bims-plasge 2020-08-02 papers

Methods Mol Biol. 2021 ;2181 1-12

Substitutional RNA Editing in Plant Organelles.

RNA editing by cytidine (C) to uridine (U) conversions frequently occurs in land plant mitochondria and plastids. Target cytidines are specifically recognized by nuclear-encoded pentatricopeptide repeat (PPR) proteins in a sequence-specific manner. In the moss Physcomitrella patens, all PPR editing factors possess the DYW-deaminase domain at the C-terminus. Here, we describe methods for the direct sequencing of cDNA to detect RNA editing events and the RNA electrophoresis mobility shift assay (REMSA) to analyze the specific binding of PPR editing factors to their target RNA.

Keywords: C-to-U editing; Mitochondria; Pentatricopeptide repeat; Physcomitrella patens; Plastid; RNA-protein interaction

DOI: https://doi.org/10.1007/978-1-0716-0787-9_1

Breed Sci. 2020 Jun;70(3): 355-362

Characterization of cytoplasmic female sterility in an alloplasmic and monosomic addition line of Brassica rapa carrying the cytoplasm and one chromosome of Diplotaxis tenuifolia.

Yoshiaki Fujita, Yuriko Nagashima, Mei Yamaguchi, Su-Hyeun Shim, Takayuki Ohnishi, Sang Woo Bang.

Alloplasmic plants exhibit various phenotypic changes such as cytoplasmic male sterility (CMS). We have been attempting to produce an alloplasmic Brassica rapa CMS line (2n = 20) carrying Diplotaxis tenuifolia cytoplasm (cyt-Dt) for several years, but a single extra chromosome always remained in all lines produced. We confirmed a D. tenuifolia-specific band in the alloplasmic line carrying D. tenuifolia cytoplasm by RAPD analysis, indicating that the additional chromosome was derived from D. tenuifolia. Here, we observed the phenotypic characteristics of the alloplasmic B. rapa monosomic addition line, named (cyt-Dt) B. rapa MAL, and investigated why a single extra chromosome is required in its genetic background for viability. When the (cyt-Dt) B. rapa MALs were crossed with pollen of several B. rapa lines, approximately 50% of the ovules attracted pollen tubes, and all the progeny had the additional chromosome. These results suggested that only the female gametes with n = 11 rather than n = 10 were fertilized and developed into mature seeds, and that cytoplasmic female sterility was overcome by nuclear restorer gene(s) derived from the cytoplasmic donor species.

Keywords: Brassica rapa; Diplotaxis tenuifolia; cytoplasmic female sterility; cytoplasmic male sterility; embryogenesis; intergeneric hybridization; pollen tube attraction

DOI: https://doi.org/10.1270/jsbbs.19147

Front Plant Sci. 2020 ;11 1020

Electron Microscopy Views of Dimorphic Chloroplasts in C4 Plants.

Keith Ka Ki Mai, Peng Gao, Byung-Ho Kang.

C4 plants enhance photosynthesis efficiency by concentrating CO2 to the site of Rubisco action. Chloroplasts in C4 plants exhibit structural dimorphism because thylakoid architectures vary depending on energy requirements. Advances in electron microscopy imaging capacity and sample preparation technologies allowed characterization of thylakoid structures and their macromolecular arrangements with unprecedented precision mostly in C3 plants. The thylakoid is assembled during chloroplast biogenesis through collaboration between the plastid and nuclear genomes. Recently, the membrane dynamics involved in the assembly process has been investigated with 3D electron microscopy, and molecular factors required for thylakoid construction have been characterized. The two classes of chloroplasts in C4 plants arise from common precursors, but little is known about how a single type of chloroplasts grow, divide, and differentiate to mature into distinct chloroplasts. Here, we outline the thylakoid structure and its assembly processes in C3 plants to discuss ultrastructural analyses of dimorphic chloroplast biogenesis in C4 plant species. Future directions for electron microscopy research of C4 photosynthetic systems are also proposed.

Keywords: C4 photosynthesis; chloroplast; electron microscopy; electron tomography; single-cell C4 plants; thylakoid

DOI: https://doi.org/10.3389/fpls.2020.01020

G3 (Bethesda). 2020 Jul 31. pii: g3.401479.2020. [Epub ahead of print]

Genomic Patterns of Introgression in Interspecific Populations Created by Crossing Wheat with Its Wild Relative.

Moses Nyine, Elina Adhikari, Marshall Clinesmith, Katherine W Jordan, Allan K Fritz, Eduard Akhunov.

