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plant chloroplast mitochondrial genome

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https://www.readbyqxmd.com/read/27908230/dna-import-into-mitochondria
#1
REVIEW
Yu M Konstantinov, A Dietrich, F Weber-Lotfi, N Ibrahim, E S Klimenko, V I Tarasenko, T A Bolotova, M V Koulintchenko
In recent decades, it has become evident that the condition for normal functioning of mitochondria in higher eukaryotes is the presence of membrane transport systems of macromolecules (proteins and nucleic acids). Natural competence of the mitochondria in plants, animals, and yeasts to actively uptake DNA may be directly related to horizontal gene transfer into these organelles occurring at much higher rate compared to the nuclear and chloroplast genomes. However, in contrast with import of proteins and tRNAs, little is known about the biological role and molecular mechanism underlying import of DNA into eukaryotic mitochondria...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27903241/abundant-rna-editing-sites-of-chloroplast-protein-coding-genes-in-ginkgo-biloba-and-an-evolutionary-pattern-analysis
#2
Peng He, Sheng Huang, Guanghui Xiao, Yuzhou Zhang, Jianing Yu
BACKGROUND: RNA editing is a posttranscriptional modification process that alters the RNA sequence so that it deviates from the genomic DNA sequence. RNA editing mainly occurs in chloroplasts and mitochondrial genomes, and the number of editing sites varies in terrestrial plants. Why and how RNA editing systems evolved remains a mystery. Ginkgo biloba is one of the oldest seed plants and has an important evolutionary position. Determining the patterns and distribution of RNA editing in the ancient plant provides insights into the evolutionary trend of RNA editing, and helping us to further understand their biological significance...
December 1, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/27847816/analysis-of-the-complete-mitochondrial-genome-sequence-of-the-diploid-cotton-gossypium-raimondii-by-comparative-genomics-approaches
#3
Changwei Bi, Andrew H Paterson, Xuelin Wang, Yiqing Xu, Dongyang Wu, Yanshu Qu, Anna Jiang, Qiaolin Ye, Ning Ye
Cotton is one of the most important economic crops and the primary source of natural fiber and is an important protein source for animal feed. The complete nuclear and chloroplast (cp) genome sequences of G. raimondii are already available but not mitochondria. Here, we assembled the complete mitochondrial (mt) DNA sequence of G. raimondii into a circular genome of length of 676,078 bp and performed comparative analyses with other higher plants. The genome contains 39 protein-coding genes, 6 rRNA genes, and 25 tRNA genes...
2016: BioMed Research International
https://www.readbyqxmd.com/read/27829020/comparative-genome-wide-analysis-of-the-malate-dehydrogenase-gene-families-in-cotton
#4
Muhammad Imran, Kai Tang, Jin-Yuan Liu
Malate dehydrogenases (MDHs) play crucial roles in the physiological processes of plant growth and development. In this study, 13 and 25 MDH genes were identified from Gossypium raimondii and Gossypium hirsutum, respectively. Using these and 13 previously reported Gossypium arboretum MDH genes, a comparative molecular analysis between identified MDH genes from G. raimondii, G. hirsutum, and G. arboretum was performed. Based on multiple sequence alignments, cotton MDHs were divided into five subgroups: mitochondrial MDH, peroxisomal MDH, plastidial MDH, chloroplastic MDH and cytoplasmic MDH...
2016: PloS One
https://www.readbyqxmd.com/read/27793078/genome-wide-investigation-and-expression-analyses-of-the-pentatricopeptide-repeat-protein-gene-family-in-foxtail-millet
#5
Jia-Ming Liu, Zhao-Shi Xu, Pan-Pan Lu, Wei-Wei Li, Ming Chen, Chang-Hong Guo, You-Zhi Ma
BACKGROUND: Pentatricopeptide repeat (PPR) proteins are encoded by a large gene family of approximately 450 members in Arabidopsis and 477 in rice, which characterized by tandem repetitions of a degenerate 35 amino acid characteristic sequence motifs. A large majority of the PPR genes in the higher plants are localized in organelles. Their functions remain as yet largely unknown. The majority of characterized PPR proteins have been found to function in modulating the expression plastid and mitochondrial genes in plants...
