A combined proteome and transcriptome analysis of developing Medicago truncatula seeds

Gallardo K, Firnhaber C, Zuber H, Hericher D, Belghazi M, Henry C, Kuester H, Thompson R (2007)
MOLECULAR & CELLULAR PROTEOMICS 6(12): 2165-2179.

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Abstract / Bemerkung
A comparative study of proteome and transcriptome changes during Medicago truncatula ( cultivar Jemalong) seed development has been carried out. Transcript and protein profiles were parallel across the time course for 50% of the comparisons made, but divergent patterns were also observed, indicative of post-transcriptional events. These data, combined with the analysis of transcript and protein distribution in the isolated seed coat, endosperm, and embryo, demonstrated the major contribution made to the embryo by the surrounding tissues. First, a remarkable compartmentalization of enzymes involved in methionine biosynthesis between the seed tissues was revealed that may regulate the availability of sulfur-containing amino acids for embryo protein synthesis during seed filling. This intertissue compartmentalization, which was also apparent for enzymes of sulfur assimilation, is relevant to strategies for modifying the nutritional value of legume seeds. Second, decreasing levels during seed filling of seed coat and endosperm metabolic enzymes, including essential steps in Met metabolism, are indicative of a metabolic shift from a highly active to a quiescent state as the embryo assimilates nutrients. Third, a concomitant persistence of several proteases in seed coat and endosperm highlighted the importance of proteolysis in these tissues as a supplementary source of amino acids for protein synthesis in the embryo. Finally, the data revealed the sites of expression within the seed of a large number of transporters implied in nutrient import and intraseed translocations. Several of these, including a sulfate transporter, were preferentially expressed in seeds compared with other plant organs. These findings provide new directions for genetic improvement of grain legumes.
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Zeitschriftentitel
MOLECULAR & CELLULAR PROTEOMICS
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6
Zeitschriftennummer
12
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2165-2179
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Gallardo K, Firnhaber C, Zuber H, et al. A combined proteome and transcriptome analysis of developing Medicago truncatula seeds. MOLECULAR & CELLULAR PROTEOMICS. 2007;6(12):2165-2179.
Gallardo, K., Firnhaber, C., Zuber, H., Hericher, D., Belghazi, M., Henry, C., Kuester, H., et al. (2007). A combined proteome and transcriptome analysis of developing Medicago truncatula seeds. MOLECULAR & CELLULAR PROTEOMICS, 6(12), 2165-2179. doi:10.1074/mcp.M700171-MCP200
Gallardo, K., Firnhaber, C., Zuber, H., Hericher, D., Belghazi, M., Henry, C., Kuester, H., and Thompson, R. (2007). A combined proteome and transcriptome analysis of developing Medicago truncatula seeds. MOLECULAR & CELLULAR PROTEOMICS 6, 2165-2179.
Gallardo, K., et al., 2007. A combined proteome and transcriptome analysis of developing Medicago truncatula seeds. MOLECULAR & CELLULAR PROTEOMICS, 6(12), p 2165-2179.
K. Gallardo, et al., “A combined proteome and transcriptome analysis of developing Medicago truncatula seeds”, MOLECULAR & CELLULAR PROTEOMICS, vol. 6, 2007, pp. 2165-2179.
Gallardo, K., Firnhaber, C., Zuber, H., Hericher, D., Belghazi, M., Henry, C., Kuester, H., Thompson, R.: A combined proteome and transcriptome analysis of developing Medicago truncatula seeds. MOLECULAR & CELLULAR PROTEOMICS. 6, 2165-2179 (2007).
Gallardo, Karine, Firnhaber, Christian, Zuber, Helene, Hericher, Delphine, Belghazi, Maya, Henry, Celine, Kuester, Helge, and Thompson, Richard. “A combined proteome and transcriptome analysis of developing Medicago truncatula seeds”. MOLECULAR & CELLULAR PROTEOMICS 6.12 (2007): 2165-2179.

