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plant mitochondrial genome

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https://www.readbyqxmd.com/read/29044717/a-genome-scale-analysis-of-mrnas-targeting-to-plant-mitochondria-upstream-augs-in-5-utrs-reduce-mitochondrial-association
#1
Timothée Vincent, Audrey Vingadassalon, Elodie Ubrig, Kevin Azeredo, Ola Srour, Valérie Cognat, Stéfanie Graindorge, Thalia Salinas, Laurence Maréchal-Drouard, Anne-Marie Duchêne
Intracellular sorting of mRNAs is an essential process to regulate gene expression and protein localization. Most of mitochondrial proteins are nuclear-encoded and imported into mitochondria, through post-translational or co-translational processes. In the latter case, mRNAs are found enriched in the vicinity of mitochondria. A genome-scale analysis of mRNAs associated with mitochondria has been performed to determine plant cytosolic mRNAs targeted to the mitochondrial surface. Many messengers encoding mitochondrial proteins were found associated with mitochondria...
October 17, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28988325/advances-in-understanding-the-molecular-mechanisms-of-cytoplasmic-male-sterility-and-restoration-in-rice
#2
Huiwu Tang, Yongyao Xie, Yao-Guang Liu, Letian Chen
Cytoplasmic male sterility (CMS) in plants is a male reproductive defect determined by mitochondrial genes and inherited maternally. CMS can be suppressed by nuclear restorer of fertility (Rf) genes. Therefore, CMS/Rf systems provide a classic model for the study of mitochondrial-nuclear interactions in plants. Moreover, CMS/Rf systems are economical, effective tools for the production of hybrid seeds. For example, CMS/Rf systems have been applied in over forty countries to breed hybrid rice (Oryza sativa L...
October 7, 2017: Plant Reproduction
https://www.readbyqxmd.com/read/28987861/genome-wide-transcriptome-profiling-of-genes-associated-with-arsenate-toxicity-in-an-arsenic-tolerant-rice-mutant
#3
Sun-Goo Hwang, Sandeep Chapagain, Jae Woo Lee, A-Reum Han, Cheol Seong Jang
The presence of arsenic (As) in polluted environments, such as ground water, affects the accumulation of As in rice grains and causes a serious threat to human health. However, the precise molecular regulations related to As toxicity and tolerance in rice remain largely unknown. In the present study, we developed an arsenic-tolerant type 1 (ATT1) rice mutant by γ-irradiation mutagenesis and performed genome-wide transcriptome analysis for the characterization of As-responsive genes. Toxicity inhibited transcriptional regulation of putative genes involved in photosynthesis, mitochondrial electron transport, and lipid biosynthesis metabolism in wild-type (WT) and ATT1 rice mutant...
September 27, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28986910/ribosome-profiling-in-maize
#4
Prakitchai Chotewutmontri, Nicholas Stiffler, Kenneth P Watkins, Alice Barkan
Ribosome profiling (also known as Ribo-seq) provides a genome-wide, high-resolution, and quantitative accounting of mRNA segments that are occupied by ribosomes in vivo. The method has been used to address numerous questions in bacteria, yeast, and metazoa, but its application to questions in plant biology is just beginning. This chapter provides a detailed protocol for profiling ribosomes in plant leaf tissue. The method was developed and optimized with maize, but it has been used successfully with Arabidopsis and tobacco as well...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28984842/intercompartmental-piecewise-gene-transfer
#5
REVIEW
Przemyslaw Szafranski
Gene relocation from the residual genomes of organelles to the nuclear genome still continues, although as a scaled down evolutionary phenomenon, limited in occurrence mostly to protists (sensu lato) and land plants. During this process, the structural integrity of transferred genes is usually preserved. However, the relocation of mitochondrial genes that code for respiratory chain and ribosomal proteins is sometimes associated with their fragmentation into two complementary genes. Herein, this review compiles cases of piecewise gene transfer from the mitochondria to the nucleus, and discusses hypothesized mechanistic links between the fission and relocation of those genes...
