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"Essential gene"

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https://www.readbyqxmd.com/read/28542621/enzymatic-activity-necessary-to-restore-the-lethality-due-to-escherichia-coli-rnase-e-deficiency-is-distributed-among-bacteria-lacking-rnase-e-homologues
#1
Masaru Tamura, Daisuke Kageyama, Naoko Honda, Hirofumi Fujimoto, Atsushi Kato
Escherichia coli RNase E (Eco-RNase E), encoded by rne (Eco-rne), is considered the global RNA decay initiator. Although Eco-RNase E is an essential gene product in E. coli, some bacterial species, such as Bacillus subtilis, do not possess Eco-RNase E sequence homologues. B. subtilis instead possesses RNase J1/J2 (Bsu-RNase J1/J2) and RNase Y (Bsu-RNase Y) to execute RNA decay. Here we found that E. coli lacking the Eco-rne gene (Δrne E. coli) was viable conditional on M9 minimal media by introducing Bsu-RNase J1/J2 or Bsu-RNase Y...
2017: PloS One
https://www.readbyqxmd.com/read/28542262/the-role-of-the-innate-immune-response-regulatory-gene-abcf1-in-mammalian-embryogenesis-and-development
#2
Sara M Wilcox, Hitesh Arora, Lonna Munro, Jian Xin, Franz Fenninger, Laura A Johnson, Cheryl G Pfeifer, Kyung Bok Choi, Juan Hou, Pamela A Hoodless, Wilfred A Jefferies
ABCF1 is an ABC transporter family protein that has been shown to regulate innate immune response and is a risk gene for autoimmune pancreatitis and arthritis. Unlike other members of ABC transporter family, ABCF1 lacks trans-membrane domains and is thought to function in translation initiation through an interaction with eukaryotic translation initiation factor 2 (eIF2). To study ABCF1 expression and function in development and disease, we used a single gene trap insertion in the Abcf1 gene in murine embryonic stem cells (ES cells) that allowed lineage tracing of the endogenous Abcf1 promoter by following the expression of a β-galactosidase reporter gene...
2017: PloS One
https://www.readbyqxmd.com/read/28534478/complementary-information-derived-from-crispr-cas9-mediated-gene-deletion-and-suppression
#3
Joseph Rosenbluh, Han Xu, William Harrington, Stanley Gill, Xiaoxing Wang, Francisca Vazquez, David E Root, Aviad Tsherniak, William C Hahn
CRISPR-Cas9 provides the means to perform genome editing and facilitates loss-of-function screens. However, we and others demonstrated that expression of the Cas9 endonuclease induces a gene-independent response that correlates with the number of target sequences in the genome. An alternative approach to suppressing gene expression is to block transcription using a catalytically inactive Cas9 (dCas9). Here we directly compare genome editing by CRISPR-Cas9 (cutting, CRISPRc) and gene suppression using KRAB-dCas9 (CRISPRi) in loss-of-function screens to identify cell essential genes...
May 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28529507/a-novel-and-efficient-method-for-bacteria-genome-editing-employing-both-crispr-cas9-and-an-antibiotic-resistance-cassette
#4
Hong Zhang, Qiu-Xiang Cheng, Ai-Min Liu, Guo-Ping Zhao, Jin Wang
As Cas9-mediated cleavage requires both protospacer and protospacer adjacent motif (PAM) sequences, it is impossible to employ the CRISPR/Cas9 system to directly edit genomic sites without available PAM sequences nearby. Here, we optimized the CRISPR/Cas9 system and developed an innovative two-step strategy for efficient genome editing of any sites, which did not rely on the availability of PAM sequences. An antibiotic resistance cassette was employed as both a positive and a negative selection marker. By integrating the optimized two-plasmid CRISPR/Cas system and donor DNA, we achieved gene insertion and point mutation with high efficiency in Escherichia coli, and importantly, obtained clean mutants with no other unwanted mutations...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28529506/roles-of-regulatory-rnas-for-antibiotic-resistance-in-bacteria-and-their-potential-value-as-novel-drug-targets
#5
REVIEW
Petra Dersch, Muna A Khan, Sabrina Mühlen, Boris Görke
The emergence of antibiotic resistance mechanisms among bacterial pathogens increases the demand for novel treatment strategies. Lately, the contribution of non-coding RNAs to antibiotic resistance and their potential value as drug targets became evident. RNA attenuator elements in mRNA leader regions couple expression of resistance genes to the presence of the cognate antibiotic. Trans-encoded small RNAs (sRNAs) modulate antibiotic tolerance by base-pairing with mRNAs encoding functions important for resistance such as metabolic enzymes, drug efflux pumps, or transport proteins...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28528409/polychlorinated-biphenyl-related-alterations-of-the-expression-of-essential-genes-in-harbour-seals-phoca-vitulina-from-coastal-sites-in-canada-and-the-united-states
#6
Marie Noël, Neil Dangerfield, Steve Jeffries, Dyanna Lambourn, Monique Lance, Caren Helbing, Michel Lebeuf, Peter S Ross
As long-lived marine mammals found throughout the temperate coastal waters of the North Pacific and Atlantic Oceans, harbour seals (Phoca vitulina) have become an invaluable sentinel of food-web contamination. Their relatively high trophic position predisposes harbour seals to the accumulation of harmful levels of persistent organic pollutants (POPs). We obtained skin/blubber biopsy samples from live-captured young harbour seals from various sites in the northeastern Pacific (British Columbia, Canada, and Washington State, USA) as well as the northwestern Atlantic (Newfoundland and Quebec, Canada)...
