bims-plasge 2018-10-07 papers

on Plastid genes

Issue of 2018‒10‒07
six papers selected by
Vera S. Bogdanova
Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences

Mapping of quantitative trait loci related to cold resistance in Brassica napus L.
Arabidopsis thaliana egy2 mutants display altered expression level of genes encoding crucial photosystem II proteins.
De novo sequencing of the Lavandula angustifolia genome reveals highly duplicated and optimized features for essential oil production.
Overexpression of Cicer arietinum βIII-Gal but not βIV-Gal in arabidopsis causes a reduction of cell wall β-(1,4)-galactan compensated by an increase in homogalacturonan.
Phyto-miRNAs-based regulation of metabolites biosynthesis in medicinal plants.
Drought timing, not previous drought exposure, determines sensitivity of two shortgrass species to water stress.

J Plant Physiol. 2018 Sep 21. pii: S0176-1617(18)30631-X. [Epub ahead of print]231 147-154

Mapping of quantitative trait loci related to cold resistance in Brassica napus L.

Zhen Huang, Na Zhao, Mengfan Qin, Aixia Xu.

  Cold stress is one of the major abiotic stresses that seriously limit rapeseed production worldwide. However, few studies on the mechanism of cold resistance in Brassica napus have been reported. In this study, an F2:3 population including 147 lines was developed to identify the quantitative trait loci (QTLs) related to cold resistance in B. napus. As a result, a genetic linkage map based on 333 simple sequence repeat (SSR) markers covering 1317.70 cM was constructed. Up to 11 QTLs for four indicators were identified in the two locations. These QTLs accounted for 1.09% to 42.50% of the phenotypic variations, and six major QTLs accounted for more than 10% of the phenotypic variations. Three QTLs, qSPADYL-6, qSPADYS-6, and qMDAYS-6, were mapped to the same region of linkage group 6 (LG6). Blast analysis indicated that the sequences of the markers related to these three QTLs showed great collinearity with those on the A08 chromosome of Brassica rapa, and that the target genes might exist in the region from 1.069 to 15.652 M on A08. Two genes, BnaA08g05330D and BnaA08g15470D, encoding the respective cold-regulated proteins in B. napus, were identified. They exhibited high similarity with Bra039858 and Bra010579 (stress-responsive proteins) in the candidate region. RT-qPCR analysis showed a significant difference in gene expression between the two parents. These two genes were hence identified as the genes responsible for cold resistance.

Keywords:  Brassica napus; Candidate genes; Cold resistance; QTLs

DOI:  https://doi.org/10.1016/j.jplph.2018.09.012
J Plant Physiol. 2018 Sep 21. pii: S0176-1617(18)30161-5. [Epub ahead of print]231 155-167

Arabidopsis thaliana egy2 mutants display altered expression level of genes encoding crucial photosystem II proteins.

Małgorzata Adamiec, Lucyna Misztal, Ewa Kosicka, Ewelina Paluch-Lubawa, Robert Luciński.

  EGY2 is a zinc-containing, intramembrane protease located in the thylakoid membrane. It is considered to be involved in the regulated intramembrane proteolysis - a mechanism leading to activation of membrane-anchored transcription factors through proteolytic cleavage, which causes them to be released from the membrane. The physiological functions of EGY2 in chloroplasts remains poorly understood. To answer the question of what the significance is of EGY2 in chloroplast functioning, two T-DNA insertion lines devoid of EGY2 protein were obtained and the mutant phenotype and photosystem II parameters were analyzed. Chlorophyll fluorescence measurements revealed that the lack of EGY2 protease caused changes in non-photochemical quenching (NPQ) and minimum fluorescence yield (F0) as well as a higher sensitivity of photosystem II (PSII) to photoinhibition. Further immunoblot analysis revealed significant changes in the accumulation levels of the three chloroplast-encoded PSII core apoproteins: PsbA (D1) and PsbD (D2) forming the PSII reaction center and PsbC - a protein component of CP43, a part of the inner PSII antenna. The accumulation levels of nuclear-encoded proteins,Lhcb1-3, components of the major light-harvesting complex II (LHCII) as well as proteins forming minor peripheral antennae complexes, namely Lhcb4 (CP29), Lhcb5 (CP26), and Lhcb6 (CP24) remain, however, unchanged. The lack of EGY2 led to a significant increase in the level of PsbA (D1) with a simultaneous decrease in the accumulation levels of PsbC (CP43) and PsbD (D2). To test the hypothesis that the observed changes in the abundance of chloroplast-encoded proteins are a consequence of changes in gene expression levels, real-time PCR was performed. The results obtained show that egy2 mutants display an increased expression of PSBA and a reduction in the PSBD and PSBC genes. Simultaneously pTAC10, pTAC16 and FLN1 proteins were found to accumulate in thylakoid membranes of analyzed mutant lines. These proteins interact with the core complex of plastid-encoded RNA polymerase and may be involved in the regulation of chloroplast gene expression.