October 6, 2017: Genes
https://www.readbyqxmd.com/read/28981788/empty-pericarp11-serves-as-a-factor-for-splicing-of-mitochondrial-nad1-intron-and-is-required-to-ensure-proper-seed-development-in-maize
#6
Xuemei Ren, Zhenyuan Pan, Hailiang Zhao, Junli Zhao, Manjun Cai, Jiang Li, Zuxin Zhang, Fazhan Qiu, Gerhard Leubner
Group II introns are common in the mitochondrial genome of higher plant species. The splicing of these introns is a complex process involving the synergistic action of multiple factors. However, few of these factors have been characterized in maize. In this study, we found that the Empty pericarp11 (Emp11) gene, which encodes a P-type pentatricopeptide repeat (PPR) protein, is required for the development of maize seeds. The loss of Emp11 function seriously impairs embryo and endosperm development, resulting in empty pericarp seeds in maize, and alteration in Emp11 expression leads to quantitative variation in kernel size and weight...
July 20, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28977655/plant-organellar-dna-polymerases-are-replicative-and-translesion-dna-synthesis-polymerases
#7
Noe Baruch-Torres, Luis G Brieba
Genomes acquire lesions that can block the replication fork and some lesions must be bypassed to allow survival. The nuclear genome of flowering plants encodes two family-A DNA polymerases (DNAPs), the result of a duplication event, that are the sole DNAPs in plant organelles. These DNAPs, dubbed Plant Organellar Polymerases (POPs), resemble the Klenow fragment of bacterial DNAP I and are not related to metazoan and fungal mitochondrial DNAPs. Herein we report that replicative POPs from the plant model Arabidopsis thaliana (AtPolI) efficiently bypass one the most insidious DNA lesions, an apurinic/apyrimidinic (AP) site...
August 30, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28972995/the-mitochondrial-genome-of-the-plant-pathogenic-fungus-stemphylium-lycopersici-uncovers-a-dynamic-structure-due-to-repetitive-and-mobile-elements
#8
Mario Emilio Ernesto Franco, Silvina Marianela Yanil López, Rocio Medina, César Gustavo Lucentini, Maria Inés Troncozo, Graciela Noemí Pastorino, Mario Carlos Nazareno Saparrat, Pedro Alberto Balatti
Stemphylium lycopersici (Pleosporales) is a plant-pathogenic fungus that has been associated with a broad range of plant-hosts worldwide. It is one of the causative agents of gray leaf spot disease in tomato and pepper. The aim of this work was to characterize the mitochondrial genome of S. lycopersici CIDEFI-216, to use it to trace taxonomic relationships with other fungal taxa and to get insights into the evolutionary history of this phytopathogen. The complete mitochondrial genome was assembled into a circular double-stranded DNA molecule of 75,911 bp that harbors a set of 37 protein-coding genes, 2 rRNA genes (rns and rnl) and 28 tRNA genes, which are transcribed from both sense and antisense strands...
2017: PloS One
https://www.readbyqxmd.com/read/28947489/the-plastid-and-mitochondrial-peptidase-network-in-arabidopsis-thaliana-a-foundation-for-testing-genetic-interactions-and-functions-in-organellar-proteostasis
#9
Kristina Majsec, Nazmul H Bhuiyan, Qi Sun, Sunita Kumari, Vivek Kumar, Doreen Ware, Klaas Jan van Wijk
Plant plastids and mitochondria have dynamic proteomes. Protein homeostasis in these organelles is maintained by a proteostasis network containing protein chaperones, peptidases and their substrate recognition factors. However, many peptidases, as well as their functional connections and substrates, are poorly characterized. This review provides a systematic insight into the organellar peptidase network in Arabidopsis. We present a compendium of known and putative Arabidopsis peptidases and inhibitors, and compare the distribution of plastid and mitochondrial peptidases to the total peptidase complement...