Introgression from wild relatives is a valuable source of novel allelic diversity for breeding. We investigated the genomic patterns of introgression from Aegilops tauschii, the diploid ancestor of the wheat D genome, into winter wheat (Triticum aestivum) cultivars. The population of 351 BC1F3:5 lines was selected based on phenology from crosses between six hexaploid wheat lines and 21 wheat-Ae. tauschii octoploids. SNP markers developed for this population and a diverse panel of 116 Ae. tauschii accessions by complexity-reduced genome sequencing were used to detect introgression based on the identity-by-descent analysis. Overall, introgression frequency positively correlated with recombination rate, with a high incidence of introgression at the ends of chromosomes and low in the pericentromeric regions, and was negatively related to sequence divergence between the parental genomes. Reduced introgression in the pericentromeric low-recombining regions spans nearly 2/3 of each chromosome arm, suggestive of the polygenic nature of introgression barriers that could be associated with multilocus negative epistasis between the alleles of wild and cultivated wheat. On the contrary, negative selection against the wild allele of Tg, controlling free-threshing trait and located in the high-recombining chromosomal region, led to reduced introgression only within ~10 Mbp region around Tg These results are consistent with the effect of selection on linked variation described by the Hill-Robertson effect, and offer insights into the introgression population development for crop improvement to maximize retention of introgressed diversity across entire genome.

Keywords: Aegilops tauschii; hexaploid wheat; introgression; recombination; tenacious glume; wild relative

DOI: https://doi.org/10.1534/g3.120.401479

Biochim Biophys Acta Bioenerg. 2020 Jul 23. pii: S0005-2728(20)30125-0. [Epub ahead of print]1861(11): 148275

Clingy genes: Why were genes for ribosomal proteins retained in many mitochondrial genomes?

Lea Bertgen, Timo Mühlhaus, Johannes M Herrmann.

Why mitochondria still retain their own genome is a puzzle given the enormous effort to maintain a mitochondrial translation machinery. Most mitochondrially encoded proteins are membrane-embedded subunits of the respiratory chain. Their hydrophobicity presumably impedes their import into mitochondria. However, many mitochondrial genomes also encode protein subunits of the mitochondrial ribosome. These proteins lack transmembrane domains and hydrophobicity cannot explain why their genes remained in mitochondria. In this review, we provide an overview about mitochondrially encoded subunits of mitochondrial ribosomes of fungi, plants and protists. Moreover, we discuss and evaluate different hypotheses which were put forward to explain why (ribosomal) proteins remained mitochondrially encoded. It seems likely that the synthesis of ribosomal proteins in the mitochondrial matrix is used to regulate the assembly of the mitochondrial ribosome within mitochondria and to avoid problems that mitochondrial proteins might pose for cytosolic proteostasis and for the assembly of cytosolic ribosomes.

Keywords: Eukaryotes; Evolution; Gene transfer; Mitochondria; Respiratory chain; Ribosomes

DOI: https://doi.org/10.1016/j.bbabio.2020.148275

J Exp Bot. 2020 Jul 06. pii: eraa316. [Epub ahead of print]

Generating and characterizing single- and multigene mutants of the Rubisco small subunit family in Arabidopsis.

Panupon Khumsupan, Marta A Kozlowska, Douglas J Orr, Andreas I Andreou, Naomi Nakayama, Nicola Patron, Elizabete Carmo-Silva, Alistair J McCormick.

The primary CO2-fixing enzyme Rubisco limits the productivity of plants. The small subunit of Rubisco (SSU) can influence overall Rubisco levels and catalytic efficiency, and is now receiving increasing attention as a potential engineering target to improve the performance of Rubisco. However, SSUs are encoded by a family of nuclear rbcS genes in plants, which makes them challenging to engineer and study. Here we have used CRISPR/Cas9 [clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9] and T-DNA insertion lines to generate a suite of single and multiple gene knockout mutants for the four members of the rbcS family in Arabidopsis, including two novel mutants 2b3b and 1a2b3b. 1a2b3b contained very low levels of Rubisco (~3% relative to the wild-type) and is the first example of a mutant with a homogenous Rubisco pool consisting of a single SSU isoform (1B). Growth under near-outdoor levels of light demonstrated Rubisco-limited growth phenotypes for several SSU mutants and the importance of the 1A and 3B isoforms. We also identified 1a1b as a likely lethal mutation, suggesting a key contributory role for the least expressed 1B isoform during early development. The successful use of CRISPR/Cas here suggests that this is a viable approach for exploring the functional roles of SSU isoforms in plants.

Keywords: Arabidopsis thaliana ; CRISPR/Cas9; Rubisco; SpCas9; T-DNA; chloroplast; photosynthesis; protoplasts

DOI: https://doi.org/10.1093/jxb/eraa316