bims-plasge 2018-09-30 papers

bims-plasge

Biomed News

on Plastid genes

Issue of 2018–09–30
seven papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

Genetic analysis and identification of a candidate gene associated with in vitro regeneration ability of cucumber.
Dehydration-induced proteomic landscape of mitochondria in chickpea reveals large-scale coordination of key biological processes.
Evolutionary divergence of the rye Pm17 and Pm8 resistance genes reveals ancient diversity.
Molecular and Functional Diversity of RNA Editing in Plant Mitochondria.
Fine mapping and candidate gene screening of the downy mildew resistance gene RPF1 in Spinach.
B-family subunits of protein phosphatase 2A are necessary for pollen development but not for female gametophyte development in Arabidopsis.
Carbon isotope composition, water use efficiency, and drought sensitivity are controlled by a common genomic segment in maize.

Theor Appl Genet. 2018 Sep 22.

Genetic analysis and identification of a candidate gene associated with in vitro regeneration ability of cucumber.

Ye Wang, Qian Zhou, Guangtao Zhu, Shenhao Wang, Yongshuo Ma, Han Miao, Shengping Zhang, Sanwen Huang, Zhonghua Zhang, Xingfang Gu.

KEY MESSAGE: Candidate genes associated with in vitro regeneration were identified in cucumber. The ability to regenerate shoots or whole plants from differentiated plant tissues is essential for plant transformation. In cucumber (Cucumis sativus L.), regeneration ability varies considerably across accessions, but the genetic mechanism has not yet been demonstrated. In the present study, 148 recombinant inbred lines and a core collection were examined to identify candidate genes involved in cucumber regeneration. Four QTL for cotyledon regeneration that explained 9.7-16.6% of the phenotypic variation in regeneration were identified on cucumber chromosomes 1, 3, and 6. The loci Fcrms1.1 and Fcrms+1.1 were consistently detected in the same genetic interval on two regeneration media. A genome-wide association study revealed 18 SNPs (- log(p) > 5) significantly associated with cotyledon regeneration. Three candidate genes in this region were identified. RT-PCR analyses revealed that Csa1G642540 was significantly more highly expressed in genotypes with high cotyledon regeneration rates than in those with low regeneration. The Csa1G642540 CDS driven by its native promoter was transformed into cucumber line 9110Gt; molecular analyses showed that the T-DNA had integrated into the genomes of 8.6% of regenerated plantlets. The seeds from T0 plants expressing Csa1G642540 were tested for regeneration from cotyledon explants, and the segregate ratio in regeneration frequency is 3:1. The AT3G44110.1, the homologue gene of Csa1G642540 in Arabidopsis, has been reported as PM H+-ATPase activity regulation, integrating flowering signals and enlarging meristem function. These results demonstrate that Csa1G642540 might play an important role in regeneration in cucumber and could serve as a selectable marker for regeneration from cotyledons.

DOI: https://doi.org/10.1007/s00122-018-3182-7
J Proteomics. 2018 Sep 19. pii: S1874-3919(18)30349-X. [Epub ahead of print]

Dehydration-induced proteomic landscape of mitochondria in chickpea reveals large-scale coordination of key biological processes.

Dipak Gayen, Saurabh Gayali, Pragya Barua, Nilesh Vikram Lande, Swati Varshney, Shantanu Sengupta, Subhra Chakraborty, Niranjan Chakraborty.

