sorting signals. Bioinforma 18:298-305
6. Bassi R, Sandona D, Croe R (1997) Novel aspects of chlorophyll a/b-binding proteins. Physiol Plant 100:769-779
7. Blackstock WP, Weir MP (1999) Proteomics: quantitative and physical mapping of cellular proteins. Trends Biotechnol 17:121-127
8. Boehlein SK, Sewell AK, Cross J, Stewart JD, Hannah LC (2005) Purification and characterization of adenosine diphosphate glucose pyrophosphorylase from maize/potato mosaics. Plant Physiol 138:1552-1562
9. Bradford MM (1976) A rapid and sensitive method for the quantification of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248-254
10. Carpentier SC, Coemans B, Podevin N, Laukens K, Witters E, Matsumura H, Terauchi R, Swennen R, Panis B (2008) Functional genomics in a non-model crop: transcriptomics or proteomics? Physiol Plant 133:117-130
11. Carrari F, Coll-Garcia D, Schauer N, Lytovchenko A, Palacios-Rojas N, Balbo I, Rosso M, Fernie AR (2005) Deficiency of a plastidial adenylate kinase in Arabidopsis results in elevated photosynthetic amino acid biosynthesis and enhanced growth. Plant Physiol 137:70-82
12. Claros MG, Vincens P (1996) Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur J Biochem 241:779-786
13. Cokol M, Nair R, Rost B (2000) Finding nuclear localization signals. Eur Mol Biol Organ Rep 1:411-415
14. Cvetic T, Veljovic-Jovanovic S, Vucinic Z (2008) Characterization of NAD-dependent malate dehydrogenases from spinach leaves. Protoplasma 232:247-253
15. Ding Y, Ma QH (2004) Characterization of a cytosolic malate dehydrogenase cDNA which encodes an isozyme toward oxaloacetate reduction in wheat. Biochimie 86:509-518
16. Dixon DP, Lapthorn A, Edwards R (2002) Plant glutathione transferases. Genome Biol 3:3
17. Dunn MJ, Gorg A (2001) Two-dimensional polyacrylamide gel electrophoresis for proteome analysis. In: Pennington SR, Dunn MJ (eds) Proteomics from protein sequence to function. BIOS Scientific Publishers, Oxford, pp 43-63
18. Edwards R, Dixon DP, Walbot V (2000) Plant glutathione S-transferases: enzymes with multiple functions in sickness and in health. Trends Plant Sci 5:193-198
19. Emanuelsson O, Brunak S, von Heijne G, Nielsen H (2007) Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2:953-971
20. 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 300:1005-1016
21. Fechter MH, Griengl H (2004) Hydroxynitrile lyases: biological sources and application as biocatalysts. Food Technol Biotechnol 42:287-294
22. Fridlyand LE, Backhausen JE, Scheibe R (1998) Flux control of the malate valve in leaf cells. Arch Biochem Biophys 349:290-298
23. Friso G, Giacomelli L, Ytterberg AJ, Peltier JB, Rudella A, Sun Q, van Wijk KJ (2004) In-depth analysis of the thylakoid membrane proteome of Arabidopsis thaliana chloroplasts: new proteins, new functions, and a plastid proteome database. Plant Cell 16:478-499
24. Ganeteg U, Strand A, Gustafsson P, Jansson S (2001) The properties of the chlorophyll a/b-binding proteins Lhca2 and Lhca3 studied in vivo using antisense inhibition. Plant Physiol 127:150-158
25. Gorg A, Obermaier C, Boguth G, Harder A, Scheibe B, Wildgruber R, Weiss W (2000) The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 21: 1037-1053
26. Gorg A, Weiss W (2004) Protein profile comparisons of microorganisms, cells and tissues using 2D gels. In: Speicher DW (ed) Proteome analysis: interpreting the genome. Elsevier, New York, pp 19-73
