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https://www.readbyqxmd.com/read/29330702/ptac10-an-s1-domain-containing-component-of-the-transcriptionally-active-chromosome-complex-is-essential-for-plastid-gene-expression-in-arabidopsis-thaliana-and-is-phosphorylated-by-chloroplast-targeted-casein-kinase-ii
#1
Qing-Bo Yu, Tuan-Tuan Zhao, Lin-Shan Ye, Ling Cheng, Ying-Qian Wu, Chao Huang, Zhong-Nan Yang
In higher plant chloroplasts, the plastid-encoded RNA polymerase (PEP) consists of four catalytic subunits and numerous nuclear-encoded accessory proteins, including pTAC10, an S1-domain-containing protein. In this study, pTAC10 knockout lines were characterized. Two ptac10 mutants had an albino phenotype and severely impaired chloroplast development. The pTAC10 genomic sequence fused to a four-tandem MYC tag driven by its own promoter functionally complemented the ptac10-1 mutant phenotype. pTAC10 was present in both the chloroplast stroma and thylakoids...
January 12, 2018: Photosynthesis Research
https://www.readbyqxmd.com/read/29300816/phylogeographic-analysis-of-the-east-asian-goldenrod-solidago-virgaurea-complex-asteraceae-reveals-hidden-ecological-diversification-with-recurrent-formation-of-ecotypes
#2
Shota Sakaguchi, Takuma Kimura, Ryuta Kyan, Masayuki Maki, Takako Nishino, Naoko Ishikawa, Atsushi J Nagano, Mie N Honjo, Masaki Yasugi, Hiroshi Kudoh, Pan Li, Hyeok Jae Choi, Olga A Chernyagina, Motomi Ito
Background and Aims: The processes and mechanisms underlying lineage diversification are major topics in evolutionary biology. Eurasian goldenrod species of the Solidago virgaurea complex show remarkable morphological and ecological diversity in the Japanese Archipelago, with ecotypic taxa well adapted to specific environments (climate, edaphic conditions and disturbance regimes). The species complex is a suitable model to investigate the evolutionary processes of actively speciating plant groups, due to its ability to evolve in relation to environmental adaptation and its historical population dynamics...
December 29, 2017: Annals of Botany
https://www.readbyqxmd.com/read/29299622/a-novel-galactolipase-from-a-green-microalga-chlorella-kessleri-purification-characterization-molecular-cloning-and-heterologous-expression
#3
Shuhei Hashiro, Koyu Fujiuchi, Daisuke Sugimori, Hisashi Yasueda
We have identified an enzyme, galactolipase (ckGL), which hydrolyzes the acyl ester bond of galactolipids such as digalactosyldiacylglycerol (DGDG), in the microalga Chlorella kessleri. Following purification of the enzyme to electrophoretic homogeneity from cell-free extract, the maximum activity toward DGDG was observed at pH 6.5 and 37 °C. ckGL was Ca2+-dependent enzyme and displayed an apparent molecular mass of approx. 53 kDa on SDS-PAGE. The substrate specificity was in the order: DGDG (100%) > monogalactosyldiacylglycerol ≈ phosphatidylglycerol (~ 40%) > sulfoquinovosyldiacylglycerol (~ 20%); the enzyme exhibited almost no activity toward glycerides and other phospholipids...
January 3, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29298822/plastid-ribosome-pausing-is-induced-by-multiple-features-and-is-linked-to-protein-complex-assembly
#4
Lars B Scharff, Piotr Gawroński, Poul Erik Jensen, Stanislaw Karpinski, Dario Leister
Many mRNAs contain pause sites that briefly interrupt the progress of translation. Specific features that induce ribosome pausing have been described; however, their individual contributions to pause-site formation, and the overall biological significance of ribosome pausing, remain largely unclear. We have taken advantage of the compact genome of chloroplasts to carry out a plastid genome-wide survey of pause sites, as a basis for studying the impact of pausing on post-translational processes. Based on ribosomal profiling of Arabidopsis thaliana chloroplast mRNAs, we demonstrate that a combination of factors - mRNA secondary structure, internal Shine-Dalgarno sequences, and positively charged amino acids in the nascent peptide chain - explains 95% of the major pause sites on plastid mRNAs, while codon usage has little impact...
