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Peng Tang, Jie Wu, Hou Liu, Youcai Liu, Xingding Zhou
One of the newly developed methods for Assimilable organic carbon (AOC) determination is leveraged on the cell enumeration by flow cytometry (FC) which could provide a rapid and automated solution for AOC measurement. However, cell samples staining with fluorescence dye is indispensable to reduce background and machine noise. This step would bring additional cost and time consuming for this method. In this study, a green fluorescence protein (GFP) tagged strain derived of AOC testing strain Pseudomonas fluorescens P-17 (GFP-P17) was generated using Tn5 transposon mutagenesis...
2018: PloS One
Jordi Morata, Marc Tormo, Konstantinos G Alexiou, Cristina Vives, Sebastián Ramos-Onsins, Jordi Garcia-Mas, Josep M Casacuberta
Transposable elements (TEs) are a major driver of plant genome evolution. A part from being a rich source of new genes and regulatory sequences, TEs can also affect plant genome evolution by modifying genome size and shaping chromosome structure. TEs tend to concentrate in heterochromatic pericentromeric regions and their proliferation may expand these regions. Here we show that after the split of melon and cucumber, TEs have expanded the pericentromeric regions of melon chromosomes that, probably as a consequence, show a very low recombination frequency...
June 13, 2018: Genome Biology and Evolution
Lifan Wei, Yanyan Wu, Haoxian Qiao, Wensheng Xu, Yuanxing Zhang, Xiaohong Liu, Qiyao Wang
Edwardsiella piscicida is an infectious Gram-negative bacterium that causes great losses to the aquaculture industry worldwide. Based on pattern analysis of conditional essentiality (PACE), a new method for transposon insertion sequencing (Tn-seq) data analysis, we investigated the genome-wide genetic requirements during the dynamic process of infection and colonization in turbot in this study. As a result, disruption of ETAE_1437 was discovered to lead to substantially reduced colonization, which was similar to the in vivo dynamic patterns of the mutants of T3SS or T6SS...
June 12, 2018: FEMS Microbiology Letters
Li-Yin Lai, Tzu-Lung Lin, Yi-Yin Chen, Pei-Fang Hsieh, Jin-Town Wang
Mycobacterium marinum is a close relative of Mycobacterium tuberculosis that can cause systemic tuberculosis-like infections in ectotherms and skin infections in humans. Sliding motility correlates with biofilm formation and virulence in most bacteria. In this study, we used a sliding motility assay to screen 2,304 transposon mutants of M. marinum NTUH-M6885 and identified five transposon mutants with decreased sliding motility. Transposons that interrupted the type VII secretion system (T7SS) ESX-1-related genes, espE ( mmar_5439 ), espF ( mmar_5440 ), and eccA1 ( mmar_5443 ), were present in 3 mutants...
2018: Frontiers in Microbiology
Benjamin O Fulton, Weina Sun, Nicholas S Heaton, Peter Palese
Influenza A and B viruses can continuously evade humoral immune responses by developing mutations in the globular head of the hemagglutinin (HA) that prevent antibody binding. However, the influenza B virus HA over time displays less antigenic variation despite being functionally and structurally similar to the influenza A virus HA. To determine if the influenza B virus HA is under constraints that limit its antigenic variation, we performed a transposon screen to compare the mutational tolerance of the currently circulating influenza A virus HAs (H1 and H3 subtypes) and influenza B virus HAs (B/Victoria87 and B/Yamagata88 antigenic lineages)...
June 13, 2018: Journal of Virology
Yee-Chin Wong, Moataz Abd El Ghany, Raeece N M Ghazzali, Soon-Joo Yap, Chee-Choong Hoh, Arnab Pain, Sheila Nathan
A Burkholderia cenocepacia infection usually leads to reduced survival and fatal cepacia syndrome in cystic fibrosis patients. The identification of B. cenocepacia essential genes for in vivo survival is key to designing new anti-infectives therapies. We used the Transposon-Directed Insertion Sequencing (TraDIS) approach to identify genes required for B. cenocepacia survival in the model infection host, Caenorhabditis elegans . A B. cenocepacia J2315 transposon pool of ∼500,000 mutants was used to infect C...
2018: Frontiers in Microbiology
Alessandra Borgognone, Raúl Castanera, Marco Morselli, Leticia López-Varas, Liudmilla Rubbi, Antonio G Pisabarro, Matteo Pellegrini, Lucía Ramírez
Transposable elements constitute an important fraction of eukaryotic genomes. Given their mutagenic potential, host-genomes have evolved epigenetic defense mechanisms to limit their expansion. In fungi, epigenetic modifications have been widely studied in ascomycetes, although we lack a global picture of the epigenetic landscape in basidiomycetes. In this study, we analysed the genome-wide epigenetic and transcriptional patterns of the white-rot basidiomycete Pleurotus ostreatus throughout its life cycle. Our results performed by using high-throughput sequencing analyses revealed that strain-specific DNA methylation profiles are primarily involved in the repression of transposon activity and suggest that 21 nt small RNAs play a key role in transposon silencing...
