The Dynamics of Transcript Abundance during Cellularization of Developing Barley Endosperm

Zhang, Runxuan; Tucker, Matthew R.; Burton, Rachel A.; Shirley, Neil J.; Little, Alan; Morris, Jennifer; Milne, Linda; Houston, Kelly; Hedley, Pete E.; Waugh, Robbie

doi:10.1104/pp.15.01690

Cited by 32 publications

(34 citation statements)

References 54 publications

(81 reference statements)

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“…Those three clusters account for most of the significantly changed proteins (in total, 962 proteins). It is known that endosperm development involves cell division, cellular differentiation events and the deposition of SSPs between early, late and mid-development (Sabelli and Larkins, 2009;Zhang et al, 2016). These findings were confirmed by toluidinestained sections prepared at 6, 12 and ≥ 20 DAP that revealed fully cellularized endosperm including three aleurone cell layers at 6 DAP (Supplemental Figure 3A).…”

Section: Multivariate Statistics Unravel Proteome Reorganization Acrosupporting

confidence: 61%

Cytoskeleton members, MVBs and the ESCRT-III HvSNF7s are putative key players for protein sorting into protein bodies during barley endosperm development

Roustan

Hilscher

Weidinger

et al. 2019

Preprint

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Twitter: @VerenaIbl m: 4; f: 7 Abbreviations AMSH1, associated molecule with the SH3 domain of Stam1; A. AbstractCereal endosperm is a short-lived tissue adapted for nutrient storage, containing specialized organelles, such as protein bodies (PBs) and protein storage vacuoles (PSVs), for the accumulation of storage proteins. PBs can be used as efficient biotechnological systems to produce high yields of stable recombinant proteins. During development, protein trafficking and storage require an extensive reorganization of the endomembrane system. Consequently, endomembrane-modifying proteins will influence the final grain quality, yield and recombinant protein production. Barley, a cereal crop of worldwide importance for the brewing industry, animal feed and to a lesser extent, human nutrition, has been identified as promising candidate for recombinant protein production. However, little is known about the molecular mechanism underlying endomembrane system remodeling during barley grain development. By using in vivo label-free quantitative proteomics profiling, we quantified 1,822 proteins across developing barley grains. Based on proteome annotation and a homology search, 95 proteins associated with the endomembrane system were identified, and 83 of these exhibited significant changes in abundance during grain development. Clustering analysis allowed characterization of three different development stages; notably, integration of proteomics data with in situ subcellular microscopic analyses showed a high abundance of cytoskeleton proteins associated with acidified protein bodies at the early development stages. Endosomal sorting complex required for transport (ESCRT)-related proteins and their transcripts are most abundant at early and mid-development. Specifically, multivesicular bodies (MVBs), and the ESCRT-III HvSNF7 proteins are associated with protein bodies (PBs) during barley endosperm development. Taken together, our proteomics results specifically identified members of the cytoskeleton, MVBs, and ESCRT as putative key players for protein sorting into PBs during barley endosperm development. These results present a comprehensive overview of proteins involved in the rearrangement of the endomembrane system during barley early grain development and will provide the basis for future work on engineering the endomembrane system to optimize nutrient content and to produce high yields of recombinant proteins.

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Section: Multivariate Statistics Unravel Proteome Reorganization Acrosupporting

confidence: 61%

Cytoskeleton members, MVBs and the ESCRT-III HvSNF7s are putative key players for protein sorting into protein bodies during barley endosperm development

Roustan

Hilscher

Weidinger

et al. 2019

Preprint

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“…Himalaya. Furthermore, the focus of this study was on transcript profiles during the very early stages of germination, namely 0–24 h. While there have been several studies on total transcript development in whole developing cereal grains (Wan et al ., ; Pfeifer et al ., ; Zhan et al ., ; Zhang et al ., ), transcriptional activity in developing grain is dominated by a single tissue, namely the endosperm. In contrast, germinated grain contains several living and non‐living tissues at different stages of development or degradation.…”