September 25, 2017: Plant Cell
https://www.readbyqxmd.com/read/28922794/genome-wide-variation-patterns-uncover-the-origin-and-selection-in-cultivated-ginseng-panax-ginseng-meyer
#10
Ming-Rui Li, Feng-Xue Shi, Ya-Ling Li, Peng Jiang, Lili Jiao, Bao Liu, Lin-Feng Li
Chinese ginseng (Panax ginseng Meyer) is a medicinally important herb and plays crucial roles in traditional Chinese medicine. Pharmacological analyses identified diverse bioactive components from Chinese ginseng. However, basic biological attributes including domestication and selection of the ginseng plant remain under-investigated. Here, we presented a genome-wide view of the domestication and selection of cultivated ginseng based on the whole genome data. A total of 8,660 protein-coding genes were selected for genome-wide scanning of the 30 wild and cultivated ginseng accessions...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28871540/isolation-of-mitochondria-from-model-and-crop-plants
#11
Sandra M Kerbler, Nicolas L Taylor
The ability to isolate intact and functional mitochondria has greatly deepened our understanding of mitochondrial structure and function. With the advancement of molecular biology techniques and progression into omics-based research over recent decades, mitochondrial research has shifted from crop species such as wheat, pea, and potato to genetically sequenced models such as Arabidopsis thaliana and rice. Although there are many attributes that make model species particularly appealing for plant research, they are often less than ideal for conducting biochemical investigations and as such, considerable modification to mitochondrial isolation methods has been made...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28854599/mitochondrial-genome-assemblies-of-elysia-timida-and-elysia-cornigera-and-the-response-of-mitochondrion-associated-metabolism-during-starvation
#12
Cessa Rauch, Gregor Christa, Jan de Vries, Christian Woehle, Sven B Gould
Some sacoglossan sea slugs sequester functional plastids (kleptoplasts) from their food, which continue to fix CO2 in a light dependent manner inside the animals. In plants and algae, plastid and mitochondrial metabolism are linked in ways that reach beyond the provision of energy-rich carbon compounds through photosynthesis, but how slug mitochondria respond to starvation or alterations in plastid biochemistry has not been explored. We assembled the mitochondrial genomes of the plastid-sequestering sea slugs Elysia timida and Elysia cornigera from RNA-Seq data that was complemented with standard sequencing of mitochondrial DNA through primer walking...
July 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28852146/the-extraordinary-variation-of-the-organellar-genomes-of-the-aneura-pinguis-revealed-advanced-cryptic-speciation-of-the-early-land-plants
#13
Kamil Myszczyński, Alina Bączkiewicz, Katarzyna Buczkowska, Monika Ślipiko, Monika Szczecińska, Jakub Sawicki
Aneura pinguis is known as a species complex with several morphologically indiscernible species, which are often reproductively isolated from each other and show distinguishable genetic differences. Genetic dissimilarity of cryptic species may be detected by genomes comparison. This study presents the first complete sequences of chloroplast and mitochondrial genomes of six cryptic species of A. pinguis complex: A. pinguis A, B, C, E, F, J. These genomes have been compared to each other in order to reconstruct phylogenetic relationships and to gain better understanding of the evolutionary process of cryptic speciation in this complex...
August 29, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821607/two-plant-derived-aporphinoid-alkaloids-exert-their-antifungal-activity-by-disrupting-mitochondrial-iron-sulfur-cluster-biosynthesis
#14
Siddharth K Tripathi, Tao Xu, Qin Feng, Bharathi Avula, Xiaomin Shi, Xuewen Pan, Melanie M Mask, Scott R Baerson, Melissa R Jacob, Ranga Rao Ravu, Shabana I Khan, Xing-Cong Li, Ikhlas A Khan, Alice M Clark, Ameeta K Agarwal
Eupolauridine and liriodenine are plant-derived aporphinoid alkaloids that exhibit potent inhibitory activity against the opportunistic fungal pathogens Candida albicans and Cryptococcus neoformans However, the molecular mechanism of this antifungal activity is unknown. In this study, we show that eupolauridine 9591 (E9591), a synthetic analog of eupolauridine, and liriodenine methiodide (LMT), a methiodide salt of liriodenine, mediate their antifungal activities by disrupting mitochondrial iron-sulfur (Fe-S) cluster synthesis...
October 6, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28754635/the-little-brown-bat-nuclear-genome-contains-an-entire-mitochondrial-genome-real-or-artifact
#15
Huizhen Shi, Yutong Xing, Xiuguang Mao
Nuclear mitochondrial DNA sequences (NUMTs) have been documented in almost all eukaryotic genomes studied. Recently, with the number of sequenced genomes increasing, extremely large NUMTs, even a nearly entire mitochondrial genome, have been reported in some plants and animals. However, few such studies provided strong experimental evidences for these important discoveries. In this study using a computer-based search method an entire mitochondrial genome (NUMT-1) was found in the nuclear genome of a bat species (Myotis lucifugus)...