May 20, 2017: Archives of Environmental Contamination and Toxicology
https://www.readbyqxmd.com/read/28512187/neutral-competition-for-drosophila-follicle-and-cyst-stem-cell-niches-requires-vesicle-trafficking-genes
#7
Matthew S Cook, Coralie Cazin, Marc Amoyel, Shinya Yamamoto, Erika Bach, Todd Nystul
The process of selecting for cellular fitness through competition plays a critical role in both development and disease. The germarium, a structure at the tip of the ovariole of a Drosophila ovary, contains two follicle stem cells (FSCs) that undergo neutral competition for the stem cell niche. Using the FSCs as a model, we performed a genetic screen through a collection of 126 mutants in essential genes on the X chromosome to identify candidates that increase or decrease competition for the FSC niche. We identified approximately 55% and 6% of the mutations screened as putative FSC hypo- or hypercompetitors, respectively...
May 16, 2017: Genetics
https://www.readbyqxmd.com/read/28507937/the-utilization-of-rna-silencing-technology-to-mitigate-the-voriconazole-resistance-of-aspergillus-flavus-lipofectamine-based-delivery
#8
Sanam Nami, Behzad Baradaran, Behzad Mansoori, Parivash Kordbacheh, Sasan Rezaie, Mehraban Falahati, Leila Mohamed Khosroshahi, Mahin Safara, Farideh Zaini
Purpose: Introducing the effect of RNAi in fungi to downregulate essential genes has made it a powerful tool to investigate gene function, with potential strategies for novel disease treatments. Thus, this study is an endeavor to delve into the silencing potentials of siRNA on cyp51A and MDR1 in voriconazole-resistant Aspergillus flavus as the target genes. Methods: In this study, we designed three cyp51A-specific siRNAs and three MDR1-specific siRNAs and after the co-transfection of siRNA into Aspergillus flavus, using lipofectamine, we investigated the effect of different siRNA concentrations (5, 15, 25, 50nM) on cyp51A and MDR1 expressions by qRT-PCR...
April 2017: Advanced Pharmaceutical Bulletin
https://www.readbyqxmd.com/read/28501989/negative-control-of-candida-albicans-filamentation-associated-gene-expression-by-essential-protein-kinase-gene-kin28
#9
C A Woolford, K Lagree, T Aleynikov, A P Mitchell
The fungus Candida albicans can grow as either yeast or filaments, which include hyphae and pseudohyphae, depending on environmental conditions. Filamentous growth is of particular interest because it is required for biofilm formation and for pathogenesis. Environmentally induced filamentous growth is associated with expression of filamentation-associated genes, and both filamentous growth and associated gene expression depend upon several well-characterized transcription factors. Surprisingly, strains with reduced expression of many essential genes display filamentous growth under non-inducing conditions-those in which the wild type grows as yeast...
May 13, 2017: Current Genetics
https://www.readbyqxmd.com/read/28495877/a-maternal-effect-selfish-genetic-element-in-caenorhabditis-elegans
#10
Eyal Ben-David, Alejandro Burga, Leonid Kruglyak
Selfish genetic elements spread in natural populations and have an important role in genome evolution. We discovered a selfish element causing embryonic lethality in crosses between wild strains of the nematode Caenorhabditis elegans The element is made up of sup-35, a maternal-effect toxin that kills developing embryos, and pha-1, its zygotically expressed antidote. pha-1 has long been considered essential for pharynx development on the basis of its mutant phenotype, but this phenotype arises from a loss of suppression of sup-35 toxicity...