27. Goward CR, Nicholls DJ (1994) Malate dehydrogenase: a model for structure, evolution, and catalysis. Protein Sci 3:1883-1888
28. Guan HP, Keeling PL (1998) Starch Biosynthesis: understanding the functions and interactions of multiple isoenzymes of starch synthase and branching enzyme. Trends Glycosci Glycotechnol 10:307-319
29. Gummadova JO, Fletcher GJ, Moolna A, Hanke GT, Hase T, Bowsher CG (2007) Expression of multiple forms of ferredoxin NADP+oxidoreductase in wheat leaves. J Exp Bot 58:3971-3985
30. Harris EH, Boynton JE, Gillham NW (1994) Chloroplast ribosomes and protein synthesis. Microbiol Rev 58:700-754
31. Heazlewood JL, Millar AH (2003) Integrated plant proteomics - putting the green genomes to work. Funct Plant Biol 30:471-482
32. Heide H, Kalisz HM, Follmann H (2004) The oxygen evolving enhancer protein 1 (OEE) of photosystem II in green algae exhibits thioredoxin activity. J Plant Physiol 161:139-149
33. Heldt HW (1997) Plant biochemistry and molecular biology. Oxford University Press, Oxford
34. Hickel A, Hasslacher M, Griengl H (1996) Hydroxynitrile lyases: functions and properties. Physiol Plant 98:891-898
35. Hua S, Sun Z (2001) Support vector machine approach for protein subcellular localization prediction. Bioinformatics 17:721-728
36. Hurkman WJ, Tanaka CK (2007) High-resolution two-dimensional gel electrophoresis: a cornerstone for plant proteomics. In: Samaj J, Thelen JJ (eds) Plant proteomics. Springer, Berlin, pp 14-28
37. Ifuku K, Nakatsu T, Shimamoto R, Yamamoto Y, Ishihara S, Kato H, Sato F (2005) Structure and function of the PsbP protein of photosystem II from higher plants. Photosyn Res 84:251-255
38. Igamberdiev AU, Kleczkowski LA (2006) Equilibration of adenylates in the mitochondrial intermembrane space maintains respiration and regulates cytosolic metabolism. J Exp Bot 57: 2133-2141
39. International rice genome sequencing project (2005) The map-based sequence of the rice genome. Nature 436:793-800
40. Jangpromma N, Kitthaisong S, Daduang S, Jaisil P, Thammasirirak S (2007) 18 kDa protein accumulation in sugarcane leaves under drought stress conditions. KMITL Sci Technol J 7:44-54
41. Jorrin JV, Maldonado AM, Castillejo MA (2007) Plant proteome analysis: a 2006 update. Proteomics 7:2947-2962
42. Jorrin-Novo JV, Maldonado AM, Echevarria-Zomeno S, Valledor L, Castillejo MA, Curto M, Valero J, Sghaier B, Donoso G, Redondo I (2009) Plant proteomics update (2007-2008): second-generation proteomic techniques, an appropriate experimental design, and data analysis to fulfill MIAPE standards, increase plant proteome coverage and expand biological knowledge. J Proteomics 72:285-314
43. Kang IH, Lee JW, Lee JH, Kang CJ, Sim W-S, Kim J-K (1998) Light-independent regulation of chloroplast translational elongation factor Tu gene expression in three types of grass: rice, maize, and barley. J Plant Biol 41:324-329
44. Kellogg EA, Juliano ND (1997) The structure and function of RuBisCo and their implications for systematic studies. Am J Bot 84:413-428
45. Komatsu S (2006) Plant proteomics databases: their status in 2005. Curr Bioinform 1:33-36
46. Krishnamurthy L, Serraj R, Hash CT, Dakheel AJ, Reddy BVS (2007) Screening sorghum genotypes for salinity tolerant biomass production. Euphytica 156:15-24
