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Transposons

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https://www.readbyqxmd.com/read/28813413/polylox-barcoding-reveals-haematopoietic-stem-cell-fates-realized-in-vivo
#1
Weike Pei, Thorsten B Feyerabend, Jens Rössler, Xi Wang, Daniel Postrach, Katrin Busch, Immanuel Rode, Kay Klapproth, Nikolaus Dietlein, Claudia Quedenau, Wei Chen, Sascha Sauer, Stephan Wolf, Thomas Höfer, Hans-Reimer Rodewald
Developmental deconvolution of complex organs and tissues at the level of individual cells remains challenging. Non-invasive genetic fate mapping has been widely used, but the low number of distinct fluorescent marker proteins limits its resolution. Much higher numbers of cell markers have been generated using viral integration sites, viral barcodes, and strategies based on transposons and CRISPR-Cas9 genome editing; however, temporal and tissue-specific induction of barcodes in situ has not been achieved. Here we report the development of an artificial DNA recombination locus (termed Polylox) that enables broadly applicable endogenous barcoding based on the Cre-loxP recombination system...
August 16, 2017: Nature
https://www.readbyqxmd.com/read/28811374/recruitment-of-crispr-cas-systems-by-tn7-like-transposons
#2
Joseph E Peters, Kira S Makarova, Sergey Shmakov, Eugene V Koonin
A survey of bacterial and archaeal genomes shows that many Tn7-like transposons contain minimal type I-F CRISPR-Cas systems that consist of fused cas8f and cas5f, cas7f, and cas6f genes and a short CRISPR array. Several small groups of Tn7-like transposons encompass similarly truncated type I-B CRISPR-Cas. This minimal gene complement of the transposon-associated CRISPR-Cas systems implies that they are competent for pre-CRISPR RNA (precrRNA) processing yielding mature crRNAs and target binding but not target cleavage that is required for interference...
August 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28808156/the-identification-of-staphylococcus-aureus-factors-required-for-pathogenicity-and-growth-in-human-blood
#3
John Connolly, Emma Boldock, Lynne R Prince, Stephen A Renshaw, Moira K Whyte, Simon J Foster
Staphylococcus aureus is a human commensal but also has devastating potential as an opportunist pathogen. S. aureus bacteraemia is often associated with an adverse outcome. To identify potential targets for novel control approaches we have identified S. aureus components that are required for growth on human blood. An ordered transposon mutant library was screened, identifying 9 genes involved specifically in haemolysis or growth on human blood agar compared to the parental strain. Three genes (purA, purB and pabA) were subsequently found to be required for pathogenesis in the zebrafish embryo infection model...
August 14, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28807594/thyroid-hormone-receptor-beta-agonist-gc-1-inhibits-met-%C3%AE-catenin-driven-hepatocellular-cancer
#4
Elisabetta Puliga, Qian Min, Junyan Tao, Rong Zhang, Tirthadipa Pradhan-Sundd, Minakshi Poddar, Sucha Singh, Amedeo Columbano, Jinming Yu, Satdarshan P Monga
The thyromimetic agent GC-1 induces hepatocyte proliferation via Wnt/β-catenin signaling and may promoting regeneration in both acute and chronic liver insufficiencies. However, β-catenin activation particularly due to mutations in CTNNB1 is seen in a subset of hepatocellular carcinomas (HCC). Thus, it will be critical to address any effect of GC-1 on HCC growth and development, before its use can be advocated to stimulate regeneration in chronic liver diseases. In the current study, we first examine the effect of GC-1 on β-catenin-TCF4 activity in HCC cell lines harboring wild-type or mutated-CTNNB1...
August 11, 2017: American Journal of Pathology
https://www.readbyqxmd.com/read/28806924/essential-genome-of-campylobacter-jejuni
#5
Rabindra K Mandal, Tieshan Jiang, Young Min Kwon
BACKGROUND: Campylobacter species are a leading cause of bacterial foodborne illness worldwide. Despite the global efforts to curb them, Campylobacter infections have increased continuously in both developed and developing countries. The development of effective strategies to control the infection by this pathogen is warranted. The essential genes of bacteria are the most prominent targets for this purpose. In this study, we used transposon sequencing (Tn-seq) of a genome-saturating library of Tn5 insertion mutants to define the essential genome of C...
