Co-expression analysis as tool for the discovery of transport proteins in photorespiration

Plant Biology

Volumn 15, Issue 4, 2013, Pages 686-693

  Bordych, C ^a   Eisenhut, M ^a   Pick, T R ^a   Kuelahoglu, C ^a   Weber, A P M ^a  

^a HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

Arabidopsis; Co expression; Photorespiration; Transporters

Indexed keywords

ARABIDOPSIS PROTEIN; CARBON DIOXIDE; CARRIER PROTEIN;

BIOINFORMATICS; DATA ACQUISITION; GENE EXPRESSION; PROTEIN; RESPIRATION;

ARABIDOPSIS; CELL RESPIRATION; GENE EXPRESSION; GENETICS; ISOLATION AND PURIFICATION; LIGHT; METABOLISM; PHOTOSYNTHESIS; PLANT LEAF; RADIATION EXPOSURE; REVERSE GENETICS; REVIEW; TRANSGENIC PLANT; TRANSPORT AT THE CELLULAR LEVEL;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; BIOLOGICAL TRANSPORT; CARBON DIOXIDE; CARRIER PROTEINS; CELL RESPIRATION; GENE EXPRESSION; LIGHT; PHOTOSYNTHESIS; PLANT LEAVES; PLANTS, GENETICALLY MODIFIED; REVERSE GENETICS;

EID: 84879468199     PISSN: 14358603     EISSN: 14388677     Source Type: Journal    
DOI: 10.1111/plb.12027     Document Type: Review

References (47)

