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https://www.readbyqxmd.com/read/27911809/unique-attributes-of-cyanobacterial-metabolism-revealed-by-improved-genome-scale-metabolic-modeling-and-essential-gene-analysis
#1
Jared T Broddrick, Benjamin E Rubin, David G Welkie, Niu Du, Nathan Mih, Spencer Diamond, Jenny J Lee, Susan S Golden, Bernhard O Palsson
The model cyanobacterium, Synechococcus elongatus PCC 7942, is a genetically tractable obligate phototroph that is being developed for the bioproduction of high-value chemicals. Genome-scale models (GEMs) have been successfully used to assess and engineer cellular metabolism; however, GEMs of phototrophic metabolism have been limited by the lack of experimental datasets for model validation and the challenges of incorporating photon uptake. Here, we develop a GEM of metabolism in S. elongatus using random barcode transposon site sequencing (RB-TnSeq) essential gene and physiological data specific to photoautotrophic metabolism...
December 1, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27903821/construction-of-a-minimal-genome-as-a-chassis-for-synthetic-biology
#2
REVIEW
Bong Hyun Sung, Donghui Choe, Sun Chang Kim, Byung-Kwan Cho
Microbial diversity and complexity pose challenges in understanding the voluminous genetic information produced from whole-genome sequences, bioinformatics and high-throughput '-omics' research. These challenges can be overcome by a core blueprint of a genome drawn with a minimal gene set, which is essential for life. Systems biology and large-scale gene inactivation studies have estimated the number of essential genes to be ∼300-500 in many microbial genomes. On the basis of the essential gene set information, minimal-genome strains have been generated using sophisticated genome engineering techniques, such as genome reduction and chemical genome synthesis...
November 30, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27903241/abundant-rna-editing-sites-of-chloroplast-protein-coding-genes-in-ginkgo-biloba-and-an-evolutionary-pattern-analysis
#3
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/27899661/duplication-insertion-recombineering-a-fast-and-scar-free-method-for-efficient-transfer-of-multiple-mutations-in-bacteria
#4
Joakim Näsvall, Anna Knöppel, Dan I Andersson
We have developed a new λ Red recombineering methodology for generating transient selection markers that can be used to transfer mutations between bacterial strains of both Escherichia coli and Salmonella enterica The method is fast, simple and allows for the construction of strains with several mutations without any unwanted sequence changes (scar-free). The method uses λ Red recombineering to generate a marker-held tandem duplication, termed Duplication-Insertion (Dup-In). The Dup-Ins can easily be transferred between strains by generalized transduction and are subsequently rapidly lost by homologous recombination between the two copies of the duplicated sequence, leaving no scar sequence or antibiotic resistance cassette behind...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899637/a-genome-wide-dosage-suppressor-network-reveals-genomic-robustness
#5
Biranchi Patra, Yoshiko Kon, Gitanjali Yadav, Anthony W Sevold, Jesse P Frumkin, Ravishankar R Vallabhajosyula, Arend Hintze, Bjørn Østman, Jory Schossau, Ashish Bhan, Bruz Marzolf, Jenna K Tamashiro, Amardeep Kaur, Nitin S Baliga, Elizabeth J Grayhack, Christoph Adami, David J Galas, Alpan Raval, Eric M Phizicky, Animesh Ray
Genomic robustness is the extent to which an organism has evolved to withstand the effects of deleterious mutations. We explored the extent of genomic robustness in budding yeast by genome wide dosage suppressor analysis of 53 conditional lethal mutations in cell division cycle and RNA synthesis related genes, revealing 660 suppressor interactions of which 642 are novel. This collection has several distinctive features, including high co-occurrence of mutant-suppressor pairs within protein modules, highly correlated functions between the pairs and higher diversity of functions among the co-suppressors than previously observed...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27896428/xci-escaping-gene-kdm5c-contributes-to-ovarian-development-via-downregulating-mir-320a
#6
Yi-Xi Sun, Yi-Xin Zhang, Dan Zhang, Chen-Ming Xu, Song-Chang Chen, Jun-Yu Zhang, Ye-Chun Ruan, Feng Chen, Run-Ju Zhang, Ye-Qing Qian, Yi-Feng Liu, Lu-Yang Jin, Tian-Tian Yu, Hai-Yan Xu, Yu-Qin Luo, Xin-Mei Liu, Fei Sun, Jian-Zhong Sheng, He-Feng Huang
Mechanisms underlying female gonadal dysgenesis remain unclarified and relatively unstudied. Whether X-chromosome inactivation (XCI)-escaping genes and microRNAs (miRNAs) contribute to this condition is currently unknown. We compared 45,X Turner Syndrome women with 46,XX normal women, and investigated differentially expressed miRNAs in Turner Syndrome through plasma miRNA sequencing. We found that miR-320a was consistently upregulated not only in 45,X plasma and peripheral blood mononuclear cells (PBMCs), but also in 45,X fetal gonadal tissues...