47. Kruger NJ (1997) Carbohydrate synthesis and degradation. In: Dennis DT, Turpin DH, Lefebvre DD, Layzell DB (eds) Plant metabolism, 2nd edn. Addison Wesley Longman, Essex, pp 83-104
48. Kumar A, Agarwal S, Heyman JA, Matson S, Heidtman M, Piccirillo S, Umansky L, Drawid A, Jansen R, Liu Y, Cheung KH, Miller P, Gerstein M, Roeder GS, Snyder M (2002) Subcellular localization of the yeast proteome. Genes Dev 16:707-719
49. Lange PR, Geserick C, Tischendorf G, Zrenner R (2008) Functions of chloroplastic adenylate kinases in Arabidopsis. Plant Physiol 146:492-504
50. Lauble H, Miehlich B, Forster S, Wajant H, Effenberger F (2002) Crystal structure of hydroxynitrile lyase from Sorghum bicolor in complex with the inhibitor benzoic acid: a novel cyanogenic enzyme. Biochemie 41:12043-12050
51. Liebler DC (ed) (2004) Proteomics in cancer research. Wiley, New Jersey
52. Lin D, Tabb DL, Yates JR 3rd (2003) Large-scale protein identification using mass spectrometry. Biochim Biophys 1646:1-10
53. Macdonald FD, Buchanan BB (1997) The reductive pentose phosphate pathway and its regulation. In: Dennis DT, Turpin DH, Lefebvre DD, Layzell DB (eds) Plant metabolism, 2nd edn. Addison Wesley Longman, Essex, pp 299-313
54. Marengo E, Robotti E, Antonucci F, Cecconi D, Campostrini N, Righetti PG (2005) Numerical approaches for quantitative analysis of two-dimensional maps: a review of commercial software and home-made systems. Proteomics 5:654-666
55. Marrs KA (1996) The functions and regulation of glutathione S-transferases in plants. Annu Rev Plant Physiol Plant Mol Biol 47:127-158
56. Martin C, Smith AM (1995) Starch biosynthesis. Plant Cell 7:971-985
57. Matthiesen R, Mutenda KE (2007) Introduction to proteomics. Methods Mol Biol 367:1-35
58. McCarty RE (1992) A plant biochemist's view of H + -ATPases and ATP synthesases. J Exp Bot 172:431-441
59. McEvoy JP, Brudvig GW (2006) Water-splitting chemistry of photosystem II. Chem Rev 106:4455-4483
60. Minarik P, Tomaskova N, Kollarova M, Antalik M (2002) Malate dehydrogenases-structure and function. Gen Physiol Biophys 21:257-265
61. Molloy MP (2000) Two-dimensional electrophoresis of membrane proteins using immobilized pH gradients. Anal Biochem 280:1-10
62. Morant AV, Jorgensen K, Jorgensen C, Paquette SM, Sanchez-Perez R, Moller BL, Bak S (2008) Beta-glucosidases as detonators of plant chemical defense. Phytochemistry 69:1795-1813
63. Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15:473-497
64. Nakai K, Horton P (1999) PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem Sci 24:34-36
65. Ndimba BK, Chivasa S, Hamilton JM, Simon WJ, Slabas AR (2003) Proteomic analysis of changes in the extracellular matrix of Arabidopsis cell suspension cultures induced by fungal elicitors. Proteomics 3:1047-1059
66. Ndimba BK, Thomas LA (2008) Proteomics in South Africa: current status, challenges and prospects. Biotechnol J 3:1368-1374
67. Ng JH, Ilag LL (2002) Functional proteomics: separating the substance from the hype. Drug Discov Today 7:504-505
68. Ngara R (2009) A Proteomic analysis of drought and salt stress responsive proteins of different sorghum varieties. Biotechnology. University of the Western Cape, Cape Town, p 346
69. Ngara R, Rees J, Ndimba BK (2008) Establishment of sorghum cell suspension culture system for proteomics studies. Afr J Biotechnol 7:744-749