Keywords:  Arabidopsis thaliana; Chloroplast proteases; EGY2; Photosystem II; regulated intramembrane proteolysis

DOI:  https://doi.org/10.1016/j.jplph.2018.09.010
Planta. 2018 Sep 29.

De novo sequencing of the Lavandula angustifolia genome reveals highly duplicated and optimized features for essential oil production.

Radesh P N Malli, Ayelign M Adal, Lukman S Sarker, Ping Liang, Soheil S Mahmoud.

  MAIN CONCLUSION: The first draft genome for a member of the genus Lavandula is described. This 870 Mbp genome assembly is composed of over 688 Mbp of non-gap sequences comprising 62,141 protein-coding genes. Lavenders (Lavandula: Lamiaceae) are economically important plants widely grown around the world for their essential oils (EOs), which contribute to the cosmetic, personal hygiene, and pharmaceutical industries. To better understand the genetic mechanisms involved in EO production, identify genes involved in important biological processes, and find genetic markers for plant breeding, we generated the first de novo draft genome assembly for L. angustifolia (Maillette). This high-quality draft reveals a moderately repeated (> 48% repeated elements) 870 Mbp genome, composed of over 688 Mbp of non-gap sequences in 84,291 scaffolds with an N50 value of 96,735 bp. The genome contains 62,141 protein-coding genes and 2003 RNA-coding genes, with a large proportion of genes showing duplications, possibly reflecting past genome polyploidization. The draft genome contains full-length coding sequences for all genes involved in both cytosolic and plastidial pathways of isoprenoid metabolism, and all terpene synthase genes previously described from lavenders. Of particular interest is the observation that the genome contains a high copy number (14 and 7, respectively) of DXS (1-deoxyxylulose-5-phosphate synthase) and HDR (4-hydroxy-3-methylbut-2-enyl diphosphate reductase) genes, encoding the two known regulatory steps in the plastidial isoprenoid biosynthetic pathway. The latter generates precursors for the production of monoterpenes, the most abundant essential oil constituents in lavender. Furthermore, the draft genome contains a variety of monoterpene synthase genes, underlining the production of several monoterpene essential oil constituents in lavender. Taken together, these findings indicate that the genome of L. angustifolia is highly duplicated and optimized for essential oil production.

Keywords:  Essential oil; Genome; Illumina sequencing; Isoprenoid; Lavandula angustifolia; Transcriptome

DOI:  https://doi.org/10.1007/s00425-018-3012-9
J Plant Physiol. 2018 Sep 21. pii: S0176-1617(18)30423-1. [Epub ahead of print]231 135-146

Overexpression of Cicer arietinum βIII-Gal but not βIV-Gal in arabidopsis causes a reduction of cell wall β-(1,4)-galactan compensated by an increase in homogalacturonan.

Lucía Izquierdo, Ignacio Martín, Lucía Albornos, Josefina Hernández-Nistal, Pablo Hueso, Berta Dopico, Emilia Labrador.

  In Cicer arietinum, as in several plant species, the β-galactosidases are encoded by multigene families, although the role of the different proteins is not completely elucidated. Here, we focus in 2 members of this family, βIII-Gal and βIV-Gal, with high degree of amino acid sequence identity (81%), but involved in different developmental processes according to previous studies. Our objective is to deepen in the function of these proteins by establishing their substrate specificity and the possible alterations caused in the cell wall polysaccharides when they are overproduced in Arabidopsis thaliana by constructing the 35S::βIII-Gal and 35S::βIV-Gal transgenic plants. βIII-Gal does cause visible alterations of the morphology of the transgenic plant, all related to a decrease in growth at different stages of development. FTIR spectroscopy and immunological studies showed that βIII-Gal causes changes in the structure of the arabidopsis cell wall polysaccharides, mainly a reduction of the galactan side chains which is compensated by a marked increase in homogalacturonan, which allows us to attribute to galactan a role in the control of the architecture of the cell wall, and therefore in the processes of growth. The 35S::βIV-Gal plants do not present any phenotypic changes, neither in their morphology nor in their cell walls. In spite of the high sequence homology, our results show different specificity of substrate for these proteins, maybe due to other dissimilar characteristics, such as isoelectric points or the number of N-glycosylation sites, which could determine their enzymatic properties and their distinct action in the cell walls.