November 28, 2016: Human Genetics
https://www.readbyqxmd.com/read/27879333/the-genome-wide-interaction-network-of-nutrient-stress-genes-in-escherichia-coli
#7
Jean-Philippe Côté, Shawn French, Sebastian S Gehrke, Craig R MacNair, Chand S Mangat, Amrita Bharat, Eric D Brown
: Conventional efforts to describe essential genes in bacteria have typically emphasized nutrient-rich growth conditions. Of note, however, are the set of genes that become essential when bacteria are grown under nutrient stress. For example, more than 100 genes become indispensable when the model bacterium Escherichia coli is grown on nutrient-limited media, and many of these nutrient stress genes have also been shown to be important for the growth of various bacterial pathogens in vivo To better understand the genetic network that underpins nutrient stress in E...
November 22, 2016: MBio
https://www.readbyqxmd.com/read/27875099/the-rhob-small-gtpase-in-physiology-and-disease
#8
Francisco M Vega, Anne J Ridley
RhoB is a Rho family GTPase that is highly similar to RhoA and RhoC, yet has distinct functions in cells. Its unique C-terminal region is subject to specific post-translational modifications that confer different localization and functions to RhoB. Apart from the common role with RhoA and RhoC in actin organization and cell migration, RhoB is also implicated in a variety of other cellular processes including membrane trafficking, cell proliferation, DNA-repair and apoptosis. RhoB is not an essential gene in mice, but it is implicated in several physiological and pathological processes...
November 22, 2016: Small GTPases
https://www.readbyqxmd.com/read/27874310/ancient-microrna-families-that-regulate-transcription-factors-are-preferentially-preserved-during-plant-radiation
#9
Tao Shi, Kun Wang, Pingfang Yang
Essential genes are usually less likely to be lost during evolution, whereas dispensable genes are lost more frequently. Integrating sacred lotus and other plant microRNA (miRNA) data, we found different ancient miRNA families that arose before eudicot radiation exhibit different evolutionary trajectories. Those ancient miRNA families with higher copy and target numbers, and older age are more likely to be retained in plant descendants and more conserved in (hairpin-structured) miRNA gene sequences. Interestingly, a large portion of the well conserved miRNA families in plant lineages can target transcription factors (TFs)...
November 22, 2016: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/27861562/digitor-dasciz-has-multiple-roles-in-drosophila-development
#10
Saheli Sengupta, Uttama Rath, Changfu Yao, Michael Zavortink, Chao Wang, Jack Girton, Kristen M Johansen, Jørgen Johansen
In this study we provide evidence that the spindle matrix protein Skeletor in Drosophila interacts with the human ASCIZ (also known as ATMIN and ZNF822) ortholog, Digitor/dASCIZ. This interaction was first detected in a yeast two-hybrid screen and subsequently confirmed by pull-down assays. We also confirm a previously documented function of Digitor/dASCIZ as a regulator of Dynein light chain/Cut up expression. Using transgenic expression of a mCitrine-labeled Digitor construct, we show that Digitor/dASCIZ is a nuclear protein that is localized to interband and developmental puff chromosomal regions during interphase but redistributes to the spindle region during mitosis...