August 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28800125/large-introns-of-5-to-10-kilo-base-pairs-can-be-spliced-out-in-arabidopsis
#6
Ning Chang, Qingqing Sun, Jinglei Hu, Chuanjing An, And Hongbo Gao
Most of the eukaryotic genes contain introns, which are removed from the pre-RNA during RNA processing. In contrast to the introns in animals, which are usually several kilo base pairs (kb), those in plants generally are very small, which are mostly from dozens of base pairs (bp) to a few hundred bp. According to annotation version 10.0 of the genome of Arabidopsis thaliana, there are 127,854 introns in the nuclear genes; 99.23% of them are less than 1 kb, and only 16 introns are annotated to be larger than 5 kb, which are extremely large introns (ELI) in Arabidopsis...
August 11, 2017: Genes
https://www.readbyqxmd.com/read/28797225/environmentally-triggered-genomic-plasticity-and-capsular-polysaccharide-formation-are-involved-in-increased-ethanol-and-acetic-acid-tolerance-in-kozakia-baliensis-nbrc-16680
#7
Julia U Brandt, Friederike-Leonie Born, Frank Jakob, Rudi F Vogel
BACKGROUND: Kozakia baliensis NBRC 16680 secretes a gum-cluster derived heteropolysaccharide and forms a surface pellicle composed of polysaccharides during static cultivation. Furthermore, this strain exhibits two colony types on agar plates; smooth wild-type (S) and rough mutant colonies (R). This switch is caused by a spontaneous transposon insertion into the gumD gene of the gum-cluster, resulting in a heteropolysaccharide secretion deficient, rough phenotype. To elucidate, whether this is a directed switch triggered by environmental factors, we checked the number of R and S colonies under different growth conditions including ethanol and acetic acid supplementation...
August 10, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28796162/the-variation-analysis-of-dna-methylation-in-wheat-carrying-gametocidal-chromosome-3c-from-aegilops-triuncialis
#8
Dan Wang, Jieyu Zhao, Yan Bai, You Ao, Changhong Guo
Gametocidal (Gc) chromosomes can ensure their preferential transmission by killing the gametes without themselves through causing chromosome breakage and therefore have been exploited as an effective tool for genetic breeding. However, to date very little is known about the molecular mechanism of Gc action. In this study, we used methylation-sensitive amplified polymorphism (MSAP) technique to assess the extent and pattern of cytosine methylation alterations at the whole genome level between two lines of wheat Gc addition line and their common wheat parent...
August 10, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28790987/comparative-analysis-of-the-flavobacterium-columnare-genomovar-i-and-ii-genomes
#9
Salih Kumru, Hasan C Tekedar, Nagihan Gulsoy, Geoffrey C Waldbieser, Mark L Lawrence, Attila Karsi
Columnaris disease caused by Gram-negative rod Flavobacterium columnare is one of the most common diseases of catfish. F. columnare is also a common problem in other cultured fish species worldwide. F. columnare has three major genomovars; we have sequenced a representative strain from genomovar I (ATCC 49512, which is avirulent in catfish) and genomovar II (94-081, which is highly pathogenic in catfish). Here, we present a comparative analysis of the two genomes. Interestingly, F. columnare ATCC 49512 and 94-081 meet criteria to be considered different species based on the Average Nucleotide Identity (90...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28790983/nitrate-sensing-and-metabolism-inhibit-biofilm-formation-in-the-opportunistic-pathogen-burkholderia-pseudomallei-by-reducing-the-intracellular-concentration-of-c-di-gmp
#10
Mihnea R Mangalea, Brooke A Plumley, Bradley R Borlee
The opportunistic pathogen Burkholderia pseudomallei is a saprophytic bacterium and the causative agent of melioidosis, an emerging infectious disease associated with high morbidity and mortality. Although melioidosis is most prevalent during the rainy season in endemic areas, domestic gardens and farms can also serve as a reservoir for B. pseudomallei during the dry season, in part due to irrigation and fertilizer use. In the environment, B. pseudomallei forms biofilms and persists in soil near plant root zones...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28783426/characterization-of-the-pirna-pathway-during-development-of-the-sea-anemone-nematostella-vectensis
#11
Daniela Praher, Bob Zimmermann, Grigory Genikhovich, Yaara Columbus-Shenkar, Vengamanaidu Modepalli, Reuven Aharoni, Yehu Moran, Ulrich Technau
PIWI-interacting RNAs (piRNAs) and associated proteins comprise a conserved pathway for silencing transposons in metazoan germlines. piRNA pathway components are also expressed in multipotent somatic stem cells in various organisms. piRNA functions have been extensively explored in bilaterian model systems, however, comprehensive studies in non-bilaterian phyla remain limited. Here we investigate the piRNA pathway during the development of Nematostella vectensis, a well-established model system belonging to Cnidaria, the sister group to Bilateria...