January 3, 2018: Plant Physiology
https://www.readbyqxmd.com/read/29297850/the-algal-chloroplast-as-a-synthetic-biology-platform-for-production-of-therapeutic-proteins
#5
Yuliya M Dyo, Saul Purton
The chloroplast of Chlamydomonas reinhardtii and other microalgae represents an attractive new platform for the synthesis of recombinant therapeutics using synthetic biology (synbio) approaches. Transgenes can be designed in silico, assembled from validated DNA parts and inserted at precise and predetermined locations within the chloroplast genome to give stable synthesis of a desired recombinant protein. Numerous recent examples of different therapeutic proteins produced successfully in the C. reinhardtii chloroplast highlight the potential of this green alga as a simple, low-cost and benign host...
January 3, 2018: Microbiology
https://www.readbyqxmd.com/read/29297348/comparative-analysis-of-inverted-repeats-of-polypod-fern-polypodiales-plastomes-reveals-two-hypervariable-regions
#6
Maria D Logacheva, Anastasiya A Krinitsina, Maxim S Belenikin, Kamil Khafizov, Evgenii A Konorov, Sergey V Kuptsov, Anna S Speranskaya
BACKGROUND: Ferns are large and underexplored group of vascular plants (~ 11 thousands species). The genomic data available by now include low coverage nuclear genomes sequences and partial sequences of mitochondrial genomes for six species and several plastid genomes. RESULTS: We characterized plastid genomes of three species of Dryopteris, which is one of the largest fern genera, using sequencing of chloroplast DNA enriched samples and performed comparative analysis with available plastomes of Polypodiales, the most species-rich group of ferns...
December 28, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29274739/herbarium-collection-based-phylogenetics-of-the-ragweeds-ambrosia-asteraceae
#7
Michael D Martin, Elva Quiroz-Claros, Grace S Brush, Elizabeth A Zimmer
Ambrosia (Asteraceae) is a taxonomically difficult genus of weedy, wind-pollinated plants with an apparent center of diversity in the Sonoran Desert of North America. Determining Ambrosia's evolutionary relationships has been the subject of much interest, with numerous studies using morphological characters, cytology, comparative phytochemistry, and chloroplast restriction site variation to produce conflicting accounts the relationships between Ambrosia species, as well as the classification of their close relatives in Franseria and Hymenoclea...
December 21, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29274579/6-0%C3%A2-k-microarray-reveals-differential-transcriptomic-responses-in-the-dinoflagellate-prorocentrum-minimum-exposed-to-polychlorinated-biphenyl-pcb
#8
Hui Wang, Ruoyu Guo, Jang-Seu Ki
Endocrine disrupting chemicals (EDCs) have toxic effects on algae; however, their molecular genomic responses have not been sufficiently elucidated. Here, we evaluated genome-scaled responses of the dinoflagellate alga Prorocentrum minimum exposed to an EDC, polychlorinated biphenyl (PCB), using a 6.0 K microarray. Based on two-fold change cut-off, we identified that 609 genes (∼10.2%) responded to the PCB treatment. KEGG pathway analysis showed that differentially expressed genes (DEGs) were related to ribosomes, biosynthesis of amino acids, spliceosomes, and cellular processes...
December 14, 2017: Chemosphere
https://www.readbyqxmd.com/read/29250098/reconstruction-of-oryza-sativa-indica-genome-scale-metabolic-model-and-its-responses-to-varying-rubisco-activity-light-intensity-and-enzymatic-cost-conditions
#9
Ankita Chatterjee, Benazir Huma, Rahul Shaw, Sudip Kundu
To combat decrease in rice productivity under different stresses, an understanding of rice metabolism is needed. Though there are different genome scale metabolic models (GSMs) of Oryza sativa japonica, no GSM with gene-protein-reaction association exist for Oryza sativa indica. Here, we report a GSM, OSI1136 of O.s. indica, which includes 3602 genes and 1136 metabolic reactions and transporters distributed across the cytosol, mitochondrion, peroxisome, and chloroplast compartments. Flux balance analysis of the model showed that for varying RuBisCO activity (Vc/Vo) (i) the activity of the chloroplastic malate valve increases to transport reducing equivalents out of the chloroplast under increased photorespiratory conditions and (ii) glyceraldehyde-3-phosphate dehydrogenase and phosphoglycerate kinase can act as source of cytosolic ATP under decreased photorespiration...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29247278/analysis-of-chloroplast-differences-in-leaves-of-rice-isonuclear-alloplasmic-lines
#10
Danfeng Tang, Fan Wei, Muhammad Haneef Kashif, Aziz Khan, Zengqiang Li, Qiqi Shi, Ruixing Jia, Hongying Xie, Li Zhang, Bin Li, Peng Chen, Ruiyang Zhou
The chloroplast being an important organelle of plant cells could possibly be associated with plant cytoplasmic male sterility (CMS). To better understand the correlation between (CMS) and chloroplast, we presented a comprehensive analysis based on the changes of photosynthetic parameters, chloroplasts ultrastructure, soluble sugar and starch content, the relative expression of sugar and starch metabolism genes, and chloroplast genome in rice isonuclear alloplasmic CMS lines at the flowering stage. Leaf gas exchange parameters did not affect by CMS lines (M2BS and M2A), although intercellular CO2 concentration (C i) was influenced in both M2BS and M2A...
