bims-plasge 2019-01-13 papers

on Plastid genes

Issue of 2019‒01‒13
six papers selected by
Vera S. Bogdanova
Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences

The nucleoid-associated protein WHIRLY1 is required for the coordinate assembly of plastid and nucleus-encoded proteins during chloroplast development.
Genetic diversity and relationship between domesticated rye and its wild relatives as revealed through genotyping-by-sequencing.
Decrease of gene expression diversity during domestication of animals and plants.
Small is big in Arabidopsis mitochondrial ribosome.
Self-incompatibility in the Brassicaceae: Regulation and mechanism of self-recognition.
The signal distinguishing between targeting of outer membrane β-barrel protein to plastids and mitochondria in plants.

Planta. 2019 Jan 11.

The nucleoid-associated protein WHIRLY1 is required for the coordinate assembly of plastid and nucleus-encoded proteins during chloroplast development.

Karin Krupinska, Susanne Braun, Monireh Saeid Nia, Anke Schäfer, Götz Hensel, Wolfgang Bilger.

  MAIN CONCLUSION: Chloroplasts deficient in the major chloroplast nucleoid-associated protein WHIRLY1 have an enhanced ratio of LHCs to reaction centers, indicating that WHIRLY1 is required for a coordinate assembly of the photosynthetic apparatus during chloroplast development. Chloroplast development was found to be delayed in barley plants with an RNAi-mediated knockdown of WHIRLY1 encoding a major nucleoid-associated protein of chloroplasts. The plastids of WHIRLY1 deficient plants had a reduced ribosome content. Accordingly, plastid-encoded proteins of the photosynthetic apparatus showed delayed accumulation during chloroplast development coinciding with a delayed increase in photosystem II efficiency measured by chlorophyll fluorescence. In contrast, light harvesting complex proteins being encoded in the nucleus had a high abundance as in the wild type. The unbalanced assembly of the proteins of the photosynthetic apparatus in WHIRLY1-deficient plants coincided with the enhanced contents of chlorophyll b and xanthophylls. The lack of coordination was most obvious at the early stages of development. Overaccumulation of LHC proteins in comparison to reaction center proteins at the early stages of chloroplast development did not correlate with enhanced expression levels of the corresponding genes in the nucleus. This work revealed that WHIRLY1 does not influence LHC abundance at the transcriptional level. Rather, WHIRLY1 in association with nucleoids might play a structural role for both the assembly of ribosomes and the complexes of the photosynthetic apparatus.

Keywords:  Barley; Chlorophyll b; LHC; Pigment–protein complexes; Plastid ribosomes; Plastid signaling

DOI:  https://doi.org/10.1007/s00425-018-03085-z
Evol Appl. 2019 Jan;12(1): 66-77

Genetic diversity and relationship between domesticated rye and its wild relatives as revealed through genotyping-by-sequencing.

Mona Schreiber, Axel Himmelbach, Andreas Börner, Martin Mascher.

  Rye (Secale cereale L.) is a cereal grass that is an important food crop in Central and Eastern Europe. In contrast to its close relatives wheat and barley, it was not a founder crop of Neolithic agriculture, but is considered a secondary domesticate that may have become a crop plant only after a transitory phase as a weed. As a minor crop of only local importance, genomic resources in rye are underdeveloped, and few population genetic studies using genomewide markers have been published to date. We collected genotyping-by-sequencing data for 603 individuals from 101 genebank accessions of domesticated rye and its wild progenitor S. cereale subsp. vavilovii and related species in the genus Secale. Variant detection in the context of a recently published draft sequence assembly of cultivated rye yielded 55,744 single nucleotide polymorphisms with present genotype calls in 90% of samples. Analysis of population structure recapitulated the taxonomy of the genus Secale. We found only weak genetic differentiation between wild and domesticated rye with likely gene flow between the two groups. Moreover, incomplete lineage sorting was frequent between Secale species because of either ongoing gene flow or recent speciation. Our study highlights the necessity of gauging the representativeness of ex situ germplasm collections for domestication studies and motivates a more in-depth analysis of the interplay between sequence divergence and reproductive isolation in the genus Secale.

Keywords:  Secale cereale; crop wild relatives; crop‐wild hybridization; gene flow; genebank collections; genotyping‐by‐sequencing; population genomics; rye

DOI:  https://doi.org/10.1111/eva.12624
BMC Evol Biol. 2019 Jan 11. 19(1): 19

Decrease of gene expression diversity during domestication of animals and plants.

Wei Liu, Lei Chen, Shilai Zhang, Fengyi Hu, Zheng Wang, Jun Lyu, Bao Wang, Hui Xiang, Ruoping Zhao, Zhixi Tian, Song Ge, Wen Wang.

  BACKGROUND: The genetic mechanisms underlying the domestication of animals and plants have been of great interest to biologists since Darwin. To date, little is known about the global pattern of gene expression changes during domestication.RESULTS: We generated and collected transcriptome data for seven pairs of domestic animals and plants including dog, silkworm, chicken, rice, cotton, soybean and maize and their wild progenitors and compared the expression profiles between the domestic and wild species. Intriguingly, although the number of expressed genes varied little, the domestic species generally exhibited lower gene expression diversity than did the wild species, and this lower diversity was observed for both domestic plants and different kinds of domestic animals including insect, bird and mammal in the whole-genome gene set (WGGS), candidate selected gene set (CSGS) and non-CSGS, with CSGS exhibiting a higher degree of decreased expression diversity. Moreover, different from previous reports which found 2 to 4% of genes were selected by human, we identified 6892 candidate selected genes accounting for 7.57% of the whole-genome genes in rice and revealed that fewer than 8% of the whole-genome genes had been affected by domestication.
CONCLUSIONS: Our results showed that domestication affected the pattern of variation in gene expression throughout the genome and generally decreased the expression diversity across species, and this decrease may have been associated with decreased genetic diversity. This pattern might have profound effects on the phenotypic and physiological changes of domestic animals and plants and provide insights into the genetic mechanisms at the transcriptome level other than decreased genetic diversity and increased linkage disequilibrium underpinning artificial selection.

