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"Essential gene"

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https://www.readbyqxmd.com/read/29230204/a-comprehensive-overview-of-online-resources-to-identify-and-predict-bacterial-essential-genes
#1
REVIEW
Chong Peng, Yan Lin, Hao Luo, Feng Gao
Genes critical for the survival or reproduction of an organism in certain circumstances are classified as essential genes. Essential genes play a significant role in deciphering the survival mechanism of life. They may be greatly applied to pharmaceutics and synthetic biology. The continuous progress of experimental method for essential gene identification has accelerated the accumulation of gene essentiality data which facilitates the study of essential genes in silico. In this article, we present some available online resources related to gene essentiality, including bioinformatic software tools for transposon sequencing (Tn-seq) analysis, essential gene databases and online services to predict bacterial essential genes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29229007/de-novo-synthesis-of-thiamine-vitamin-b1-is-the-ancestral-state-in-plasmodium-parasites-evidence-from-avian-haemosporidians
#2
Olof Hellgren, Staffan Bensch, Elin Videvall
Parasites often have reduced genomes as their own genes become redundant when utilizing their host as a source of metabolites, thus losing their own de novo production of metabolites. Primate malaria parasites can synthesize vitamin B1 (thiamine) de novo but rodent malaria and other genome-sequenced apicomplexans cannot, as the three essential genes responsible for this pathway are absent in their genomes. The unique presence of functional thiamine synthesis genes in primate malaria parasites and their sequence similarities to bacterial orthologues, have led to speculations that this pathway was horizontally acquired from bacteria...
December 12, 2017: Parasitology
https://www.readbyqxmd.com/read/29222103/a-novel-non-antibiotic-lgt-based-selection-system-for-stable-maintenance-of-expression-vectors-in-escherichia-coli-and-vibrio-cholerae
#3
Manuela Terrinoni, Stefan L Nordqvist, Susanne Källgård, Jan Holmgren, Michael Lebens
Antibiotic selection for maintenance of expression plasmids is discouraged in production of recombinant proteins for pharmaceutical or other human uses due to the risks of antibiotic residue contamination of the final products and release of DNA encoding antibiotic resistance into the environment. We describe the construction of expression plasmids that are instead maintained by complementation of the lgt gene encoding a (pro)lipoprotein glyceryl transferase essential for biosynthesis of bacterial lipoprotein...
December 8, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29216381/de-novo-gene-evolution-of-antifreeze-glycoproteins-in-codfishes-revealed-by-whole-genome-sequence-data
#4
Helle Tessand Baalsrud, Ole Kristian Tørresen, Monica Hongrø Solbakken, Walter Salzburger, Reinhold Hanel, Kjetill S Jakobsen, Sissel Jentoft
New genes can arise through duplication of a pre-existing gene or de novo from non-coding DNA, providing raw material for evolution of new functions in response to a changing environment. A prime example is the independent evolution of antifreeze glycoprotein genes (afgps) in the Arctic codfishes and Antarctic notothenioids to prevent freezing. However, the highly repetitive nature of these genes complicates studies of their organization. In notothenioids, afgps evolved from an extant gene, yet the evolutionary origin of afgps in codfishes is unknown...
December 5, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29208119/comparative-analysis-of-the-burkholderia-cenocepacia-k56-2-essential-genome-reveals-cell-envelope-functions-that-are-uniquely-required-for-survival-in-species-of-the-genus-burkholderia
#5
April S Gislason, Keith Turner, Mike Domaratzki, Silvia T Cardona
Burkholderia cenocepacia K56-2 belongs to the Burkholderia cepacia complex, a group of Gram-negative opportunistic pathogens that have large and dynamic genomes. In this work, we identified the essential genome of B. cenocepacia K56-2 using high-density transposon mutagenesis and insertion site sequencing (Tn-seq circle). We constructed a library of one million transposon mutants and identified the transposon insertions at an average of one insertion per 27 bp. The probability of gene essentiality was determined by comparing of the insertion density per gene with the variance of neutral datasets generated by Monte Carlo simulations...
November 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29206858/extreme-metal-adapted-knockout-and-knockdown-strains-reveal-a-coordinated-gene-expression-among-different-tetrahymena-thermophila-metallothionein-isoforms
#6
Patricia de Francisco, Ana Martín-González, Aaron P Turkewitz, Juan Carlos Gutiérrez
Metallothioneins (MT) constitute a superfamily of small cytosolic proteins that are able to bind metal cations through numerous cysteine (Cys) residues. Like other organisms the ciliate Tetrahymena thermophila presents several MT isoforms, which have been classified into two subfamilies (Cd- and Cu-metallothioneins). The main aim of this study was to examine the specific functions and transcriptional regulation of the five MT isoforms present in T. thermophila, by using several strains of this ciliate. After a laboratory evolution experiment over more than two years, three different T...