May 11, 2017: Science
https://www.readbyqxmd.com/read/28490437/high-throughput-crispri-phenotyping-identifies-new-essential-genes-in-streptococcus-pneumoniae
#11
Xue Liu, Clement Gallay, Morten Kjos, Arnau Domenech, Jelle Slager, Sebastiaan P van Kessel, Kèvin Knoops, Robin A Sorg, Jing-Ren Zhang, Jan-Willem Veening
Genome-wide screens have discovered a large set of essential genes in the opportunistic human pathogen Streptococcus pneumoniae However, the functions of many essential genes are still unknown, hampering vaccine development and drug discovery. Based on results from transposon sequencing (Tn-seq), we refined the list of essential genes in S. pneumoniae serotype 2 strain D39. Next, we created a knockdown library targeting 348 potentially essential genes by CRISPR interference (CRISPRi) and show a growth phenotype for 254 of them (73%)...
May 10, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28481201/functional-mapping-of-yeast-genomes-by-saturated-transposition
#12
Agnès Henria Michel, Riko Hatakeyama, Philipp Kimmig, Meret Arter, Matthias Peter, Joao Matos, Claudio De Virgilio, Benoît Kornmann
Yeast is a powerful model for systems genetics. We present a versatile, time- and labor-efficient method to functionally explore the Saccharomyces cerevisiae genome using saturated transposon mutagenesis coupled to high-throughput sequencing. SAturated Transposon Analysis in Yeast (SATAY) allows one-step mapping of all genetic loci in which transposons can insert without disrupting essential functions. SATAY is particularly suited to discover loci important for growth under various conditions. SATAY (1) reveals positive and negative genetic interactions in single and multiple mutant strains, (2) can identify drug targets, (3) detects not only essential genes, but also essential protein domains, (4) generates both null and other informative alleles...
May 8, 2017: ELife
https://www.readbyqxmd.com/read/28476020/the-role-of-autophagy-in-hepatocellular-carcinoma-friend-or-foe
#13
REVIEW
Lian Liu, Jia-Zhi Liao, Xing-Xing He, Pei-Yuan Li
Autophagy is an evolutionarily conserved lysosome-dependent catabolic process which degrades cell's components in order to recycle substrates to exert optimally and adapt to tough circumstances. It is a critical cellular homeostatic mechanism with stress resistance, immunity, antiaging, and pro-tumor or anti-tumor effects. Among these, the role of autophagy in cancer is the most eye-catching that is not immutable but dynamic and highly complex. Basal autophagy acts as a tumor suppressor by maintaining genomic stability in normal cells...
April 18, 2017: Oncotarget
https://www.readbyqxmd.com/read/28472505/the-antibiotic-resistant-target-seeker-arts-an-exploration-engine-for-antibiotic-cluster-prioritization-and-novel-drug-target-discovery
#14
Mohammad Alanjary, Brent Kronmiller, Martina Adamek, Kai Blin, Tilmann Weber, Daniel Huson, Benjamin Philmus, Nadine Ziemert
With the rise of multi-drug resistant pathogens and the decline in number of potential new antibiotics in development there is a fervent need to reinvigorate the natural products discovery pipeline. Most antibiotics are derived from secondary metabolites produced by microorganisms and plants. To avoid suicide, an antibiotic producer harbors resistance genes often found within the same biosynthetic gene cluster (BGC) responsible for manufacturing the antibiotic. Existing mining tools are excellent at detecting BGCs or resistant genes in general, but provide little help in prioritizing and identifying gene clusters for compounds active against specific and novel targets...
May 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28472465/precise-integration-of-inducible-transcriptional-elements-priite-enables-absolute-control-of-gene-expression
#15
Rita Pinto, Lars Hansen, John Hintze, Raquel Almeida, Sylvester Larsen, Mehmet Coskun, Johanne Davidsen, Cathy Mitchelmore, Leonor David, Jesper Thorvald Troelsen, Eric Paul Bennett
Tetracycline-based inducible systems provide powerful methods for functional studies where gene expression can be controlled. However, the lack of tight control of the inducible system, leading to leakiness and adverse effects caused by undesirable tetracycline dosage requirements, has proven to be a limitation. Here, we report that the combined use of genome editing tools and last generation Tet-On systems can resolve these issues. Our principle is based on precise integration of inducible transcriptional elements (coined PrIITE) targeted to: (i) exons of an endogenous gene of interest (GOI) and (ii) a safe harbor locus...