Keywords:  Decrease; Domestication; Gene expression diversity

DOI:  https://doi.org/10.1186/s12862-018-1340-9
Nat Plants. 2019 Jan;5(1): 106-117

Small is big in Arabidopsis mitochondrial ribosome.

Florent Waltz, Tan-Trung Nguyen, Mathilde Arrivé, Anthony Bochler, Johana Chicher, Philippe Hammann, Lauriane Kuhn, Martine Quadrado, Hakim Mireau, Yaser Hashem, Philippe Giegé.

Mitochondria are responsible for energy production through aerobic respiration, and represent the powerhouse of eukaryotic cells. Their metabolism and gene expression processes combine bacterial-like features and traits that evolved in eukaryotes. Among mitochondrial gene expression processes, translation remains the most elusive. In plants, while numerous pentatricopeptide repeat (PPR) proteins are involved in all steps of gene expression, their function in mitochondrial translation remains unclear. Here we present the biochemical characterization of Arabidopsis mitochondrial ribosomes and identify their protein subunit composition. Complementary biochemical approaches identified 19 plant-specific mitoribosome proteins, of which ten are PPR proteins. The knockout mutations of ribosomal PPR (rPPR) genes result in distinct macroscopic phenotypes, including lethality and severe growth delay. The molecular analysis of rppr1 mutants using ribosome profiling, as well as the analysis of mitochondrial protein levels, demonstrate rPPR1 to be a generic translation factor that is a novel function for PPR proteins. Finally, single-particle cryo-electron microscopy (cryo-EM) reveals the unique structural architecture of Arabidopsis mitoribosomes, characterized by a very large small ribosomal subunit, larger than the large subunit, bearing an additional RNA domain grafted onto the head. Overall, our results show that Arabidopsis mitoribosomes are substantially divergent from bacterial and other eukaryote mitoribosomes, in terms of both structure and protein content.

DOI: https://doi.org/10.1038/s41477-018-0339-y
Curr Top Dev Biol. 2019 ;pii: S0070-2153(18)30073-5. [Epub ahead of print]131 435-452

Self-incompatibility in the Brassicaceae: Regulation and mechanism of self-recognition.

June B Nasrallah.

  Self-incompatibility is one of the most common mechanisms used by plants to prevent self-fertilization. In the Brassicaceae, the inhibition of self-pollen is triggered right at the stigma surface by interaction of two highly polymorphic self-recognition proteins that are encoded by tightly linked genes of the S-locus haplotype: a receptor protein kinase displayed at the surface of stigma epidermal cells and its small diffusible ligand that is localized in the outer coat of pollen grains. It is the specific interaction between receptor and ligand encoded in the same S haplotype that determines specificity in the rejection of self-pollen. The chapter reviews recent results that have shed light on the genetic control, cell biology, and regulation of the self-recognition molecules, as well as the structural basis of ligand recognition. Models that aim to explain how diversification of the self-recognition repertoire can occur in this two-gene self-recognition system are discussed.

Keywords:  Arabidopsis thaliana; Brassicaceae; Crystal structure; Live imaging; Receptor-ligand interaction; S-locus cysteine-rich protein; S-locus receptor kinase; Self-incompatibility

DOI:  https://doi.org/10.1016/bs.ctdb.2018.10.002
Biochim Biophys Acta Mol Cell Res. 2019 Jan 08. pii: S0167-4889(18)30382-3. [Epub ahead of print]

The signal distinguishing between targeting of outer membrane β-barrel protein to plastids and mitochondria in plants.

Anna Klinger, Victoria Gosch, Uwe Bodensohn, Roman Ladig, Enrico Schleiff.

  The proteome of the outer membrane of mitochondria and chloroplasts consists of membrane proteins anchored by α-helical or β-sheet elements. While proteins with α-helical transmembrane domains are present in all cellular membranes, proteins with β-barrel structure are specific for these two membranes. The organellar β-barrel proteins are encoded in the nuclear genome and thus, have to be targeted to the outer organellar membrane where they are recognized by surface exposed translocation complexes. In the last years, the signals that ensure proper targeting of these proteins have been investigated as essential base for an understanding of the regulation of cellular protein distribution. However, the organellar β-barrel proteins are unique as most of them do not contain a typical targeting information in form of an N-terminal cleavable targeting signal. Recently, it was discovered that targeting and surface recognition of mitochondrial β-barrel proteins in yeast, humans and plants depends on the hydrophobicity of the last β-hairpin of the β-barrel. However, we demonstrate that the hydrophobicity is not sufficient for the discrimination of targeting to chloroplasts or mitochondria. By domain swapping between mitochondrial and chloroplast targeted β-barrel proteins atVDAC1 and psOEP24 we demonstrate that the presence of a hydrophilic amino acid at the C-terminus of the penultimate β-strand is required for mitochondrial targeting. A mutation of the chloroplast β-barrel protein psOEP24 which mimics such profile is efficiently targeted to mitochondria. Thus, we present the properties of the signal for mitochondrial targeting of β-barrel proteins in plants.

Keywords:  Intracellular protein sorting; Membrane proteins; Protein targeting; targeting signal; β-Barrel proteins

DOI:  https://doi.org/10.1016/j.bbamcr.2019.01.004