  Mitochondria play crucial roles in regulating multiple biological processes particularly electron transfer and energy metabolism in eukaryotic cells. Exposure to water-deficit or dehydration may affect mitochondrial function, and dehydration response may dictate cell fate decisions. iTRAQ-based quantitative proteome of a winter legume, chickpea, demonstrated the central metabolic alterations in mitochondria, presumably involved in dehydration adaptation. Three-week-old chickpea seedlings were subjected to progressive dehydration and the magnitude of dehydration-induced compensatory physiological responses was monitored in terms of physicochemical characteristics and mitochondrial architecture. The proteomics analysis led to the identification of 40 dehydration-responsive proteins whose expressions were significantly modulated by dehydration. The differentially expressed proteins were implicated in different metabolic processes, with obvious functional tendencies toward purine-thiamine metabolic network, pathways of carbon fixation and oxidative phosphorylation. The linearity of dehydration-induced proteome alteration was examined with transcript abundance of randomly selected candidates under multivariate stress conditions. The differentially regulated proteins were validated through sequence analysis. An extensive sequence based localization prediction revealed >62.5% proteins to be mitochondrial resident by, at least, one prediction algorithm. The results altogether provide intriguing insights into the dehydration-responsive metabolic pathways and useful clues to identify crucial proteins linked to stress tolerance.
BIOLOGICAL SIGNIFICANCE: Investigation on plant mitochondrial proteome is of significance because it would allow a better understanding of mitochondrial function in plant adaptation to stress. Mitochondria are the unique organelles, which play a crucial role in energy metabolism and cellular homeostasis, particularly when exposed to stress conditions. Chickpea is one of the cultivated winter legumes, which enriches soil nitrogen and has very low water footprint and thus contributes to fortification of sustainable agriculture. We therefore examined the dehydration-responsive mitochondrial proteome landscape of chickpea and queried whether molecular interplay of mitochondrial proteins modulate dehydration tolerance. A total of 40 dehydration-induced mitochondrial proteins were identified, predicted to be involved in key metabolic processes. Our future efforts would focus on understanding both posttranslational modification and processing for comprehensive characterization of mitochondrial protein function. This approach will facilitate mining of more biomarkers linked to the tolerance trait and contribute to crop adaptation to climate change.

Keywords:  Cell defense; Cultivated legume; Dehydration; Metabolic alterations; Mitochondrial proteins; Proteomic landscape

DOI:  https://doi.org/10.1016/j.jprot.2018.09.008
Plant Mol Biol. 2018 Sep 22.

Evolutionary divergence of the rye Pm17 and Pm8 resistance genes reveals ancient diversity.

Simrat Pal Singh, Severine Hurni, Michela Ruinelli, Susanne Brunner, Javier Sanchez-Martin, Patricia Krukowski, David Peditto, Gabriele Buchmann, Helen Zbinden, Beat Keller.

   KEY MESSAGE: We have isolated a novel powdery mildew resistance gene in wheat that was originally introgressed from rye. Further analysis revealed evolutionary divergent history of wheat and rye orthologous resistance genes. Wheat production is under constant threat from a number of fungal pathogens, among them is wheat powdery mildew (Blumeria graminis f. sp. tritici). Deployment of resistance genes is the most economical and sustainable method for mildew control. However, domestication and selective breeding have narrowed genetic diversity of modern wheat germplasm, and breeders have relied on wheat relatives for enriching its gene pool through introgression. Translocations where the 1RS chromosome arm was introgressed from rye to wheat have improved yield and resistance against various pathogens. Here, we isolated the Pm17 mildew resistance gene located on the 1RS introgression in wheat cultivar 'Amigo' and found that it is an allele or a close paralog of the Pm8 gene isolated earlier from 'Petkus' rye. Functional validation using transient and stable transformation confirmed the identity of Pm17. Analysis of Pm17 and Pm8 coding regions revealed an overall identity of 82.9% at the protein level, with the LRR domains being most divergent. Our analysis also showed that the two rye genes are much more diverse compared to the variants encoded by the Pm3 gene in wheat, which is orthologous to Pm17/Pm8 as concluded from highly conserved upstream sequences in all these genes. Thus, the evolutionary history of these orthologous loci differs in the cereal species rye and wheat and demonstrates that orthologous resistance genes can take different routes towards functionally active genes. These findings suggest that the isolation of Pm3/Pm8/Pm17 orthologs from other grass species, additional alleles from the rye germplasm as well as possibly synthetic variants will result in novel resistance genes useful in wheat breeding.