October 28, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27764252/the-chloroplast-genome-of-utricularia-reniformis-sheds-light-on-the-evolution-of-the-ndh-gene-complex-of-terrestrial-carnivorous-plants-from-the-lentibulariaceae-family
#6
Saura R Silva, Yani C A Diaz, Helen Alves Penha, Daniel G Pinheiro, Camila C Fernandes, Vitor F O Miranda, Todd P Michael, Alessandro M Varani
Lentibulariaceae is the richest family of carnivorous plants spanning three genera including Pinguicula, Genlisea, and Utricularia. Utricularia is globally distributed, and, unlike Pinguicula and Genlisea, has both aquatic and terrestrial forms. In this study we present the analysis of the chloroplast (cp) genome of the terrestrial Utricularia reniformis. U. reniformis has a standard cp genome of 139,725bp, encoding a gene repertoire similar to essentially all photosynthetic organisms. However, an exclusive combination of losses and pseudogenization of the plastid NAD(P)H-dehydrogenase (ndh) gene complex were observed...
2016: PloS One
https://www.readbyqxmd.com/read/27736909/complete-sequence-and-analysis-of-coconut-palm-cocos-nucifera-mitochondrial-genome
#7
Hasan Awad Aljohi, Wanfei Liu, Qiang Lin, Yuhui Zhao, Jingyao Zeng, Ali Alamer, Ibrahim O Alanazi, Abdullah O Alawad, Abdullah M Al-Sadi, Songnian Hu, Jun Yu
Coconut (Cocos nucifera L.), a member of the palm family (Arecaceae), is one of the most economically important crops in tropics, serving as an important source of food, drink, fuel, medicine, and construction material. Here we report an assembly of the coconut (C. nucifera, Oman local Tall cultivar) mitochondrial (mt) genome based on next-generation sequencing data. This genome, 678,653bp in length and 45.5% in GC content, encodes 72 proteins, 9 pseudogenes, 23 tRNAs, and 3 ribosomal RNAs. Within the assembly, we find that the chloroplast (cp) derived regions account for 5...
2016: PloS One
https://www.readbyqxmd.com/read/27609835/plant-mitochondria-contain-the-protein-translocase-subunits-tatb-and-tatc
#8
Chris Carrie, Stefan Weißenberger, Jürgen Soll
Twin-arginine translocation (Tat) pathways have been well-characterized in bacteria and chloroplasts. Genes encoding a TatC protein are found in almost all plant mitochondrial genomes but to date these have not been extensively investigated. For the first time it could be demonstrated that this mitochondrial-encoded TatC is a functional gene that is translated into a protein in the model plant Arabidopsis thaliana A TatB--like subunit localized to the inner membrane was also identified that is nuclear-encoded and is essential for plant growth and development, indicating that plants potentially require a Tat pathway for mitochondrial biogenesis...
October 15, 2016: Journal of Cell Science
https://www.readbyqxmd.com/read/27563303/alternative-oxidase-gene-family-in-hypericum-perforatum-l-characterization-and-expression-at-the-post-germinative-phase
#9
Isabel Velada, Hélia G Cardoso, Carla Ragonezi, Amaia Nogales, Alexandre Ferreira, Vera Valadas, Birgit Arnholdt-Schmitt
Alternative oxidase (AOX) protein is located in the inner mitochondrial membrane and is encoded in the nuclear genome being involved in plant response upon a diversity of environmental stresses and also in normal plant growth and development. Here we report the characterization of the AOX gene family of Hypericum perforatum L. Two AOX genes were identified, both with a structure of four exons (HpAOX1, acc. KU674355 and HpAOX2, acc. KU674356). High variability was found at the N-terminal region of the protein coincident with the high variability identified at the mitochondrial transit peptide...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27503298/mitochondrion-to-chloroplast-dna-transfers-and-intragenomic-proliferation-of-chloroplast-group-ii-introns-in-gloeotilopsis-green-algae-ulotrichales-ulvophyceae
#10
Monique Turmel, Christian Otis, Claude Lemieux
To probe organelle genome evolution in the Ulvales/Ulotrichales clade, the newly sequenced chloroplast and mitochondrial genomes of Gloeotilopsis planctonica and Gloeotilopsis sarcinoidea (Ulotrichales) were compared with those of Pseudendoclonium akinetum (Ulotrichales) and of the few other green algae previously sampled in the Ulvophyceae. At 105,236 bp, the G planctonica mitochondrial DNA (mtDNA) is the largest mitochondrial genome reported so far among chlorophytes, whereas the 221,431-bp G planctonica and 262,888-bp G sarcinoidea chloroplast DNAs (cpDNAs) are the largest chloroplast genomes analyzed among the Ulvophyceae...