70. Nozu Y, Tsugita A, Kamijo K (2006) Proteomic analysis of rice leaf, stem and root tissues during growth course. Proteomics 6:3665-3670
71. Pandey A, Mann M (2000) Proteomics to study genes and genomes. Nature 405:837-846
72. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob-ur R, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551-556
73. Patterson SD (2000) Mass spectrometry and proteomics. Physiol Genomics 2:59-65
74. Patterson SD (2004) How much of the proteome do we see with discovery-based proteomics methods and how much do we need to see? Curr Proteomics 1:3-12
75. Patterson SD, Aebersold R, Goodlett DR (2001) Mass spectrometry-based methods for protein identification and phosphorylation site analysis. In: Pennington SR, Dunn MJ (eds) Proteomics from protein sequence to function. BIOS Scientific Publishers, Oxford, pp 87-130
76. Patterson SD, Aebersold RH (2003) Proteomics: the first decade and beyond. Nat Genet 33(Suppl):311-323
77. Patton WF (2000) A thousand points of light: the application of fluorescence detection technologies to two-dimensional gel electrophoresis and proteomics. Electrophoresis 21:1123-1144
78. Podolak E (2010) Sequencing's new race. Biotechniques 48:105-111
79. Porubleva L, Vander Velden K, Kothari S, Oliver DJ, Chitnis PR (2001) The proteome of maize leaves: use of gene sequences and expressed sequence tag data for identification of proteins with peptide mass fingerprints. Electrophoresis 22:1724-1738
80. Poulton JE (1990) Cyanogenesis in plants. Plant Physiol 94:401-405
81. Preiss J (1997) Modulation of starch synthesis. In: Foyer CH, Quick WP (eds) A molecular approach to primary metabolism in higher plants. Taylor and Francis Publishers, London, pp 81-104
82. Purkarthofer T, Skranc W, Schuster C, Griengl H (2007) Potential and capabilities of hydroxynitrile lyases as biocatalysts in the chemical industry. Appl Microbiol Biotechnol 76:309-320
83. Rabilloud T (2002) Two-dimensional gel electrophoresis in proteomics: old, old fashioned, but it still climbs up the mountains. Proteomics 2:3-10
84. Raines CA (2003) The Calvin cycle revisited. Photosyn Res 75:1-10
85. Raymond J, Blankenship RE (2008) The origin of the oxygen-evolving complex. Coord Chem Rev 252:377-383
86. Salekdeh GH, Komatsu S (2007) Crop proteomics: aim at sustainable agriculture of tomorrow. Proteomics 7:2976-2996
87. Santoni V, Kieffer S, Desclaux D, Masson F, Rabilloud T (2000) Membrane proteomics: use of additive main effects with multiplicative interaction model to classify plasma membrane proteins according to their solubility and electrophoretic properties. Electrophoresis 21:3329-3344
88. Scheibe R (2004) Malate valves to balance cellular energy supply. Physiol Plant 120:21-26
89. Schiltz E, Burger S, Grafmuller R, Deppert WR, Haehnel W, Wagner E (1994) Primary structure of maize chloroplast adenylate kinase. Eur J Biochem 222:949-954
90. Schiltz S, Gallardo K, Huart M, Negroni L, Sommerer N, Burstin J (2004) Proteome reference maps of vegetative tissues in pea. An investigation of nitrogen mobilization from leaves during seed filling. Plant Physiol 135:2241-2260
91. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112-1115
92. Small I, Peeters N, Legeai F, Lurin C (2004) Predotar: a tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics 4:1581-1590