December 15, 2017: Protoplasma
https://www.readbyqxmd.com/read/29246263/the-complete-chloroplast-genome-sequence-of-asian-palmyra-palm-borassus-flabellifer
#11
Arpakorn Sakulsathaporn, Passorn Wonnapinij, Supachai Vuttipongchaikij, Somsak Apisitwanich
OBJECTIVE: Borassus flabellifer or Asian Palmyra palm is widely distributed in South and Southeast Asia and is horticultural and economic importance for its fruit and palm sugar production. However, its population is in rapid decline, and only a few genetic data are available. We sequenced the complete chloroplast (cp) genome of B. flabellifer to provide its genetic data for further utilization. RESULTS: The cp genome was obtained by Illumina sequencing and manual gap fillings providing 160,021 bp in length containing a pair of inverted repeats (IRs) with 27,256 bp...
December 16, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/29244730/isolation-and-characterization-of-ftsz-genes-in-cassava
#12
Meng-Ting Geng, Yi Min, Yuan Yao, Xia Chen, Jie Fan, Shuai Yuan, Lei Wang, Chong Sun, Fan Zhang, Lu Shang, Yun-Lin Wang, Rui-Mei Li, Shao-Ping Fu, Rui-Jun Duan, Jiao Liu, Xin-Wen Hu, Jian-Chun Guo
The filamenting temperature-sensitive Z proteins (FtsZs) play an important role in plastid division. In this study, three FtsZ genes were isolated from the cassava genome, and named MeFtsZ1, MeFtsZ2-1, and MeFtsZ2-2, respectively. Based on phylogeny, the MeFtsZs were classified into two groups (FtsZ1 and FtsZ2). MeFtsZ1 with a putative signal peptide at N-terminal, has six exons, and is classed to FtsZ1 clade. MeFtsZ2-1 and MeFtsZ2-2 without a putative signal peptide, have seven exons, and are classed to FtsZ2 clade...
December 15, 2017: Genes
https://www.readbyqxmd.com/read/29240932/homogenization-of-populations-in-the-wildflower-texas-bluebonnet-lupinus-texensis
#13
Kathryn G Turner, Daisie I Huang, Quentin C B Cronk, Loren H Rieseberg
Wildflower seeds are routinely spread along highways and thoroughfares throughout North America as part of federal beautification policy, but the genetic effect of the introduction of these cultivated populations on wild populations of the same species is unknown. Interbreeding may occur between these seeded and wild populations, resulting in several possible outcomes. Here we sample 187 individuals in 12 matched pairs of neighboring wild and seeded populations of the Texas bluebonnet (Lupinus texensis), a species popular in commercially available wildflower seed mixes used by both the Texas Department of Transportation and the public...
December 12, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29230609/comparative-assessment-of-chloroplast-transcriptional-responses-highlights-conserved-and-unique-patterns-across-triticeae-members-under-salt-stress
#14
Saeid Mirzaei, Mehdi Mansouri, Ghasem Mohammadi-Nejad, Gaurav Sablok
Chloroplast functional genomics, in particular understanding the chloroplast transcriptional response is of immense importance mainly due to its role in oxygenic photosynthesis. As a photosynthetic unit, its efficiency and transcriptional activity is directly regulated by reactive oxygen species during abiotic and biotic stress and subsequently affects carbon assimilation, and plant biomass. In crops, understanding photosynthesis is crucial for crop domestication by identifying the traits that could be exploited for crop improvement...
