Systems Analysis of Seed Filling in Arabidopsis: Using General Linear Modeling to Assess Concordance of Transcript and Protein Expression

Hajdúch, Marián; Hearne, Leonard B.; Miernyk, Ján A.; Casteel, Jill E.; Joshi, Trupti; Agrawal, Ganesh Kumar; Song, Zhao; Zhou, Mingyi; Xu, Dong; Thelen, Jay J.

doi:10.1104/pp.109.152413

Cited by 115 publications

(118 citation statements)

References 38 publications

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“…In a comparison of transcriptome and proteome study during Arabidopsis seeds filling, Hajduch et al (2010) reported that the observed correlation was only 56%. Galland et al (2012) also pointed out a poor correlation between RNA and protein abundance during seed germination of Arabidopsis.…”

Section: Comparison Of Fluctuation In Gene Expression At the Protein mentioning

confidence: 99%

Proteomic analysis of stress-related proteins in rice seeds during the desiccation phase of grain filling

Sano

Masaki

Tanabata

et al. 2013

Plant Biotechnology

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During seed maturation, the water content of seeds decreases remarkably. Mature seeds can germinate after imbibition since the embryos are protected by mechanism of desiccation tolerance. To better understand the mechanism of desiccation tolerance in seeds, we analyzed the fluctuation of stress-related proteins in the desiccation phase of rice seeds by a real-time RT-PCR and gel-based proteomic approach. Based on the changes in water content of developing rice seeds, we defined stages from the beginning of dehydration (10 to 20 days after flowering) and the desiccation phase (20 to 40 days after flowering). The proteomic analysis revealed that late embryogenesis abundant proteins, small heat shock proteins and antioxidative proteins accumulate at the beginning of dehydration and remain at a high level in the desiccation phase, suggesting that these proteins are involved in acquisition of desiccation tolerance. The fluctuation in levels of mRNA encoding some stress-related proteins did not precisely reflect the change in levels of these proteins. Therefore, proteomic analysis, which provides an accurate assessment of changes in protein levels, is a more efficient technique than transcriptomics for inferring the role of stress-related proteins in rice seeds.

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Section: Comparison Of Fluctuation In Gene Expression At the Protein mentioning

confidence: 99%

Proteomic analysis of stress-related proteins in rice seeds during the desiccation phase of grain filling

Sano

Masaki

Tanabata

et al. 2013

Plant Biotechnology

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“…In Arabidopsis (Arabidopsis thaliana), about 17,500 distinct mRNAs (approximately 60% of the full gene complement) are transcribed in the seed during its development, with about 1,300 of these being seed specific (Belmonte et al, 2013). While this set of genes no doubt provides a full picture of the stage-and tissue-specific framework of gene activity, many examples have been described in plants where the pairs of transcript versus protein or protein versus flux are rather discordant (Junker et al, 2007;Hajduch et al, 2010;Fernie and Stitt, 2012;Schwender et al, 2014). Thus, monitoring of gene expression is not sufficient to define metabolic activities in vivo.…”

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confidence: 99%

Quantitative Multilevel Analysis of Central Metabolism in Developing Oilseeds of Oilseed Rape during in Vitro Culture