September 20, 2017: Gene
https://www.readbyqxmd.com/read/28723946/the-mitochondrial-genome-of-the-terrestrial-carnivorous-plant-utricularia-reniformis-lentibulariaceae-structure-comparative-analysis-and-evolutionary-landmarks
#16
Saura R Silva, Danillo O Alvarenga, Yani Aranguren, Helen A Penha, Camila C Fernandes, Daniel G Pinheiro, Marcos T Oliveira, Todd P Michael, Vitor F O Miranda, Alessandro M Varani
The carnivorous plants of the family Lentibulariaceae have attained recent attention not only because of their interesting lifestyle, but also because of their dynamic nuclear genome size. Lentibulariaceae genomes span an order of magnitude and include species with the smallest genomes in angiosperms, making them a powerful system to study the mechanisms of genome expansion and contraction. However, little is known about mitochondrial DNA (mtDNA) sequences of this family, and the evolutionary forces that shape this organellar genome...
2017: PloS One
https://www.readbyqxmd.com/read/28701376/the-nuclear-and-mitochondrial-genomes-of-the-facultatively-eusocial-orchid-bee-euglossa-dilemma
#17
Philipp Brand, Nicholas Saleh, Hailin Pan, Cai Li, Karen M Kapheim, Santiago R Ramírez
Bees provide indispensable pollination services to both agricultural crops and wild plant populations, and several species of bees have become important models for the study of learning and memory, plant-insect interactions, and social behavior. Orchid bees (Apidae: Euglossini) are especially important to the fields of pollination ecology, evolution, and species conservation. Here we report the nuclear and mitochondrial genome sequences of the orchid bee Euglossa dilemma Bembé & Eltz. E. dilemma was selected because it is widely distributed, highly abundant, and it was recently naturalized in the southeastern United States...
September 7, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28645767/assessing-the-potential-of-rad-sequencing-to-resolve-phylogenetic-relationships-within-species-radiations-the-fly-genus-chiastocheta-diptera-anthomyiidae-as-a-case-study
#18
Tomasz Suchan, Anahí Espíndola, Sereina Rutschmann, Brent C Emerson, Kevin Gori, Christophe Dessimoz, Nils Arrigo, Michał Ronikier, Nadir Alvarez
Determining phylogenetic relationships among recently diverged species has long been a challenge in evolutionary biology. Cytoplasmic DNA markers, which have been widely used, notably in the context of molecular barcoding, have not always proved successful in resolving such phylogenies. However, with the advent of next-generation-sequencing technologies and associated techniques of reduced genome representation, phylogenies of closely related species have been resolved at a much higher detail in the last couple of years...
June 21, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28638050/de-novo-yeast-genome-assemblies-from-minion-pacbio-and-miseq-platforms
#19
Francesca Giordano, Louise Aigrain, Michael A Quail, Paul Coupland, James K Bonfield, Robert M Davies, German Tischler, David K Jackson, Thomas M Keane, Jing Li, Jia-Xing Yue, Gianni Liti, Richard Durbin, Zemin Ning
Long-read sequencing technologies such as Pacific Biosciences and Oxford Nanopore MinION are capable of producing long sequencing reads with average fragment lengths of over 10,000 base-pairs and maximum lengths reaching 100,000 base- pairs. Compared with short reads, the assemblies obtained from long-read sequencing platforms have much higher contig continuity and genome completeness as long fragments are able to extend paths into problematic or repetitive regions. Many successful assembly applications of the Pacific Biosciences technology have been reported ranging from small bacterial genomes to large plant and animal genomes...
June 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28614601/genomewide-transcriptional-reprogramming-in-the-seagrass-cymodocea-nodosa-under-experimental-ocean-acidification
#20
Miriam Ruocco, Francesco Musacchia, Irene Olivé, Monya M Costa, Isabel Barrote, Rui Santos, Remo Sanges, Gabriele Procaccini, João Silva
Here, we report the first use of massive-scale RNA-sequencing to explore seagrass response to CO2 -driven ocean acidification (OA). Large-scale gene expression changes in the seagrass Cymodocea nodosa occurred at CO2 levels projected by the end of the century. C. nodosa transcriptome was obtained using Illumina RNA-Seq technology and de novo assembly, and differential gene expression was explored in plants exposed to short-term high CO2 /low pH conditions. At high pCO2 , there was a significant increased expression of transcripts associated with photosynthesis, including light reaction functions and CO2 fixation, and also to respiratory pathways, specifically for enzymes involved in glycolysis, in the tricarboxylic acid cycle and in the energy metabolism of the mitochondrial electron transport...
June 14, 2017: Molecular Ecology
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