June 8, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
Zhilong Lu, Qi Lu, Ying Chen, Renzhi Wu, Jun Huang, Xiaoling Chen, Dong Chen, Ribo Huang
Spt proteins are defined as a large family of transcription regulators of the yeast Saccharomyces cerevisiae. They are crucial components of the SAGA complex that regulates transcription through interaction with the TATA box in the upstream region of the target genes. About 10% of total gene transcriptions are related to Spt proteins and these genes are highly related to environmental stress response. Such vast regulation network and complex mechanisms have become a hotspot. Spt proteins are also important to suppress transposon-induced mutations, being a switch on regulation of transposon behaviors and adaptive evolution of Saccharomyces cerevisiae...
May 25, 2018: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
Li-Qin Xie, Ping-Lan Wang, Shen-Hua Jiang, Ze Zhang, Hua-Hao Zhang
TC1/Mariner transposons belong to class II transposable elements (TEs) that use DNA-mediated "cut and paste" mechanism to transpose, and they have been identified in almost all organisms. Although silkworm (Bombyx mori) has a large amount of TC1/Mariner elements, the genome wide information of this superfamily in the silkworm is unknown. In this study, we have identified 2670 TC1/Mariner (Bmmar) elements in the silkworm genome. All the TEs were classified into 22 families by means of fgclust, a tool of repetitive sequence classification, seven of which was first reported in this study...
May 2018: Genes & Genomics
Andrew P-A Karalewitz, Samuel I Miller
Acinetobacter baumannii is a Gram negative organism that is a cause of hospital acquired multidrug resistant (MDR) infections. A. baumannii has a unique cell surface compared to many other Gram-negative pathogens in that it can live without LPS and it has a high content of cardiolipin in the outer membrane. Therefore, to better understand the cell envelope and mechanisms of A. baumannii MDR, we screened a transposon library for mutants with defective permeability barrier function, as defined as a deficiency in the ability to exclude the phosphatase chromogenic substrate, 5-Bromo-4-chloro-3-indolyl phosphate (XP)...
June 11, 2018: Antimicrobial Agents and Chemotherapy
Yohsuke Ogawa, Kazumasa Shiraiwa, Sayaka Nishikawa, Masahiro Eguchi, Yoshihiro Shimoji
Erysipelothrix rhusiopathiae causes swine erysipelas, an infection characterized by acute septicemia or chronic endocarditis and polyarthritis. Among seventeen E. rhusiopathiae serovars, determined based on heat-stable peptidoglycan antigens, serovars 1 and 2 are most commonly associated with the disease; however, the molecular basis for the association between these serovars and virulence is unknown. To search for the genetic region defining serovar 1a (Fujisawa) strain antigenicity, we examined the 15-kb chromosomal region encompassing a putative pathway for polysaccharide biosynthesis, which was previously identified in the E...
June 11, 2018: Infection and Immunity
Jessica Mendez, Desirée Cascales, Ana I Garcia-Torrico, Jose A Guijarro
Yersinia ruckeri is a bacterium causing fish infection processes at temperatures below the optimum for growth. A derivative Tn5 transposon was used to construct a library of Y. ruckeri mutants with transcriptional fusions between the interrupted genes and the promoterless luxCDABE and lacZY operons. In vitro analysis of β-galactosidase activity allowed the identification of 168 clones having higher expression at 18°C than at 28°C. Among the interrupted genes a SAM-dependent methyltransferase, a diguanylated cyclase, three genes involved in legionaminic acid synthesis and three transcriptional regulators were defined...
2018: Frontiers in Microbiology
Li Wang, Min Fan, Chao Zeng, Wei Li, Qikang Hu, Wenliang Liu, Xingchun Huang, Guiyuan Li, Fenglei Yu
TMEM8B-a protein is the longer, predominant isoform of the TMEM8B gene product, which is a tumor metastasis suppressor in nasopharyngeal carcinoma (NPC) and lung cancer. TMEM8B-a is rapidly degraded via the proteasome pathway mediated by ezrin in many NPC and lung cancer cell lines, but TMEM8B-a is not ubiquitinated. In this study, we report the recombinant production of full-length modified TMEM8B-a in mammalian cells. We used the PiggyBac transposon system to efficiently generate normal and lung cancer cell lines with stable TMEM8B-a protein expression...