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Developmental analysis of maize endosperm proteome suggests a pivotal role for pyruvate orthophosphate dikinase.
Mechin V, Thevenot C, Le Guilloux M, Prioul JL, Damerval C., Plant Physiol. 143(3), 2007
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AUTHOR UNKNOWN, accharomyces cerevisiae. 18(), 2001

AUTHOR UNKNOWN, Saccharomyces cerevisiae 4(), 2005

AUTHOR UNKNOWN, Methanosarcina acetivorans 6(), 2007

AUTHOR UNKNOWN, Staphylococcus aureus 6(), 2006

AUTHOR UNKNOWN, Cell Cycle 5(), 2006
The heterogeneity of human mesenchymal stem cell preparations--evidence from simultaneous analysis of proteomes and transcriptomes.
Wagner W, Feldmann RE Jr, Seckinger A, Maurer MH, Wein F, Blake J, Krause U, Kalenka A, Burgers HF, Saffrich R, Wuchter P, Kuschinsky W, Ho AD., Exp. Hematol. 34(4), 2006
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AUTHOR UNKNOWN, Arabidopsis thaliana. 5(), 2005
Using quantitative proteomics of Arabidopsis roots and leaves to predict metabolic activity
Mooney BP, Miernyk JA, Michael Greenlief C, Thelen JJ., Physiol Plant 128(2), 2006
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Estimating genome conservation between crop and model legume species.
Choi HK, Mun JH, Kim DJ, Zhu H, Baek JM, Mudge J, Roe B, Ellis N, Doyle J, Kiss GB, Young ND, Cook DR., Proc. Natl. Acad. Sci. U.S.A. 101(43), 2004
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AUTHOR UNKNOWN, Medicago truncatula 43(), 2005
Proteome analysis of embryo and endosperm from germinating tomato seeds.
Sheoran IS, Olson DJ, Ross AR, Sawhney VK., Proteomics 5(14), 2005
PMID: 16097031
Identification of genes specifically expressed in maternal and filial tissues of barley caryopses: a cDNA array analysis.
Sreenivasulu N, Altschmied L, Panitz R, Hahnel U, Michalek W, Weschke W, Wobus U., Mol. Genet. Genomics 266(5), 2001
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Transcript profiles and deduced changes of metabolic pathways in maternal and filial tissues of developing barley grains.
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AUTHOR UNKNOWN, Medicago truncatula 137(), 2005
A small-scale procedure for the rapid isolation of plant RNAs.
Verwoerd TC, Dekker BM, Hoekema A., Nucleic Acids Res. 17(6), 1989
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AUTHOR UNKNOWN, Medicago truncatula. 108(), 2004

AUTHOR UNKNOWN, Vicia faba 191(), 1993
EMMA: a platform for consistent storage and efficient analysis of microarray data.
Dondrup M, Goesmann A, Bartels D, Kalinowski J, Krause L, Linke B, Rupp O, Sczyrba A, Puhler A, Meyer F., J. Biotechnol. 106(2-3), 2003
PMID: 14651856

AUTHOR UNKNOWN, Statistica Sinica 12(), 2002
Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses.
Usadel B, Nagel A, Thimm O, Redestig H, Blaesing OE, Palacios-Rojas N, Selbig J, Hannemann J, Piques MC, Steinhauser D, Scheible WR, Gibon Y, Morcuende R, Weicht D, Meyer S, Stitt M., Plant Physiol. 138(3), 2005
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Cluster analysis and display of genome-wide expression patterns.
Eisen MB, Spellman PT, Brown PO, Botstein D., Proc. Natl. Acad. Sci. U.S.A. 95(25), 1998
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AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, Medicago truncatula 56(), 2005

AUTHOR UNKNOWN, 0
Proteomics of Arabidopsis seed germination. A comparative study of wild-type and gibberellin-deficient seeds.
Gallardo K, Job C, Groot SP, Puype M, Demol H, Vandekerckhove J, Job D., Plant Physiol. 129(2), 2002
PMID: 12068122