2017: PloS One
https://www.readbyqxmd.com/read/29205229/crispr-cas-mediated-gene-silencing-reveals-racr-to-be-a-negative-regulator-of-ydas-and-ydat-toxins-in-escherichia-coli-k-12
#7
Gargi Bindal, Revathy Krishnamurthi, Aswin Sai Narain Seshasayee, Devashish Rath
Bacterial genomes are rich in horizontally acquired prophages. racR is an essential gene located in the rac prophage that is resident in many Escherichia coli genomes. Employing a clustered regularly interspaced short palindromic repeat (CRISPR)-Cas-based gene silencing approach, we show that RacR is a negative regulator of the divergently transcribed and adjacent ydaS-ydaT operon in Escherichia coli K-12. Overexpression of YdaS and YdaT due to RacR depletion leads to cell division defects and decrease in survival...
November 2017: MSphere
https://www.readbyqxmd.com/read/29196747/a-small-cassette-enables-conditional-gene-inactivation-by-crispr-cas9
#8
Paloma M Guzzardo, Christina Rashkova, Rodrigo L Dos Santos, Raha Tehrani, Philippe Collin, Tilmann Bürckstümmer
The availability of CRISPR/Cas9 technology has enabled the rapid establishment of gene knockouts in many cell types and even whole organisms. However, conditional inactivation of essential genes remains a challenge. We devised an approach named DECAI (DEgradation based on Cre-regulated- Artificial Intron). It utilizes a small cassette of just 201 nucleotides that is inserted into the coding exon of a target gene using CRISPR/Cas9 technology and homology-directed repair. As its sequence is derived from an artificial intron, the cassette is removed by the splicing machinery and thus leaves no trace in the "off-state"...
December 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29191012/tape-assisted-photolithographic-free-microfluidic-chip-tapmic-cell-patterning-for-tumor-metastasis-study
#9
Liang Zhao, Tengfei Guo, Lirong Wang, Yang Liu, Ganyu Chen, Hao Zhou, Meiqin Zhang
Cancer metastatic dissemination is a complex event during tumor progression which involves cell-cell, cell-matrix interactions. Micro-patterning of is one of the most efficient ways to study tumor development because it can tune the distribution of cells with spatial and temporal control. Extensive studies have shown that microfluidics can provide a feasible method for cell patterning. However, the current technique requires a microfabrication laboratory to manufacture the chip, which results in inaccessibility to researchers especially biologists who focus on the disclosing biological mechanisms rather than the methods...
November 30, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29187507/using-separation-of-function-mutagenesis-to-define-the-full-spectrum-of-activities-performed-by-the-est1-telomerase-subunit-in-vivo
#10
Johnathan W Lubin, Timothy M Tucey, Victoria Lundblad
A leading objective in biology is to identify the complete set of activities that each gene performs in vivo In this study, we have asked whether a genetic approach can provide an efficient means of achieving this goal, through the identification and analysis of a comprehensive set of separation-of-function (sof- ) mutations in a gene. Towards this goal, we have subjected the S. cerevisiae EST1 gene, which encodes a regulatory subunit of telomerase, to intensive mutagenesis (with an average coverage of 1 mutation for every 4...
November 29, 2017: Genetics
https://www.readbyqxmd.com/read/29186130/correcting-crispr-for-copy-number
#11
John Paul Shen, Trey Ideker
The CRISPR-Cas9 system enables global screens of gene function with high sensitivity and specificity, but off-target effects have been reported for CRISPR guide RNAs targeting genes that are amplified at high copy number. A new study describes a computational approach to correct for this copy number effect, increasing the specificity of CRIPSR screens to identify essential genes.
November 29, 2017: Nature Genetics
https://www.readbyqxmd.com/read/29186125/promoter-bound-mettl3-maintains-myeloid-leukaemia-by-m6a-dependent-translation-control
#12
Isaia Barbieri, Konstantinos Tzelepis, Luca Pandolfini, Junwei Shi, Gonzalo Millán-Zambrano, Samuel C Robson, Demetrios Aspris, Valentina Migliori, Andrew J Bannister, Namshik Han, Etienne De Braekeleer, Hannes Ponstingl, Alan Hendrick, Christopher R Vakoc, George S Vassiliou, Tony Kouzarides
N6-methyladenosine (m6A) is an abundant internal RNA modification in both coding and non-coding RNAs that is catalysed by the METTL3-METTL14 methyltransferase complex. However, the specific role of these enzymes in cancer is still largely unknown. Here we define a pathway that is specific for METTL3 and is implicated in the maintenance of a leukaemic state. We identify METTL3 as an essential gene for growth of acute myeloid leukaemia cells in two distinct genetic screens. Downregulation of METTL3 results in cell cycle arrest, differentiation of leukaemic cells and failure to establish leukaemia in immunodeficient mice...