December 11, 2017: Photosynthesis Research
https://www.readbyqxmd.com/read/29222062/evolutionary-history-of-the-cobalamin-independent-methionine-synthase-gene-family-across-the-land-plants
#15
Hugo Vianna Silva Rody, Luiz Orlando de Oliveira
Plants are successful paleopolyploids. The wide diversity of land plants is driven strongly by their gene duplicates undergoing distinct evolutionary fates after duplication. We used genomic resources from 35 model plant species to unravel the evolutionary fate of gene copies (paralogs) of the cobalamin-independent methionine synthase (metE) gene family across the land plants. To explore genealogical relationships and characterize positive selection as a driving force in the evolution of metE paralogs within a single species, we carried out complementary analyses on genomic data of 32 genotypes of soybean...
December 6, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29211049/living-organisms-author-their-read-write-genomes-in-evolution
#16
REVIEW
James A Shapiro
Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life...
December 6, 2017: Biology
https://www.readbyqxmd.com/read/29206296/comparative-plastome-genomics-and-phylogenomics-of-brachypodium-flowering-time-signatures-introgression-and-recombination-in-recently-diverged-ecotypes
#17
Rubén Sancho, Carlos P Cantalapiedra, Diana López-Alvarez, Sean P Gordon, John P Vogel, Pilar Catalán, Bruno Contreras-Moreira
Few pan-genomic studies have been conducted in plants, and none of them have focused on the intraspecific diversity and evolution of their plastid genomes. We address this issue in Brachypodium distachyon and its close relatives B. stacei and B. hybridum, for which a large genomic data set has been compiled. We analyze inter- and intraspecific plastid comparative genomics and phylogenomic relationships within a family-wide framework. Major indel differences were detected between Brachypodium plastomes. Within B...
December 5, 2017: New Phytologist
https://www.readbyqxmd.com/read/29199074/the-plastid-genome-in-cladophorales-green-algae-is-encoded-by-hairpin-chromosomes
#18
Andrea Del Cortona, Frederik Leliaert, Kenny A Bogaert, Monique Turmel, Christian Boedeker, Jan Janouškovec, Juan M Lopez-Bautista, Heroen Verbruggen, Klaas Vandepoele, Olivier De Clerck
Virtually all plastid (chloroplast) genomes are circular double-stranded DNA molecules, typically between 100 and 200 kb in size and encoding circa 80-250 genes. Exceptions to this universal plastid genome architecture are very few and include the dinoflagellates, where genes are located on DNA minicircles. Here we report on the highly deviant chloroplast genome of Cladophorales green algae, which is entirely fragmented into hairpin chromosomes. Short- and long-read high-throughput sequencing of DNA and RNA demonstrated that the chloroplast genes of Boodlea composita are encoded on 1- to 7-kb DNA contigs with an exceptionally high GC content, each containing a long inverted repeat with one or two protein-coding genes and conserved non-coding regions putatively involved in replication and/or expression...
November 22, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/29188144/an-efficient-pipeline-to-generate-data-for-studies-in-plastid-population-genomics-and-phylogeography
#19
Brendan F Kohrn, Jessica M Persinger, Mitchell B Cruzan
Premise of the study: Seed dispersal contributes to gene flow and is responsible for colonization of new sites and range expansion. Sequencing chloroplast haplotypes offers a way to estimate contributions of seed dispersal to population genetic structure and enables studies of population history. Whole-genome sequencing is expensive, but resources can be conserved by pooling samples. Unfortunately, haplotype associations among single-nucleotide polymorphisms (SNPs) are lost in pooled samples, and treating SNP allele frequencies as independent markers provides biased estimates of genetic structure...
November 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29186778/comparative-analysis-of-the-complete-chloroplast-genome-of-four-known-ziziphus-species
#20
(no author information available yet)
Ziziphus Mill. (Rhamnaceae) is comprised of about 170 species that are mainly distributed in tropical to subtropical regions, with few in the temperate zone. Several Ziziphus fruit tree species are important energy, nutrient, and medicinal resources for human populations, particularly for those living in rural regions. To date, limited genomic information is available for this genus. Here, we assembled the complete chloroplast genomes of four best known Ziziphus species, i.e., Ziziphus jujuba, Ziziphus acidojujuba, Ziziphus mauritiana, and Ziziphus spina-christi, based on the Illumina Paired-end sequencing method...
November 24, 2017: Genes
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