2016: Genome Biology and Evolution
https://www.readbyqxmd.com/read/27446158/differential-regulation-of-genes-coding-for-organelle-and-cytosolic-clpatpases-under-biotic-and-abiotic-stresses-in-wheat
#11
Senthilkumar K Muthusamy, Monika Dalal, Viswanathan Chinnusamy, Kailash C Bansal
A sub-group of class I Caseinolytic proteases (Clps) function as molecular chaperone and confer thermotolerance to plants. We identified class I Clp family consisting of five ClpB/HSP100, two ClpC, and two ClpD genes from bread wheat. Phylogenetic analysis showed that these genes were highly conserved across grass genomes. Subcellular localization prediction revealed that TaClpC and TaClpD subgroup proteins and TaClpB1 proteins are potentially targeted to chloroplast, while TaClpB5 to mitochondria, and TaClpB2, TaClpB3, and TaClpB4 to cytoplasm...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27444405/the-mitochondrial-genome-map-of-nelumbo-nucifera-reveals-ancient-evolutionary-features
#12
Songtao Gui, Zhihua Wu, Hongyuan Zhang, Yinzhen Zheng, Zhixuan Zhu, Dequan Liang, Yi Ding
Nelumbo nucifera is an evolutionary relic from the Late Cretaceous period. Sequencing the N. nucifera mitochondrial genome is important for elucidating the evolutionary characteristics of basal eudicots. Here, the N. nucifera mitochondrial genome was sequenced using single molecule real-time sequencing technology (SMRT), and the mitochondrial genome map was constructed after de novo assembly and annotation. The results showed that the 524,797-bp N. nucifera mitochondrial genome has a total of 63 genes, including 40 protein-coding genes, three rRNA genes and 20 tRNA genes...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27235415/systematic-analysis-of-plant-mitochondrial-and-chloroplast-small-rnas-suggests-organelle-specific-mrna-stabilization-mechanisms
#13
Hannes Ruwe, Gongwei Wang, Sandra Gusewski, Christian Schmitz-Linneweber
Land plant organellar genomes encode a small number of genes, many of which are essential for respiration and photosynthesis. Organellar gene expression is characterized by a multitude of RNA processing events that lead to stable, translatable transcripts. RNA binding proteins (RBPs), have been shown to generate and protect transcript termini and eventually induce the accumulation of short RNA footprints. We applied knowledge of such RBP-derived footprints to develop software (sRNA miner) that enables identification of RBP footprints, or other clusters of small RNAs, in organelles...
September 6, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27155533/identification-and-molecular-characterization-of-the-nicotianamine-synthase-gene-family-in-bread-wheat
#14
Julien Bonneau, Ute Baumann, Jesse Beasley, Yuan Li, Alexander A T Johnson
Nicotianamine (NA) is a non-protein amino acid involved in fundamental aspects of metal uptake, transport and homeostasis in all plants and constitutes the biosynthetic precursor of mugineic acid family phytosiderophores (MAs) in graminaceous plant species. Nicotianamine synthase (NAS) genes, which encode enzymes that synthesize NA from S-adenosyl-L-methionine (SAM), are differentially regulated by iron (Fe) status in most plant species and plant genomes have been found to contain anywhere from 1 to 9 NAS genes...
December 2016: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/27100569/divergent-evolution-of-the-m3a-family-of-metallopeptidases-in-plants
#15
Beata Kmiec, Pedro F Teixeira, Monika W Murcha, Elzbieta Glaser
Plants, as stationary organisms, have developed mechanisms allowing them efficient resource reallocation and a response to changing environmental conditions. One of these mechanisms is proteome remodeling via a broad peptidase network present in various cellular compartments including mitochondria and chloroplasts. The genome of the model plant Arabidopsis thaliana encodes as many as 616 putative peptidase-coding genes organized in 55 peptidase families. In this study, we describe the M3A family of peptidases, which comprises four members: mitochondrial and chloroplastic oligopeptidase (OOP), cytosolic oligopeptidase (CyOP), mitochondrial octapeptidyl aminopeptidase 1 (Oct1) and plant-specific protein of M3 family (PSPM3) of unknown function...