2016: PloS One
https://www.readbyqxmd.com/read/27834204/one-gene-and-two-proteins-a-leaderless-mrna-supports-the-translation-of-a-shorter-form-of-the-shigella-virf-regulator
#11
Maria Letizia Di Martino, Cédric Romilly, E Gerhart H Wagner, Bianca Colonna, Gianni Prosseda
: VirF, an AraC-like activator, is required to trigger a regulatory cascade that initiates the invasive program of Shigella spp., the etiological agents of bacillary dysentery in humans. VirF expression is activated upon entry into the host and depends on many environmental signals. Here, we show that the virF mRNA is translated into two proteins, the major form, VirF30 (30 kDa), and the shorter VirF21 (21 kDa), lacking the N-terminal segment. By site-specific mutagenesis and toeprint analysis, we identified the translation start sites of VirF30 and VirF21 and showed that the two different forms of VirF arise from differential translation...
November 8, 2016: MBio
https://www.readbyqxmd.com/read/27826289/pimms-pragmatic-insertional-mutation-mapping-system-laboratory-methodology-a-readily-accessible-tool-for-identification-of-essential-genes-in-streptococcus
#12
Adam M Blanchard, Sharon A Egan, Richard D Emes, Andrew Warry, James A Leigh
The Pragmatic Insertional Mutation Mapping (PIMMS) laboratory protocol was developed alongside various bioinformatics packages (Blanchard et al., 2015) to enable detection of essential and conditionally essential genes in Streptococcus and related bacteria. This extended the methodology commonly used to locate insertional mutations in individual mutants to the analysis of mutations in populations of bacteria. In Streptococcus uberis, a pyogenic Streptococcus associated with intramammary infection and mastitis in ruminants, the mutagen pGhost9:ISS1 was shown to integrate across the entire genome...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27824140/random-mutagenesis-of-the-hyperthermophilic-archaeon-pyrococcus-furiosus-using-in-vitro-mariner-transposition-and-natural-transformation
#13
Natalia Guschinskaya, Romain Brunel, Maxime Tourte, Gina L Lipscomb, Michael W W Adams, Philippe Oger, Xavier Charpentier
Transposition mutagenesis is a powerful tool to identify the function of genes, reveal essential genes and generally to unravel the genetic basis of living organisms. However, transposon-mediated mutagenesis has only been successfully applied to a limited number of archaeal species and has never been reported in Thermococcales. Here, we report random insertion mutagenesis in the hyperthermophilic archaeon Pyrococcus furiosus. The strategy takes advantage of the natural transformability of derivatives of the P...
November 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27821740/disease-resistance-through-impairment-of-%C3%AE-snap-nsf-interaction-and-vesicular-trafficking-by-soybean-rhg1
#14
Adam M Bayless, John M Smith, Junqi Song, Patrick H McMinn, Alice Teillet, Benjamin K August, Andrew F Bent
α-SNAP [soluble NSF (N-ethylmaleimide-sensitive factor) attachment protein] and NSF proteins are conserved across eukaryotes and sustain cellular vesicle trafficking by mediating disassembly and reuse of SNARE protein complexes, which facilitate fusion of vesicles to target membranes. However, certain haplotypes of the Rhg1 (resistance to Heterodera glycines 1) locus of soybean possess multiple repeat copies of an α-SNAP gene (Glyma.18G022500) that encodes atypical amino acids at a highly conserved functional site...
November 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27818647/rodz-and-pgsa-play-intertwined-roles-in-membrane-homeostasis-of-bacillus-subtilis-and-resistance-to-weak-organic-acid-stress
#15
Johan van Beilen, Christoph J Blohmke, Hendrik Folkerts, Richard de Boer, Anna Zakrzewska, Wim Kulik, Fred M Vaz, Stanley Brul, Alexander Ter Beek
Weak organic acids like sorbic and acetic acid are widely used to prevent growth of spoilage organisms such as Bacilli. To identify genes involved in weak acid stress tolerance we screened a transposon mutant library of Bacillus subtilis for sorbic acid sensitivity. Mutants of the rodZ (ymfM) gene were found to be hypersensitive to the lipophilic weak organic acid. RodZ is involved in determining the cell's rod-shape and believed to interact with the bacterial actin-like MreB cytoskeleton. Since rodZ lies upstream in the genome of the essential gene pgsA (phosphatidylglycerol phosphate synthase) we hypothesized that expression of the latter might also be affected in rodZ mutants and hence contribute to the phenotype observed...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27815544/functional-genomic-characterization-of-cancer-genomes
#16
Thomas P Howard, Francisca Vazquez, Aviad Tsherniak, Andrew L Hong, Mik Rinne, Andrew J Aguirre, Jesse S Boehm, William C Hahn
International efforts to sequence cancer genomes now provide an overview of the major genetic alterations that occur in most human cancers. These studies have identified many highly recurrent alterations in specific cancer subtypes but have also identified mutations that occur at lower frequency and unstudied variants of known cancer-associated genes. To elucidate the function of such cancer alleles, we have developed several approaches to systematically interrogate genomic changes found in human tumors. In general, we have taken two complementary approaches...
