bims-plasge 2020-09-20 papers

Issue of 2020–09–20
two papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

RNA Biol. 2020 Sep 16. 1-11

EMP32 is required for the cis-splicing of nad7 intron 2 and seed development in maize.

Yan-Zhuo Yang, Shuo Ding, Xin-Yuan Liu, Jiao-Jiao Tang, Yong Wang, Feng Sun, Chunhui Xu, Bao-Cai Tan.

Pentatricopeptide repeat (PPR) proteins play an important role in post-transcriptional regulation of mitochondrial gene expression. Functions of many PPR proteins and their roles in plant growth and development remain unknown. Through characterization of an empty pericarp32 (emp32) mutant, we identified the function of Emp32 in mitochondrial intron splicing and seed development in maize. The loss-of-function mutant emp32 shows embryo lethality with severely arrested embryo and endosperm development, and over-expression of Emp32 rescues the embryo-lethality. EMP32 is a P-type PPR protein targeted to mitochondria. Loss of function in Emp32 dramatically decreases the splicing efficiency of nad7 intron 2, while complementation of Emp32 restores the splicing efficiency. Although nad7 intron 2 is partially spliced in the wild type, over-expression of Emp32 does not increase the splicing efficiency. The splicing deficiency of nad7 intron 2 blocks the assembly of mitochondrial complex I and dramatically reduces its activity, which may explain the embryo-lethality in emp32. In addition to the one copy of nad7 in the maize mitochondrial genome, we identified one to six copies of nad7 in the nuclear genomes in different maize inbred lines. These copies appear not to be expressed. Together, our results revealed that the P-type PPR protein EMP32 is required for the cis-splicing of nad7 intron 2 and seed development in maize.

Keywords: nad7 ; Maize (Zea mays) ; intron splicing; mitochondrion; seed development

DOI: https://doi.org/10.1080/15476286.2020.1817267

Plant J. 2020 Sep 13.

Gene co-expression analysis reveals transcriptome divergence between wild and cultivated chickpea under drought stress.

Susan M Moenga, Yunpeng Gai, Noelia Carrasquilla-Garcia, Laura M Perilla-Henao, Douglas R Cook.

Ancestral adaptations in crop wild relatives can provide a genetic reservoir for crop improvement. Here we document physiological changes to mild and severe drought stress, and the associated transcriptome dynamics in both wild and cultivated chickpea. Over 60% of transcriptional changes were related to metabolism, indicating that metabolic plasticity is a core and conserved drought response. Also predominant in the data were changes in RNA processing and protein turnover, suggestive of broad restructuring of the chickpea proteome in response to drought. While 12% of the drought responsive transcripts have similar dynamics in cultivated and wild accessions, numerous transcripts had expression patterns unique to particular genotypes, or that distinguished wild from cultivated genotypes and whose divergence may be a consequence of domestication. These and other comparisons provide a transcriptional correlate of previously described species' genetic diversity, with wild accessions well differentiated from each other and from cultivars, and cultivars essentially indistinguishable at the broad transcriptome level. We identified metabolic pathways such as phenylpropanoid metabolism, and biological processes such as stomatal development, that are differentially regulated across genotypes with potential consequences on drought tolerance. These data indicate that wild C. reticulatum may provide both conserved and divergent mechanisms as a resource for breeding of drought tolerance in cultivated chickpea.

Keywords: Cicer; Domestication; RNASeq; available soil water; crop wild relative; drought; gene co-expression; legumes; transcriptome; water use efficiency

DOI: https://doi.org/10.1111/tpj.14988