July 2016: Physiologia Plantarum
https://www.readbyqxmd.com/read/26993327/genetic-composition-of-interspecific-potato-somatic-hybrids-and-autofused-4x-plants-evaluated-by-dart-and-cytoplasmic-dna-markers
#16
Paulina Smyda-Dajmund, Jadwiga Śliwka, Iwona Wasilewicz-Flis, Henryka Jakuczun, Ewa Zimnoch-Guzowska
Using DArT analysis, we demonstrated that all Solanum × michoacanum (+) S. tuberosum somatic hybrids contained all parental chromosomes. However, from 13.9 to 29.6 % of the markers from both parents were lost in the hybrids. Somatic hybrids are an interesting material for research of nucleus-cytoplasm interaction and sources of new nuclear and cytoplasmic combinations. Analyses of genomes of somatic hybrids are essential for studies on genome compatibility between species, its evolution and are important for their efficient exploitation...
June 2016: Plant Cell Reports
https://www.readbyqxmd.com/read/26951647/cell-to-cell-movement-of-mitochondria-in-plants
#17
Csanad Gurdon, Zora Svab, Yaping Feng, Dibyendu Kumar, Pal Maliga
We report cell-to-cell movement of mitochondria through a graft junction. Mitochondrial movement was discovered in an experiment designed to select for chloroplast transfer from Nicotiana sylvestris into Nicotiana tabacum cells. The alloplasmic N. tabacum line we used carries Nicotiana undulata cytoplasmic genomes, and its flowers are male sterile due to the foreign mitochondrial genome. Thus, rare mitochondrial DNA transfer from N. sylvestris to N. tabacum could be recognized by restoration of fertile flower anatomy...
March 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/26781919/the-roles-of-mitochondrial-transcription-termination-factors-mterfs-in-plants
#18
REVIEW
Víctor Quesada
Stress such as salinity, cold, heat or drought affect plant growth and development, and frequently result in diminished productivity. Unlike animals, plants are sedentary organisms that must withstand and cope with environmental stresses. During evolution, plants have developed strategies to successfully adapt to or tolerate such stresses, which might have led to the expansion and functional diversification of gene families. Some new genes may have acquired functions that could differ from those of their animal homologues, e...
July 2016: Physiologia Plantarum
https://www.readbyqxmd.com/read/26407159/organelle-simple-sequence-repeat-markers-help-to-distinguish-carpelloid-stamen-and-normal-cytoplasmic-male-sterile-sources-in-broccoli
#19
Jinshuai Shu, Yumei Liu, Zhansheng Li, Lili Zhang, Zhiyuan Fang, Limei Yang, Mu Zhuang, Yangyong Zhang, Honghao Lv
We previously discovered carpelloid stamens when breeding cytoplasmic male sterile lines in broccoli (Brassica oleracea var. italica). In this study, hybrids and multiple backcrosses were produced from different cytoplasmic male sterile carpelloid stamen sources and maintainer lines. Carpelloid stamens caused dysplasia of the flower structure and led to hooked or coiled siliques with poor seed setting, which were inherited in a maternal fashion. Using four distinct carpelloid stamens and twelve distinct normal stamens from cytoplasmic male sterile sources and one maintainer, we used 21 mitochondrial simple sequence repeat (mtSSR) primers and 32 chloroplast SSR primers to identify a mitochondrial marker, mtSSR2, that can differentiate between the cytoplasm of carpelloid and normal stamens...
2015: PloS One
https://www.readbyqxmd.com/read/26388536/intra-individual-polymorphism-in-chloroplasts-from-ngs-data-where-does-it-come-from-and-how-to-handle-it
#20
N Scarcelli, C Mariac, T L P Couvreur, A Faye, D Richard, F Sabot, C Berthouly-Salazar, Y Vigouroux
Next-generation sequencing allows access to a large quantity of genomic data. In plants, several studies used whole chloroplast genome sequences for inferring phylogeography or phylogeny. Even though the chloroplast is a haploid organelle, NGS plastome data identified a nonnegligible number of intra-individual polymorphic SNPs. Such observations could have several causes such as sequencing errors, the presence of heteroplasmy or transfer of chloroplast sequences in the nuclear and mitochondrial genomes. The occurrence of allelic diversity has practical important impacts on the identification of diversity, the analysis of the chloroplast data and beyond that, significant evolutionary questions...
March 2016: Molecular Ecology Resources
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