93. Speicher DW (2004) Overview of proteome analysis. In: Speicher DW (ed) Proteome analysis: interpreting the genome. Elsevier, New York, pp 1-18
94. Sproviero EM, Gascon JA, McEvoy JP, Brudvig GW, Batista VS (2007) Quantum mechanics/molecular mechanics structural models of the oxygen-evolving complex of photosystem II. Curr Opin Struct Biol 17:173-180
95. Sun Q, Zybailov B, Majeran W, Friso G, Olinares PD, van Wijk KJ (2009) PPDB, the plant proteomics database at Cornell. Nucleic Acids Res 37:D969-D974
96. Tabita FR, Hanson TE, Li H, Satagopan S, Singh J, Chan S (2007) Function, structure, and evolution of the RubisCO-like proteins and their RubisCO homologs. Microbiol Mol Biol Rev 71:576-599
97. Tamoi M, Nagaoka M, Yabuta Y, Shigeoka S (2005) Carbon metabolism in the Calvin cycle. Plant Biotechnol 22:355-360
98. Tetlow IJ, Davies EJ, Vardy KA, Bowsher CG, Burrell MM, Emes MJ (2003) Subcellular localization of ADP glucose pyrophosphorylase in developing wheat endosperm and analysis of the properties of a plastidial isoform. J Exp Bot 54:715-725
99. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815
100. Thiellement H, Bahrman N, Damerval C, Plomion C, Rossignol M, Santoni V, de Vienne D, Zivy M (1999) Proteomics for genetic and physiological studies in plants. Electrophoresis 20:2013-2026
101. Thomas JC, Ughy B, Lagoutte B, Ajlani G (2006) A second isoform of the ferredoxin:NADP oxidoreductase generated by an in-frame initiation of translation. Proc Natl Acad Sci U S A 103:18368-18373
102. van Wijk KJ (2001) Challenges and prospects of plant proteomics. Plant Physiol 126:501-508
103. van Wijk KJ (2004) Plastid proteomics. Plant Physiol Biochem 42:963-977
104. Vetter J (2000) Plant cyanogenic glucosides. Toxicon 38:11-36
105. Vettore AL, da Silva FR, Kemper EL, Souza GM, da Silva AM, Ferro MI, Henrique-Silva F, Giglioti EA, Lemos MV, Coutinho LL, Nobrega MP, Carrer H, Franca SC, Bacci Junior M, Goldman MH, Gomes SL, Nunes LR, Camargo LE, Siqueira WJ, Van Sluys MA, Thiemann OH, Kuramae EE, Santelli RV, Marino CL, Targon ML, Ferro JA, Silveira HC, Marini DC, Lemos EG, Monteiro-Vitorello CB, Tambor JH, Carraro DM, Roberto PG, Martins VG, Goldman GH, de Oliveira RC, Truffi D, Colombo CA, Rossi M, de Araujo PG, Sculaccio SA, Angella A, Lima MM, de Rosa Junior VE, Siviero F, Coscrato VE, Machado MA, Grivet L, Di Mauro SM, Nobrega FG, Menck CF, Braga MD, Telles GP, Cara FA, Pedrosa G, Meidanis J, Arruda P (2003) Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane. Genome Res 13:2725-2735
106. Vicentini R, Menossi M (2009) The predicted subcellular localisation of the sugarcane proteome. Funct Plant Biol 36:242-250
107. von Ballmoos C, Dimroth P (2007) Two distinct proton binding sites in the ATP synthase family. Biochemistry 46:11800-11809
108. Wajant H, Mundry K-W (1993) Hydroxynitrile lyase from Sorghum bicolor: a glycoprotein heterotetramer. Plant Sci 89:127-133
109. Washburn MP, Wolters D, Yates JR III (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19:242-247
110. Watson BS, Asirvatham VS, Wang L, Sumner LW (2003) Mapping the proteome of barrel medic (Medicago truncatula). Plant Physiol 131:1104-1123
111. Westermeier R (2005) Electrophoresis in practice, 4th edn. Wiley-VCH, Weinheim
112. White WLB, Arias-Garzon DI, McMahon JM, Sayre RT (1998) Cyanogenesis in cassava-the role of hydroxynitrile lyase in root cyanide production. Plant Physiol 116:1219-1225