title: Silencing of soybean seed storage proteins results in a rebalanced protein composition preserving seed protein content without major collateral changes in the metabolome and transcriptome.
abstract: The ontogeny of seed structure and the accumulation of seed storage substances is the result of a determinant genetic program. Using RNA interference, the synthesis of soybean (Glycine max) glycinin and conglycinin storage proteins has been suppressed. The storage protein knockdown (SP-) seeds are overtly identical to the wild type, maturing to similar size and weight, and in developmental ontogeny. The SP- seeds rebalance the proteome, maintaining wild-type levels of protein and storage triglycerides. The SP- soybeans were evaluated with systems biology techniques of proteomics, metabolomics, and transcriptomics using both microarray and next-generation sequencing transcript sequencing (RNA-Seq). Proteomic analysis shows that rebalancing of protein content largely results from the selective increase in the accumulation of only a few proteins. The rebalancing of protein composition occurs with small alterations to the seed's transcriptome and metabolome. The selectivity of the rebalancing was further tested by introgressing into the SP- line a green fluorescent protein (GFP) glycinin allele mimic and quantifying the resulting accumulation of GFP. The GFP accumulation was similar to the parental GFP-expressing line, showing that the GFP glycinin gene mimic does not participate in proteome rebalancing. The results show that soybeans make large adjustments to the proteome during seed filling and compensate for the shortage of major proteins with the increased selective accumulation of other proteins that maintains a normal protein content.
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA.
authors.forename: Monica A
authors.initials: MA
authors.lastname: Schmidt
authors.forename: W Brad
authors.initials: WB
authors.lastname: Barbazuk
authors.forename: Michael
authors.initials: M
authors.lastname: Sandford
authors.forename: Greg
authors.initials: G
authors.lastname: May
authors.forename: Zhihong
authors.initials: Z
authors.lastname: Song
authors.forename: Wenxu
authors.initials: W
authors.lastname: Zhou
authors.forename: Basil J
authors.initials: BJ
authors.lastname: Nikolau
authors.forename: Eliot M
authors.initials: EM
authors.lastname: Herman
mesh_terms: D000596:Amino Acids / Q000378:metabolism; D002849:Chromatography, Gas; D015180:Electrophoresis, Gel, Two-Dimensional; D020869:Gene Expression Profiling; D055785:Gene Knockdown Techniques; D059014:High-Throughput Nucleotide Sequencing; D013058:Mass Spectrometry; D055442:Metabolome; D020411:Oligonucleotide Array Sequence Analysis; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D030821:Plants, Genetically Modified; D020543:Proteome; D055314:Seed Storage Proteins / Q000235:genetics / Q000378:metabolism*; D012639:Seeds / Q000235:genetics / Q000378:metabolism; D013025:Glycine max / Q000235:genetics / Q000378:metabolism* / Q000648:ultrastructure; D059467:Transcriptome
chemical_list: D000596:Amino Acids; D010940:Plant Proteins; D020543:Proteome; D055314:Seed Storage Proteins