Keywords:  Blumeria graminis tritici; Pm17; Powdery mildew; Resistance gene alleles; Secale cereale (Rye); Triticum aestivum (Wheat)

DOI:  https://doi.org/10.1007/s11103-018-0780-3
Mol Biotechnol. 2018 Sep 22.

Molecular and Functional Diversity of RNA Editing in Plant Mitochondria.

Wei Tang, Caroline Luo.

  RNA editing is a fundamental biochemical process relating to the modification of nucleotides in messenger RNAs of functional genes in cells. RNA editing leads to re-establishment of conserved amino acid residues for functional proteins in nuclei, chloroplasts, and mitochondria. Identification of RNA editing factors that contributes to target site recognition increases our understanding of RNA editing mechanisms. Significant progress has been made in recent years in RNA editing studies for both animal and plant cells. RNA editing in nuclei and mitochondria of animal cells and in chloroplast of plant cells has been extensively documented and reviewed. RNA editing has been also extensively documented on plant mitochondria. However, functional diversity of RNA editing factors in plant mitochondria is not overviewed. Here, we review the biological significance of RNA editing, recent progress on the molecular mechanisms of RNA editing process, and function diversity of editing factors in plant mitochondrial research. We will focus on: (1) pentatricopeptide repeat proteins in Arabidopsis and in crop plants; (2) the progress of RNA editing process in plant mitochondria; (3) RNA editing-related RNA splicing; (4) RNA editing associated flower development; (5) RNA editing modulated male sterile; (6) RNA editing-regulated cell signaling; and (7) RNA editing involving abiotic stress. Advances described in this review will be valuable in expanding our understanding in RNA editing. The diverse functions of RNA editing in plant mitochondria will shed light on the investigation of molecular mechanisms that underlies plant development and abiotic stress tolerance.

Keywords:  Adenosine-to-inosine editing; Arabidopsis; Cytidine-to-uridine editing; Mitochondria; Pentatricopeptide repeat protein; RNA editing factor

DOI:  https://doi.org/10.1007/s12033-018-0126-z
Theor Appl Genet. 2018 Sep 22.

Fine mapping and candidate gene screening of the downy mildew resistance gene RPF1 in Spinach.

Hongbing She, Wei Qian, Helong Zhang, Zhiyuan Liu, Xiaowu Wang, Jian Wu, Chunda Feng, James C Correll, Zhaosheng Xu.

KEY MESSAGE: A SLAF-BSA approach was used to locate the RPF1 locus. The three most likely candidate genes were identified which provide a basic for cloning the resistance gene at the RPF1 locus. Spinach downy mildew is a globally devastating oomycete disease. The use of downy mildew resistance genes constitutes the most effective approach for disease management. Hence, the objective of the present study was to fine map the first-reported resistance locus RPF1. The resistance allele at this resistance locus was effective against races 1-7, 9, 11, 13, and 15 of Peronospora farinosa f. sp. spinaciae (P. effusa). The approach fine mapped RPF1 using specific-locus amplified fragment sequencing (SLAF-Seq) technology combined with bulked segregant analysis. A 1.72 Mb region localized on chromosome 3 was found to contain RPF1 based on association analysis. After screening recombinants with the SLAF markers within the region, the region was narrowed down to 0.89 Mb. Within this region, 14 R genes were identified based on the annotation information. To identify the genes involved in resistance, resequencing of two resistant inbred lines (12S2 and 12S3) and three susceptible inbred lines (12S1, 12S4, and 10S2) was performed. The three most likely candidate genes were identified via amino acid sequence analysis and conserved domain analysis between resistant and susceptible inbred lines. These included Spo12729, encoding a receptor-like protein, and Spo12784 and Spo12903, encoding a nucleotide-binding site and leucine-rich repeat domains. Additionally, based on the sequence variation in the three genes between the resistant and susceptible lines, molecular markers were developed for marker-assisted selection. The results could be valuable in cloning the RPF1 alleles and improving our understanding of the interaction between the host and pathogen.