November 4, 2016: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/27814692/a-set-of-genes-conserved-in-sequence-and-expression-traces-back-the-establishment-of-multicellularity-in-social-amoebae
#17
Christina Schilde, Hajara M Lawal, Angelika A Noegel, Ludwig Eichinger, Pauline Schaap, Gernot Glöckner
BACKGROUND: The developmental cycle of Dictyostelid amoebae represents an early form of multicellularity with cell type differentiation. Mutant studies in the model Dictyostelium discoideum revealed that its developmental program integrates the actions of genes involved in signal transduction, adhesion, motility, autophagy and cell wall and matrix biosynthesis. However, due to functional redundancy and fail safe options not required in the laboratory, this single organism approach cannot capture all essential genes...
November 4, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27804786/heavy-ion-beam-mutagenesis-identified-an-essential-gene-for-chloroplast-development-under-cold-stress-conditions-during-both-early-growth-and-tillering-stages-in-rice
#18
Ryouhei Morita, Mayu Nakagawa, Hinako Takehisa, Yoriko Hayashi, Hiroyuki Ichida, Sachiko Usuda, Katsunori Ichinose, Hiroshi Abe, Yuki Shirakawa, Tadashi Sato, Makoto T Fujiwara, Ryuuichi D Itoh, Tomoko Abe
We isolated a cold sensitive virescent1 (csv1) mutant from a rice (Oryza sativa L.) population mutagenized by carbon ion irradiation. The mutant exhibited chlorotic leaves during the early growth stages, and produced normal green leaves as it grew. The growth of csv1 plants displayed sensitivity to low temperatures. In addition, the mutant plants that were transferred to low temperatures at the fifth leaf stage produced chlorotic leaves subsequently. Genetic and molecular analyses revealed translocation of a 13-kb genomic fragment that disrupted the causative gene (CSV1; LOC_Os05g34040)...
November 2, 2016: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/27799467/ogee-v2-an-update-of-the-online-gene-essentiality-database-with-special-focus-on-differentially-essential-genes-in-human-cancer-cell-lines
#19
Wei-Hua Chen, Guanting Lu, Xiao Chen, Xing-Ming Zhao, Peer Bork
OGEE is an Online GEne Essentiality database. To enhance our understanding of the essentiality of genes, in OGEE we collected experimentally tested essential and non-essential genes, as well as associated gene properties known to contribute to gene essentiality. We focus on large-scale experiments, and complement our data with text-mining results. We organized tested genes into data sets according to their sources, and tagged those with variable essentiality statuses across data sets as conditionally essential genes, intending to highlight the complex interplay between gene functions and environments/experimental perturbations...
October 30, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27799222/competitive-growth-enhances-conditional-growth-mutant-sensitivity-to-antibiotics-and-exposes-a-two-component-system-as-an-emerging-antibacterial-target-in-burkholderia-cenocepacia
#20
April S Gislason, Matthew Choy, Ruhi A M Bloodworth, Wubin Qu, Maria S Stietz, Xuan Li, Chenggang Zhang, Silvia T Cardona
Chemogenetic approaches to profile antibiotic mode of action are based on detecting differential sensitivity of engineered bacterial strains in which the antibacterial target (usually encoded by an essential gene) or an associated process are regulated. We previously developed an essential gene-knockdown mutant library in the multidrug resistant Burkholderia cenocepacia, by transposon-delivery of a rhamnose-inducible promoter. In this work, we used Illumina sequencing of multiplex-PCR amplified transposon junctions to track individual mutants during pooled growth in the presence of antibiotics...
October 31, 2016: Antimicrobial Agents and Chemotherapy
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