June 7, 2018: Protein Expression and Purification
Sébastien Crépin, Elizabeth N Ottosen, Katharina Peters, Sara N Smith, Stephanie D Himpsl, Waldemar Vollmer, Harry L T Mobley
Acinetobacter baumannii has emerged as a leading nosocomial pathogen, infecting a wide range of anatomic sites including the respiratory tract and the bloodstream. In addition to being multi-drug resistant, little is known about the molecular basis of A. baumannii pathogenesis. To better understand A. baumannii virulence, a combination of a transposon-sequencing (TraDIS) screen and the neutropenic mouse model of bacteremia was used to identify the full set of fitness genes required during bloodstream infection...
June 8, 2018: Molecular Microbiology
Rosa Maria Ceinos, Elena Frigato, Cristina Pagano, Nadine Fröhlich, Pietro Negrini, Nicola Cavallari, Daniela Vallone, Silvia Fuselli, Cristiano Bertolucci, Nicholas S Foulkes
Light represents the principal signal driving circadian clock entrainment. However, how light influences the evolution of the clock remains poorly understood. The cavefish Phreatichthys andruzzii represents a fascinating model to explore how evolution under extreme aphotic conditions shapes the circadian clock, since in this species the clock is unresponsive to light. We have previously demonstrated that loss-of-function mutations targeting non-visual opsins contribute in part to this blind clock phenotype...
June 8, 2018: Scientific Reports
Fang-Fang Fu, R Kelly Dawe, Jonathan I Gent
Plants make use of distinct types of DNA methylation characterized by their DNA methyltransferases and modes of regulation. One type, RNA-directed DNA methylation (RdDM), is guided by small interfering RNAs (siRNAs) to the edges of transposons that are close to genes, areas called mCHH islands in maize (Zea mays). Another type, chromomethylation, is guided by histone H3 lysine 9 methylation to heterochromatin across the genome. We examined DNA methylation and small RNA expression in plant tissues that were mutant for both copies of the genes encoding chromomethylases as well as mutants for both copies of the genes encoding DECREASED DNA METHYLATION1 (DDM1)-type nucleosome remodelers, which facilitate chromomethylation...
June 8, 2018: Plant Cell
Gökhan Karakülah, Athanasia Pavlopoulou
Transposable elements of the hAT family exhibit a cross-kingdom distribution. The plant hAT transposons are proposed to play a critical role in plant adaptive evolution and DNA damage repair. The sequencing of an increasing number of plant genomes has facilitated the discovery of a plethora of hAT elements. This enabled us to perform an in-depth phylogenetic analysis of consensus hAT sequences in the fully-sequenced genomes of 11 plant species that represent diverse taxonomic divisions. Four putative nucleotide sequences were detected in cottonwood that were similar to the corresponding animal hAT elements, which are possibly sequence artifacts...
June 6, 2018: Genes
Diane Mutumwinka, Shen-Bao Zhao, Yi-Shi Liu, Emmanuel Osei Mensah, Xiao-Dong Gao, Morihisa Fujita
Glycoengineered yeast cells, which express human-compatible glycan structures, are particularly attractive host cells to produce therapeutic glycoproteins. Disruption of OCH1 gene, which encodes an α-1,6-mannosyltransferase required for mannan-type N-glycan formation, is essential for the elimination of yeast-specific N-glycan structures. However, the gene disruption causes cell wall defects leading to growth defects. Here, we tried to identify factors to rescue the growth defects of och1Δ cells by in vivo mutagenesis using piggyBac (PB)-based transposon...
June 8, 2018: Bioscience, Biotechnology, and Biochemistry
Shuaixin Sun, Yunpeng Chen, Jiejie Cheng, Qiongjie Li, Zhenchuan Zhang, Zhengliang Lan
A gram-negative bacterium GXGL-4A was originally isolated from maize roots. It displayed nitrogen-fixing (NF) ability under nitrogen-free culture condition, and had a significant promotion effect on cucumber growth in the pot inoculation test. The preliminary physiological and biochemical traits of GXGL-4A were characterized. Furthermore, a phylogenetic tree was constructed based on 16S ribosomal DNA (rDNA) sequences of genetically related species. To determine the taxonomic status of GXGL-4A and further utilize its nitrogen-fixing potential, genome sequence was obtained using PacBio RS II technology...
June 6, 2018: Folia Microbiologica
Shuai Luo, Xin-Ai Chen, Xu-Ming Mao, Yong-Quan Li
Production of secondary metabolites in Streptomyces is regulated by a complex regulatory network precisely, elaborately, and hierarchically. One of the main reasons for the low yields of some high-value secondary metabolites is the repressed expression of their biosynthetic gene clusters, supposedly by some gene cluster out-situated negative regulators. Identification of these repressors and removal of the inhibitory effects based on the regulatory mechanisms will be an effective way to improve their yields...
June 6, 2018: Applied Microbiology and Biotechnology
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