Section: Discussionmentioning

confidence: 99%

Isolation of tissues and preservation of RNA from intact, germinated barley grain

et al. 2017

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Isolated barley (Hordeum vulgare L.) aleurone layers have been widely used as a model system for studying gene expression and hormonal regulation in germinating cereal grains. A serious technological limitation of this approach has been the inability to confidently extrapolate conclusions obtained from isolated tissues back to the whole grain, where the co-location of several living and non-living tissues results in complex tissue-tissue interactions and regulatory pathways coordinated across the multiple tissues. Here we have developed methods for isolating fragments of aleurone, starchy endosperm, embryo, scutellum, pericarp-testa, husk and crushed cell layers from germinated grain. An important step in the procedure involves the rapid fixation of the intact grain to freeze the transcriptional activity of individual tissues while dissection is effected for subsequent transcriptomic analyses. The developmental profiles of 19 611 gene transcripts were precisely defined in the purified tissues and in whole grain during the first 24 h of germination by RNA sequencing. Spatial and temporal patterns of transcription were validated against well-defined data on enzyme activities in both whole grain and isolated tissues. Transcript profiles of genes involved in mitochondrial assembly and function were used to validate the very early stages of germination, while the profiles of genes involved in starch and cell wall mobilisation matched existing data on activities of corresponding enzymes. The data will be broadly applicable for the interrogation of co-expression and differential expression patterns and for the identification of transcription factors that are important in the early stages of grain and seed germination.

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“…As we had both temporal and genetic breadth in our design, we estimated the heritability of our transcriptome, a novelty compared to previous studies (Li et al , , ; Wan et al , ; Yi et al , ; Zhang et al , ). Within a TCoE set, we asked two questions: (i) which transcripts are strongly correlated with each other across genotypes such that they are similarly affected by genetic background?…”

Section: Resultsmentioning

confidence: 99%

“…Investigation of the transcriptome through time is useful for understanding physiological processes occurring during seed maturation and for conducting genetic improvement. Much effort has been made to understand biological processes underlying observed temporal gene expression patterns, including transcriptome studies in maize (Li et al , ; Yi et al , ), wheat (Li et al , ; Wan et al , ) and barley (Zhang et al , ). However, in each case, only one cultivar was examined, which may reflect genotype‐dependent or genotype‐specific results and thus may have limitations for plant improvement.…”

Section: Introductionmentioning

confidence: 99%

Heritable temporal gene expression patterns correlate with metabolomic seed content in developing hexaploid oat seed

Gutiérrez-González

Liu

et al. 2020

Plant Biotechnology Journal

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Summary Oat ranks sixth in world cereal production and has a higher content of health‐promoting compounds compared with other cereals. However, there is neither a robust oat reference genome nor transcriptome. Using deeply sequenced full‐length mRNA libraries of oat cultivar Ogle‐C, a de novo high‐quality and comprehensive oat seed transcriptome was assembled. With this reference transcriptome and QuantSeq 3′ mRNA sequencing, gene expression was quantified during seed development from 22 diverse lines across six time points. Transcript expression showed higher correlations between adjacent time points. Based on differentially expressed genes, we identified 22 major temporal co‐expression (TCoE) patterns of gene expression and revealed enriched gene ontology biological processes. Within each TCoE set, highly correlated transcripts, putatively commonly affected by genetic background, were clustered and termed genetic co‐expression (GCoE) sets. Seventeen of the 22 TCoE sets had GCoE sets with median heritabilities higher than 0.50, and these heritability estimates were much higher than that estimated from permutation analysis, with no divergence observed in cluster sizes between permutation and non‐permutation analyses. Linear regression between 634 metabolites from mature seeds and the PC1 score of each of the GCoE sets showed significantly lower p‐values than permutation analysis. Temporal expression patterns of oat avenanthramides and lipid biosynthetic genes were concordant with previous studies of avenanthramide biosynthetic enzyme activity and lipid accumulation. This study expands our understanding of physiological processes that occur during oat seed maturation and provides plant breeders the means to change oat seed composition through targeted manipulation of key pathways.

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The Dynamics of Transcript Abundance during Cellularization of Developing Barley Endosperm

Cited by 32 publications

References 54 publications

Cytoskeleton members, MVBs and the ESCRT-III HvSNF7s are putative key players for protein sorting into protein bodies during barley endosperm development

Cytoskeleton members, MVBs and the ESCRT-III HvSNF7s are putative key players for protein sorting into protein bodies during barley endosperm development

Isolation of tissues and preservation of RNA from intact, germinated barley grain

Heritable temporal gene expression patterns correlate with metabolomic seed content in developing hexaploid oat seed

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