August 7, 2017: RNA Biology
https://www.readbyqxmd.com/read/28782559/trap-seq-an-rna-sequencing-based-pipeline-for-the-identification-of-genetrap-insertions-in-mammalian-cells
#12
Cristina Mayor-Ruiz, Orlando Dominguez, Oscar Fernandez-Capetillo
The development of haploid mammalian cell lines, coupled to next generation sequencing, has recently facilitated forward genetic screenings in mammals. For mutagenesis, retrovirus- or transposon-based genetraps are frequently used. Current methods to map genetrap insertions are based on inverse- or splinkerette-PCR, which despite their efficacy are prone to artifacts and do not provide information about expression of the targeted gene. Here, we describe a new RNA-sequencing based method (Trap(Seq)) to map genetrap insertions...
August 4, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28776161/diversity-distribution-and-dynamics-of-full-length-copia-and-gypsy-ltr-retroelements-in-solanum-lycopersicum
#13
Rosalía Cristina Paz, Melisa Eliana Kozaczek, Hernán Guillermo Rosli, Natalia Pilar Andino, Maria Virginia Sanchez-Puerta
Transposable elements are the most abundant components of plant genomes and can dramatically induce genetic changes and impact genome evolution. In the recently sequenced genome of tomato (Solanum lycopersicum), the estimated fraction of elements corresponding to retrotransposons is nearly 62%. Given that tomato is one of the most important vegetable crop cultivated and consumed worldwide, understanding retrotransposon dynamics can provide insight into its evolution and domestication processes. In this study, we performed a genome-wide in silico search of full-length LTR retroelements in the tomato nuclear genome and annotated 736 full-length Gypsy and Copia retroelements...
August 3, 2017: Genetica
https://www.readbyqxmd.com/read/28774284/transcriptional-activity-of-pif-and-pong-like-class-ii-transposable-elements-in-triticeae
#14
Dragomira N Markova, Roberta J Mason-Gamer
BACKGROUND: Transposable elements are major contributors to genome size and variability, accounting for approximately 70-80% of the maize, barley, and wheat genomes. PIF and Pong-like elements belong to two closely-related element families within the PIF/Harbinger superfamily of Class II (DNA) transposons. Both elements contain two open reading frames; one encodes a transposase (ORF2) that catalyzes transposition of the functional elements and their related non-autonomous elements, while the function of the second is still debated...
August 3, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28771073/co-occurrence-of-3-different-resistance-plasmids-in-a-multi-drug-resistant-cronobacter-sakazakii-isolate-causing-neonatal-infections
#15
Lining Shi, Quanhui Liang, Zhe Zhan, Jiao Feng, Yachao Zhao, Yong Chen, Mei Huang, Yigang Tong, Weili Wu, Weijun Chen, Xiaojun Li, Zhe Yin, Jinglin Wang, Dongsheng Zhou
Cronobacter sakazakii 505108 was isolated from a sputum specimen of a neonate with severe pneumonia. C. sakazakii 505108 co-harbors 3 resistance plasmids of the IncHI2, IncX3, and IncFIB incomparability groups, respectively. These 3 plasmids have acquired several accessory modules, which carry an extremely large number of resistance genes, especially including those involved in resistance to carbapenems, aminoglycoside, tetracyclines, and phenicols and sulphonamide/trimethoprim. These plasmid-borne antibiotic resistance genes were associated with insertion sequences, integrons, and transposons, indicating that the assembly and mobilization of the corresponding accessory modules with complex chimera structures are facilitated by transposition and/or homologous recombination...