1. Aoki K., Ogata Y., Shibata D. (2007) Approaches for extracting practical information from gene co-expression networks in plant biology. Plant and Cell Physiology, 48, 381-390.
2. Bartel D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281-297.
3. Boldt R., Edner C., Kolukisaoglu U., Hagemann M., Weckwerth W., Wienkoop S., Morgenthal K., Bauwe H. (2005) D-GLYCERATE 3-KINASE, the last unknown enzyme in the photorespiratory cycle in Arabidopsis, belongs to a novel kinase family. The Plant Cell, 17, 2413-2420.
4. Brazma A., Vilo J., (2000) Gene expression data analysis. FEBS Letters, 480, 17-24.
5. 2 labeling. Journal of Magnetic Resonance, 178, 1-10.
6. 2 release. Plant Physiology, 148, 786-795.
7. Eisen M.B., Spellman P.T., Brown P.O., Botstein D. (1998) Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Sciences USA, 95, 14863-14868.
8. Eisenhut M., Pick T., Bordych C., Weber A. (2012) Towards closing the remaining gaps in photorespiration - the essential but unexplored role of transport proteins. Plant Biology, 15, 676-685.
9. 2 levels. The Plant Journal, 73, 836-849.
10. Haferkamp I., Linka N. (2012) Functional expression and characterisation of membrane transport proteins. Plant Biology, 14, 675-690.
11. Heazlewood J.L., Verboom R.E., Tonti-Filippini J., Small I., Millar A.H. (2007) SUBA: the Arabidopsis Subcellular Database. Nucleic Acids Research, 35(Database issue), D213-D218.
12. Hirai M.Y., Sugiyama K., Sawada Y., Tohge T., Obayashi T., Suzuki A., Araki R., Sakurai N., Suzuki H., Aoki K., Goda H., Nishizawa O.I., Shibata D., Saito K. (2007) Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proceedings of the National Academy of Sciences USA, 104, 6478-6483.
13. 2 evolution. Plant Physiology, 80, 390-395.
14. Jamai A., Salome P.A., Schilling S.H., Weber A.P., McClung C.R. (2009) Arabidopsis photorespiratory serine hydroxymethyltransferase activity requires the mitochondrial accumulation of ferredoxin-dependent glutamate synthase. The Plant Cell, 21, 595-606.
15. Kinoshita H., Nagasaki J., Yoshikawa N., Yamamoto A., Takito S., Kawasaki M., Sugiyama T., Miyake H., Weber A.P., Taniguchi M. (2011) The chloroplastic 2-oxoglutarate/malate transporter has dual function as the malate valve and in carbon/nitrogen metabolism. The Plant Journal, 65, 15-26.
16. Langfelder P., Horvath S. (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics, 9, 559.
17. Lee H.K., Hsu A.K., Sajdak J., Qin J., Pavlidis P. (2004) Coexpression analysis of human genes across many microarray data sets. Genome Research, 14, 1085-1094.
18. Nozawa A., Nanamiya H., Miyata T., Linka N., Endo Y., Weber A.P., Tozawa Y. (2007) A cell-free translation and proteoliposome reconstitution system for functional analysis of plant solute transporters. Plant and Cell Physiology, 48, 1815-1820.
19. Obayashi T., Kinoshita K. (2009) Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression. DNA Research, 16, 249-260.
20. Obayashi T., Kinoshita K., Nakai K., Shibaoka M., Hayashi S., Saeki M., Shibata D., Saito K., Ohta H. (2007) ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Research, 35(Database issue), D863-D869.
21. Obayashi T., Nishida K., Kasahara K., Kinoshita K. (2011) ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants. Plant and Cell Physiology, 52, 213-219.
22. Persson S., Wei H., Milne J., Page G.P., Somerville C.R. (2005) Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proceedings of the National Academy of Sciences USA, 102, 8633-8638.
23. Pick T.R., Bräutigam A., Schulz M.A., Obata T., Fernie A.R., Weber A.P.M. (2013) PLGG1, a plastidic glycolate glycerate transporter, is required for photorespiration and defines a unique class of metabolite transporters. Proceedings of the National Academy of Sciences USA, doi: 10.1073/pnas.1215142110.
24. Ren Q., Kang K.H., Paulsen I.T. (2004) TransportDB: a relational database of cellular membrane transport systems. Nucleic Acids Research, 32(Database issue), D284-D288.
25. Ren Q.H., Chen K.X., Paulsen I.T. (2007) TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. Nucleic Acids Research, 35, D274-D279.
26. Renne P., Dressen U., Hebbeker U., Hille D., Flugge U.I., Westhoff P., Weber A.P. (2003) The Arabidopsis mutant dct is deficient in the plastidic glutamate/malate translocator DiT2. The Plant Journal, 35, 316-331.
27. Reumann S., Weber A.P. (2006) Plant peroxisomes respire in the light: some gaps of the photorespiratory C2 cycle have become filled - others remain. Biochimica et Biophysica Acta, 1763, 1496-1510.
28. Schmid M., Davison T.S., Henz S.R., Pape U.J., Demar M., Vingron M., Scholkopf B., Weigel D., Lohmann J.U. (2005) A gene expression map of Arabidopsis thaliana development. Nature Genetics, 37, 501-506.
29. Schneidereit J., Hausler R.E., Fiene G., Kaiser W.M., Weber A.P. (2006) Antisense repression reveals a crucial role of the plastidic 2-oxoglutarate/malate translocator DiT1 at the interface between carbon and nitrogen metabolism. The Plant Journal, 45, 206-224.
30. Schwab R., Ossowski S., Riester M., Warthmann N., Weigel D. (2006) Highly specific gene silencing by artificial microRNAs in Arabidopsis. The Plant Cell, 18, 1121-1133.
31. Schwacke R., Schneider A., van der Graaff E., Fischer K., Catoni E., Desimone M., Frommer W.B., Flugge U.I., Kunze R. (2003) ARAMEMNON, a novel database for Arabidopsis integral membrane proteins. Plant Physiology, 131, 16-26.
32. Schwacke R., Fischer K., Ketelsen B., Krupinska K., Krause K. (2007) Comparative survey of plastid and mitochondrial targeting properties of transcription factors in Arabidopsis and rice. Molecular Genetics and Genomics, 277, 631-646.
33. Somerville C.R. (2001) An early Arabidopsis demonstration. Resolving a few issues concerning photorespiration. Plant Physiology, 125, 20-24.
34. Somerville C.R., Ogren W.L. (1979) A phosphoglycolate phosphatase-deficient mutant of Arabidopsis. Nature, 280, 833-836.
35. Somerville C.R., Ogren W.L. (1980a) Inhibition of photosynthesis in Arabidopsis mutants lacking leaf glutamate synthase activity. Nature, 286, 257-259.
36. Somerville C.R., Ogren W.L. (1980b) Photorespiration mutants of Arabidopsis thaliana deficient in serine-glyoxylate aminotransferase activity. Proceedings of the National Academy of Sciences USA, 77, 2684-2687.
37. Somerville C.R., Ogren W.L. (1981) Photorespiration-deficient mutants of Arabidopsis thaliana lacking mitochondrial serine transhydroxymethylase activity. Plant Physiology, 67, 666-671.
38. Somerville C.R., Ogren W.L. (1982) Mutants of the cruciferous plant Arabidopsis thaliana lacking glycine decarboxylase activity. The Biochemical Journal, 202, 373-380.
39. Stuart J.M., Segal E., Koller D., Kim S.K. (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science, 302, 249-255.
40. Taniguchi M., Taniguchi Y., Kawasaki M., Takeda S., Kato T., Sato S., Tabata S., Miyake H., Sugiyama T. (2002) Identifying and characterizing plastidic 2-oxoglutarate/malate and dicarboxylate transporters in Arabidopsis thaliana. Plant and Cell Physiology, 43, 706-717.
41. Taylor N.G., Howells R.M., Huttly A.K., Vickers K., Turner S.R. (2003) Interactions among three distinct CesA proteins essential for cellulose synthesis. Proceedings of the National Academy of Sciences USA, 100, 1450-1455.
42. Timm S., Bauwe H. (2012) The variety of photorespiratory phenotypes - employing the current status for future research directions on photorespiration. Plant Biology, 15, 737-747.
43. Usadel B., Obayashi T., Mutwil M., Giorgi F.M., Bassel G.W., Tanimoto M., Chow A., Steinhauser D., Persson S., Provart N.J. (2009) Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant, Cell & Environment, 32, 1633-1651.
44. Voll L.M., Jamai A., Renne P., Voll H., McClung C.R., Weber A.P. (2006) The photorespiratory Arabidopsis shm1 mutant is deficient in SHM1. Plant Physiology, 140, 59-66.
45. Werdan K., Heldt H.W. (1972) Accumulation of bicarbonate in intact chloroplasts following a pH gradient. Biochimica et Biophysica Acta, 283, 430-441.
46. Yonekura-Sakakibara K., Tohge T., Niida R., Saito K. (2007) Identification of a flavonol 7-O-rhamnosyltransferase gene determining flavonoid pattern in Arabidopsis by transcriptome coexpression analysis and reverse genetics. Journal of Biological Chemistry, 282, 14932-14941.
47. Yu C., Claybrook D.L., Huang A.H.C. (1983) Transport of glycine, serine, and proline into spinach leaf mitochondria. Archives of Biochemistry and Biophysics, 227, 180-187.