Keywords:  Arabidopsis; Cell wall; Cicer arietinum; β-(1,4)-galactan; β-Galactosidases

DOI:  https://doi.org/10.1016/j.jplph.2018.09.008
Gene. 2018 Sep 26. pii: S0378-1119(18)31013-8. [Epub ahead of print]

Phyto-miRNAs-based regulation of metabolites biosynthesis in medicinal plants.

M Sabzehzari, M R Naghavi.

  Medicinal plants, are known to produce a wide range of plant secondary metabolites (PSMs) applied as insecticides, drugs, dyes and toxins in agriculture, medicine, industry and bio-warfare plus bio-terrorism, respectively. However, production of PSMs is usually in small quantities, so we need to find novel ways to increase both quantity and quality of them. Fortunately, biotechnology suggests several options through which secondary metabolism in plants can be engineered in innovative ways to: 1) over-produce the useful metabolites, 2) down-produce the toxic metabolites, 3) produce the new metabolites. Among the ways, RNA interference (RNAi) technology which involves gene-specific regulation by small non-coding RNAs (sncRNAs) have been recently emerged as a promising tool for plant biotechnologist, not only to decipher the function of plant genes, but also for development of the plants with improved and novel traits through manipulation of both desirable and undesirable genes. Among sncRNAs, miRNAs have been recorded various regulatory roles in plants such as development, signal transduction, response to environmental stresses, metabolism. Certainly, the use of miRNAs in metabolic engineering requires identification of miRNAs involved in metabolites biosynthesis, understanding of the biosynthetic pathways, as well as the identification of key points of the pathways in which the miRNAs have their own effect. Thus, we firstly consider these three issues on metabolic engineering of medicinal plants. Our review shows, application of miRNAs can open a novel perspective to metabolic engineering of medicinal plants.

Keywords:  Medicinal plants; Metabolic engineering; MiRNAs; Phyto-medicine; Plant secondary metabolites (PSMs)

DOI:  https://doi.org/10.1016/j.gene.2018.09.049
Oecologia. 2018 Sep 29.

Drought timing, not previous drought exposure, determines sensitivity of two shortgrass species to water stress.

Nathan P Lemoine, Robert J Griffin-Nolan, Abigail D Lock, Alan K Knapp.

  Climate change will alter global precipitation patterns, making it increasingly important that we understand how ecosystems will be impacted by more frequent and severe droughts. Yet most drought studies examine a single, within-season drought, and we know relatively little about the impacts of multiple droughts that occur within a single growing season. This distinction is important because many plant species are able to acclimate physiologically, such that the effects of multiple droughts on ecosystem function deviate significantly from the effects of cumulative, independent droughts. Unfortunately, we know relatively little about the ability of dominant species to acclimate to drought in drought-sensitive ecosystems like semi-arid grasslands. Here, we tested for physiological acclimation to multiple drought events in two dominant shortgrass steppe species: Bouteloua gracilis (C4) and Elymus elymoides (C3). Neither species exhibited physiological acclimation to drought; leaf water potential, stomatal conductance, and photosynthesis rates were all similarly affected by a single, late period drought and a second, late period drought. Biomass was lowest in plants exposed to two droughts, but this is likely due to the cumulative effects of both an early and late period drought. Our results suggest that late period droughts do exert weaker effects on biomass production of two dominant shortgrass species, but that the weaker effects are due to ontogenetic changes in plant physiology as opposed to physiological acclimation against multiple droughts. As a consequence, current ecosystem models that incorporate grass phenology and seasonal physiology should provide accurate predictions of primary production under future climates.

Keywords:  Leaf water potential; Photosynthesis; Plant phenology; Soil moisture; Stomatal conductance

DOI:  https://doi.org/10.1007/s00442-018-4265-5