AUTHOR UNKNOWN, Medicago truncatula 1(), 2001

AUTHOR UNKNOWN, 0
Unmatched masses in peptide mass fingerprints caused by cross-contamination: an updated statistical result.
Ding Q, Xiao L, Xiong S, Jia Y, Que H, Guo Y, Liu S., Proteomics 3(7), 2003
PMID: 12872232
The effect of alpha-amanitin on the Arabidopsis seed proteome highlights the distinct roles of stored and neosynthesized mRNAs during germination.
Rajjou L, Gallardo K, Debeaujon I, Vandekerckhove J, Job C, Job D., Plant Physiol. 134(4), 2004
PMID: 15047896

AUTHOR UNKNOWN, clpP 44(), 2003
Importance of methionine biosynthesis for Arabidopsis seed germination and seedling growth.
Gallardo K, Job C, Groot SP, Puype M, Demol H, Vandekerckhove J, Job D., Physiol Plant 116(2), 2002
PMID: 12354201

AUTHOR UNKNOWN, 0
Global analysis of stress-regulated mRNA turnover by using cDNA arrays.
Fan J, Yang X, Wang W, Wood WH 3rd, Becker KG, Gorospe M., Proc. Natl. Acad. Sci. U.S.A. 99(16), 2002
PMID: 12149460

AUTHOR UNKNOWN, Lotus japonicus 134(), 2004

AUTHOR UNKNOWN, Picea abies 53(), 2002

AUTHOR UNKNOWN, Lemna paucicostata. 93(), 1990
Developmental changes in the metabolic protein profiles of wheat endosperm.
Vensel WH, Tanaka CK, Cai N, Wong JH, Buchanan BB, Hurkman WJ., Proteomics 5(6), 2005
PMID: 15800972

AUTHOR UNKNOWN, de novo 77(), 1985

AUTHOR UNKNOWN, de novo 279(), 2004

AUTHOR UNKNOWN, S 25(), 2001

AUTHOR UNKNOWN, Arabidopsis thaliana 281(), 2006
Sulfate transport and assimilation in plants
Leustek T, Saito K., Plant Physiol. 120(3), 1999
PMID: 10398698

AUTHOR UNKNOWN, In vitro 170(), 2006
Two subtilisin-like proteases from soybean.
Beilinson V, Moskalenko OV, Livingstone DS, Reverdatto SV, Jung R, Nielsen NC., Physiol Plant 115(4), 2002
PMID: 12121465
The seed coat-specific expression of a subtilisin-like gene, SCS1, from soybean.
Batchelor AK, Boutilier K, Miller SS, Labbe H, Bowman L, Hu M, Johnson DA, Gijzen M, Miki BL., Planta 211(4), 2000
PMID: 11030547
A subtilisin-like serine protease is required for epidermal surface formation in Arabidopsis embryos and juvenile plants.
Tanaka H, Onouchi H, Kondo M, Hara-Nishimura I, Nishimura M, Machida C, Machida Y., Development 128(23), 2001
PMID: 11731449

AUTHOR UNKNOWN, Arabidopsis thaliana 370(), 2003

AUTHOR UNKNOWN, Arabidopsis thaliana S 142(), 2006
Plant sulphate transporters: co-ordination of uptake, intracellular and long-distance transport.
Buchner P, Takahashi H, Hawkesford MJ., J. Exp. Bot. 55(404), 2004
PMID: 15258169
Evidence of a key role for photosynthetic oxygen release in oil storage in developing soybean seeds.
Rolletschek H, Radchuk R, Klukas C, Schreiber F, Wobus U, Borisjuk L., New Phytol. 167(3), 2005
PMID: 16101914
Synthesis of the sulfur amino acids: cysteine and methionine.
Wirtz M, Droux M., Photosyn. Res. 86(3), 2005
PMID: 16307301

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