August 3, 2017: Virulence
https://www.readbyqxmd.com/read/28769883/a-case-study-into-microbial-genome-assembly-gap-sequences-and-finishing-strategies
#16
Sagar M Utturkar, Dawn M Klingeman, Richard A Hurt, Steven D Brown
This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28768207/bm-muted-orthologous-to-mouse-muted-and-encoding-a-subunit-of-the-bloc-1-complex-is-responsible-for-the-otm-translucent-mutation-of-the-silkworm-bombyx-mori
#17
Haokun Zhang, Takashi Kiuchi, Lingyan Wang, Munetaka Kawamoto, Yutaka Suzuki, Sumio Sugano, Yutaka Banno, Susumu Katsuma, Toru Shimada
"Tanaka's mottled translucent" (otm) is a mutation of the silkworm Bombyx mori that exhibits translucent skin during larval stages. We performed positional cloning of the gene responsible for otm and mapped it to a 364-kb region on chromosome 5 that contains 22 hypothetical protein-coding genes. We performed RNA-seq analysis of the epidermis and fat body of otm larvae and determined that the gene BGIBMGA002619 may be responsible for the otm mutation. BGIBMGA002619 encodes the biosynthesis of lysosome-related organelles complex 1 (BLOC-1) subunit 5, whose ortholog is responsible for the Muted mutant in mouse...
July 30, 2017: Gene
https://www.readbyqxmd.com/read/28768189/genetic-metabolic-coupling-for-targeted-metabolic-engineering
#18
Stefano Cardinale, Felipe Gonzalo Tueros, Morten Otto Alexander Sommer
Production of chemicals in microbes often employs potent biosynthetic enzymes, which can interact with the microbial native metabolism to affect cell fitness and product yield. However, production optimization largely relies on data collected from wild-type strains in the absence of metabolic perturbations, thus limiting their relevance to specific conditions. Here, we address this issue by coupling cell fitness to the production of thiamine diphosphate in Escherichia coli using a synthetic RNA biosensor. We use this strategy to interrogate a library of transposon mutants and elucidate the native gene network influencing both cell fitness and thiamine production...
August 1, 2017: Cell Reports
https://www.readbyqxmd.com/read/28765224/genome-wide-sensitivity-analysis-of-the-microsymbiont-sinorhizobium-meliloti-to-symbiotically-important-defensin-like-host-peptides
#19
Markus F F Arnold, Mohammed Shabab, Jon Penterman, Kevin L Boehme, Joel S Griffitts, Graham C Walker
The model legume species Medicago truncatula expresses more than 700 nodule-specific cysteine-rich (NCR) signaling peptides that mediate the differentiation of Sinorhizobium meliloti bacteria into nitrogen-fixing bacteroids. NCR peptides are essential for a successful symbiosis in legume plants of the inverted-repeat-lacking clade (IRLC) and show similarity to mammalian defensins. In addition to signaling functions, many NCR peptides exhibit antimicrobial activity in vitro and in vivo Bacterial resistance to these antimicrobial activities is likely to be important for symbiosis...
August 1, 2017: MBio
https://www.readbyqxmd.com/read/28762778/epigenomic-analysis-in-a-cell-based-model-reveals-the-roles-of-h3k9me3-in-breast-cancer-transformation
#20
Qing-Lan Li, Pin-Ji Lei, Quan-Yi Zhao, Lianyun Li, Gang Wei, Min Wu
AIM: Epigenetic marks are critical regulators of chromatin and gene activity. Their roles in normal physiology and disease states, including cancer development, still remain elusive. Herein, the epigenomic change of H3K9me3, as well as its potential impacts on gene activity and genome stability, was investigated in an in vitro breast cancer transformation model. METHODS: The global H3K9me3 level was studied with western blotting. The distribution of H3K9me3 on chromatin and gene expression was studied with ChIP-Seq and RNA-Seq, respectively...
August 1, 2017: Epigenomics
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