et al. 2015

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Seeds provide the basis for many food, feed, and fuel products. Continued increases in seed yield, composition, and quality require an improved understanding of how the developing seed converts carbon and nitrogen supplies into storage. Current knowledge of this process is often based on the premise that transcriptional regulation directly translates via enzyme concentration into flux. In an attempt to highlight metabolic control, we explore genotypic differences in carbon partitioning for in vitro cultured developing embryos of oilseed rape (Brassica napus). We determined biomass composition as well as 79 net fluxes, the levels of 77 metabolites, and 26 enzyme activities with specific focus on central metabolism in nine selected germplasm accessions. Overall, we observed a tradeoff between the biomass component fractions of lipid and starch. With increasing lipid content over the spectrum of genotypes, plastidic fatty acid synthesis and glycolytic flux increased concomitantly, while glycolytic intermediates decreased. The lipid/starch tradeoff was not reflected at the proteome level, pointing to the significance of (posttranslational) metabolic control. Enzyme activity/flux and metabolite/flux correlations suggest that plastidic pyruvate kinase exerts flux control and that the lipid/starch tradeoff is most likely mediated by allosteric feedback regulation of phosphofructokinase and ADP-glucose pyrophosphorylase. Quantitative data were also used to calculate in vivo mass action ratios, reaction equilibria, and metabolite turnover times. Compounds like cyclic 39,59-AMP and sucrose-6-phosphate were identified to potentially be involved in so far unknown mechanisms of metabolic control. This study provides a rich source of quantitative data for those studying central metabolism.Seeds develop by absorbing nutrients from their mother plant and using these to synthesize a combination of starch, protein, and lipid. The size and number of seeds that finally develop determine the crop's yield, while their composition determines the end-use quality of the crop. The conversion of nutrients into storage products involves a complex network of metabolic reactions, many of which are subject to transcriptional, translational, and posttranslational regulation. Attempting to engineer seed composition clearly requires a firm understanding of these regulatory networks.The seed's central metabolism differs markedly from those of both a photosynthesizing leaf and a root. In most species, the immature seed is green for a period during its development, so during this phase it is regarded as being photoheterotrophic. A further level of complexity arises as a result of spatial heterogeneity within the seed (Rolletschek et al., 2011; Borisjuk et al.,

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“…Because protein levels are influenced by post-translational processing and inherent variation in stability, it is difficult to infer the representation and regulation of proteins and participating metabolic pathways from transcriptomic data alone, and the correlation between protein and transcript expression levels has been shown to vary extensively depending on the system being analyzed and the profiling approach used (Hajduch et al 2010). As proteins represent the key players in cellular activities, characterizing the proteome using appropriately targeted approaches constitutes an important component of the evolutionary analysis of polyploidy and its consequences.…”

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confidence: 99%

Genomically Biased Accumulation of Seed Storage Proteins in Allopolyploid Cotton

Houston

Pathak

et al. 2011

Genetics

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Allopolyploidy is an important process during plant evolution that results in the reunion of two divergent genomes into a common nucleus. Many of the immediate as well as longer-term genomic and epigenetic responses to polyploidy have become appreciated. To investigate the modifications of gene expression at the proteome level caused by allopolyploid formation, we conducted a comparative analysis of cotton seed proteomes from the allopolyploid Gossypium hirsutum (AD genome) and its model Agenome and D-genome diploid progenitors. An unexpectedly high level of divergence among the three proteomes was found, with about one-third of all protein forms being genome specific. Comparative analysis showed that there is a higher degree of proteomic similarity between the allopolyploid and its D-genome donor than its A-genome donor, reflecting a biased accumulation of seed proteins in the allopolyploid. Protein identification and genetic characterization of high-abundance proteins revealed that two classes of seed storage proteins, vicilins and legumins, compose the major component of cotton seed proteomes. Analyses further indicate differential regulation or modification of homoeologous gene products, as well as novel patterns in the polyploid proteome that may result from the interaction between homoeologous gene products. Our findings demonstrate that genomic merger and doubling have consequences that extend beyond the transcriptome into the realm of the proteome and that unequal expression of proteins from diploid parental genomes may occur in allopolyploids.

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Systems Analysis of Seed Filling in Arabidopsis: Using General Linear Modeling to Assess Concordance of Transcript and Protein Expression

Cited by 115 publications

References 38 publications

Proteomic analysis of stress-related proteins in rice seeds during the desiccation phase of grain filling

Proteomic analysis of stress-related proteins in rice seeds during the desiccation phase of grain filling

Quantitative Multilevel Analysis of Central Metabolism in Developing Oilseeds of Oilseed Rape during in Vitro Culture

Genomically Biased Accumulation of Seed Storage Proteins in Allopolyploid Cotton

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