May 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28469617/exploration-of-using-antisense-peptide-nucleic-acid-pna-cell-penetrating-peptide-cpp-as-a-novel-bactericide-against-fire-blight-pathogen-erwinia-amylovora
#16
Ravi R Patel, George W Sundin, Ching-Hong Yang, Jie Wang, Regan B Huntley, Xiaochen Yuan, Quan Zeng
Erwinia amylovora is a Gram-negative bacterial plant pathogen in the family Enterobacteriaceae and is the causal agent of fire blight, a devastating disease of apple and pear. Fire blight is traditionally managed by the application of the antibiotic streptomycin during bloom, but this strategy has been challenged by the development and spread of streptomycin resistance. Thus, there is an urgent need for effective, specific, and sustainable control alternatives for fire blight. Antisense antimicrobials are oligomers of nucleic acid homologs with antisense sequence of essential genes in bacteria...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28461154/pathophysiology-of-tfii-i-old-guard-wearing-new-hats
#17
REVIEW
Ananda L Roy
The biochemical properties of the signal-induced multifunctional transcription factor II-I (TFII-I) indicate that it is involved in a variety of gene regulatory processes. Although gene ablation in murine models and cell-based assays show that it is encoded by an essential gene, GTF2I/Gtf2i, its physiologic role in human disorders was relatively unknown until recently. Novel studies show that it is involved in an array of human diseases including neurocognitive disorders, systemic lupus erythematosus (SLE), and cancer...
April 28, 2017: Trends in Molecular Medicine
https://www.readbyqxmd.com/read/28460089/genome-sequence-of-the-highly-weak-acid-tolerant-zygosaccharomyces-bailii-ist302-amenable-to-genetic-manipulations-and-physiological-studies
#18
Margarida Palma, Martin Münsterkötter, João Peça, Ulrich Güldener, Isabel Sá-Correia
Zygosaccharomyces bailii is one of the most problematic spoilage yeast species found in the food and beverage industry particularly in acidic products, due to its exceptional resistance to weak acid stress. This article describes the annotation of the genome sequence of Z. bailii IST302, a strain recently proven to be amenable to genetic manipulations and physiological studies. The work was based on the annotated genomes of strain ISA1307, an interspecies hybrid between Z. bailii and a closely related species, and the Z...
April 29, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28454513/mycbase-a-database-of-functional-sites-and-biochemical-properties-of-myc-in-both-normal-and-cancer-cells
#19
Debangana Chakravorty, Tanmoy Jana, Sukhen Das Mandal, Anuradha Seth, Anubrata Bhattacharya, Sudipto Saha
BACKGROUND: Myc is an essential gene having multiple functions such as in cell growth, differentiation, apoptosis, genomic stability, angiogenesis, and disease biology. A large number of researchers dedicated to Myc biology are generating a substantial amount of data in normal and cancer cells/tissues including Burkitt's lymphoma and ovarian cancer. RESULTS: MYCbase ( http://bicresources.jcbose.ac.in/ssaha4/mycbase ) is a collection of experimentally supported functional sites in Myc that can influence the biological cellular processes...
April 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28454091/heterogeneous-nuclear-ribonucleoprotein-hnrnp-l-promotes-dna-damage-induced-cell-apoptosis-by-enhancing-the-translation-of-p53
#20
Ji-Young Seo, Do-Yeon Kim, Seong-Hoon Kim, Hyo-Jin Kim, Hye Guk Ryu, Juhyun Lee, Kyung-Ha Lee, Kyong-Tai Kim
The tumor suppressor p53 is an essential gene in the induction of cell cycle arrest, DNA repair, and apoptosis. p53 protein is induced under cellular stress, blocking cell cycle progression and inducing DNA repair. Under DNA damage conditions, it has been reported that post-transcriptional regulation of p53 mRNA contributes to the increase in p53 protein level. Here we demonstrate that heterogeneous nuclear ribonucleoprotein (hnRNP) L enhances p53 mRNA translation. We found that hnRNP L is increased and binds to the 5'UTR of p53 mRNA in response to DNA damage...
April 10, 2017: Oncotarget
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