DOI: https://doi.org/10.1007/s00122-018-3169-4
Biochem Biophys Res Commun. 2018 Sep 19. pii: S0006-291X(18)32013-8. [Epub ahead of print]

B-family subunits of protein phosphatase 2A are necessary for pollen development but not for female gametophyte development in Arabidopsis.

Daisuke Tsugama, Shenkui Liu, Kaien Fujino, Tetsuo Takano.

  Protein phosphatase 2A (PP2A) is a heterotrimeric protein complex conserved among eukaryotes. The B subunit of PP2A determines the substrate specificity of the PP2A holoenzyme, and is classified into the B, B', B″ and B‴ families. Arabidopsis thaliana has two isoforms of the B-family subunit (ATBA and ATBB). A double knockout of their genes is lethal, but which developmental process is primarily impaired by the double knockout is unclear. Identifying such a process helps understand PP2A-mediated signaling more deeply. Here, genetic characterization of new knockout mutants for these genes shows that they are necessary for pollen development but not for female gametophyte development. Compared to wild-type pollen grains, the mutant pollen grains exhibited lower enzyme activities, germinated less frequently on stigmas, and exhibited the aberrant numbers of sperm cell nuclei, suggesting that ATBA and ATBB play pleiotropic roles in pollen development. The amino acids stabilizing the interaction between the human PP2A A and B-family subunits are conserved in an Arabidopsis A subunit (AtPP2AA2), ATBA and ATBB. His-tagged AtPP2AA2 co-immunoprecipitated with either Myc-tagged ATBA or Myc-tagged ATBB in vitro, confirming their interactions. Proteins that regulate pollen development and that undergo dephosphorylation are likely primary targets of ATBA and ATBB.

Keywords:  Arabidopsis thaliana; Gametophyte; Plants; Pollen; Protein phosphatase 2A; Protein-protein interaction

DOI:  https://doi.org/10.1016/j.bbrc.2018.09.088
Theor Appl Genet. 2018 Sep 22.

Carbon isotope composition, water use efficiency, and drought sensitivity are controlled by a common genomic segment in maize.

Viktoriya Avramova, Adel Meziane, Eva Bauer, Sonja Blankenagel, Stella Eggels, Sebastian Gresset, Erwin Grill, Claudiu Niculaes, Milena Ouzunova, Brigitte Poppenberger, Thomas Presterl, Wilfried Rozhon, Claude Welcker, Zhenyu Yang, François Tardieu, Chris-Carolin Schön.

KEY MESSAGE: A genomic segment on maize chromosome 7 influences carbon isotope composition, water use efficiency, and leaf growth sensitivity to drought, possibly by affecting stomatal properties. Climate change is expected to decrease water availability in many agricultural production areas around the globe. Therefore, plants with improved ability to grow under water deficit are urgently needed. We combined genetic, phenomic, and physiological approaches to understand the relationship between growth, stomatal conductance, water use efficiency, and carbon isotope composition in maize (Zea mays L.). Using near-isogenic lines derived from a maize introgression library, we analysed the effects of a genomic region previously identified as affecting carbon isotope composition. We show stability of trait expression over several years of field trials and demonstrate in the phenotyping platform Phenodyn that the same genomic region also influences the sensitivity of leaf growth to evaporative demand and soil water potential. Our results suggest that the studied genomic region affecting carbon isotope discrimination also harbours quantitative trait loci playing a role in maize drought sensitivity possibly via stomatal behaviour and development. We propose that the observed phenotypes collectively originate from altered stomatal conductance, presumably via abscisic acid.

DOI: https://doi.org/10.1007/s00122-018-3193-4