November 27, 2017: Nature
https://www.readbyqxmd.com/read/29183982/improved-detection-of-synthetic-lethal-interactions-in-drosophila-cells-using-variable-dose-analysis-vda
#13
Benjamin E Housden, Zhongchi Li, Colleen Kelley, Yuanli Wang, Yanhui Hu, Alexander J Valvezan, Brendan D Manning, Norbert Perrimon
Synthetic sick or synthetic lethal (SS/L) screens are a powerful way to identify candidate drug targets to specifically kill tumor cells, but this approach generally suffers from low consistency between screens. We found that many SS/L interactions involve essential genes and are therefore detectable within a limited range of knockdown efficiency. Such interactions are often missed by overly efficient RNAi reagents. We therefore developed an assay that measures viability over a range of knockdown efficiency within a cell population...
November 28, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29183975/high-resolution-mapping-of-cis-regulatory-variation-in-budding-yeast
#14
Ryosuke Kita, Sandeep Venkataram, Yiqi Zhou, Hunter B Fraser
Genetic variants affecting gene-expression levels are a major source of phenotypic variation. The approximate locations of these variants can be mapped as expression quantitative trait loci (eQTLs); however, a major limitation of eQTLs is their low resolution, which precludes investigation of the causal variants and their molecular mechanisms. Here we report RNA-seq and full genome sequences for 85 diverse isolates of the yeast Saccharomyces cerevisiae-including wild, domesticated, and human clinical strains-which allowed us to perform eQTL mapping with 50-fold higher resolution than previously possible...
November 28, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29174293/improvements-in-the-crispr-cas9-system-for-high-efficiency-gene-disruption-in-trypanosoma-cruzi
#15
Bruno A A Romagnoli, Gisele F A Picchi, Priscila M Hiraiwa, Beatriz S Borges, Lysangela R Alves, Samuel Goldenberg
Chagas disease, caused by the protozoan parasite Trypanosoma cruzi, affects millions of individuals around the world. Although it has been known for more than a century, the study of T. cruzi has been a challenge, particularly due to the scarcity of tools for genome inquiries. Recently, strategies have been described allowing gene disruption in T. cruzi by the CRISPR/Cas9 nuclease system. Although these strategies demonstrated success in deleting some genes, several aspects could be improved to increase the efficiency of the CRISPR/Cas9 system in T...
November 21, 2017: Acta Tropica
https://www.readbyqxmd.com/read/29164070/generation-of-an-attenuated-tiantan-vaccinia-virus-strain-by-deletion-of-multiple-genes
#16
Yiquan Li, Yilong Zhu, Shuang Chen, Wenjie Li, Xunzhe Yin, Shanzhi Li, Pengpeng Xiao, Jicheng Han, Xiao Li, Lili Sun, Ningyi Jin
An attenuated vaccinia virus-MVTTEAB-was constructed by deletion of non-essential gene segments related to the immunomodulatory and virulence functions of the vaccinia virus Tiantan strain (VVTT). The shuttle plasmids pTC-EGFP, pTE-EGFP, pTA35-EGFP, pTB-EGFP, and pTA66-EGFP were constructed and combined with the early and late strong promoter pE/L and EGFP as an exogenous selectable marker. Then, through the homologous recombination technology and Cre/loxP system, the following gene fragments were gradually knocked out one by one: TC7L-TK2L, TE3L, TA35R, TB13R, and TA66R...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/29158625/comparative-genomic-hybridization-and-transcriptome-sequencing-reveal-that-two-genes-osi_14279-loc_os03g62620-and-osi_10794-loc_os03g14950-regulate-the-mutation-in-the-%C3%AE-rl-rice-mutant
#17
Xulong Wang, Fanhua Wang, Huiqiong Chen, Xiaoyu Liang, Yingmei Huang, Jicai Yi
We previously established the genetic locus of the rolled-leaf mutant, γ-rl, to chromosome 3. In this study, we performed a comparative genomic hybridization (CGH) analysis to identify the genes responsible for the γ-rl mutant phenotype. This was combined with RNA transcriptome sequencing (RNA-seq) to analyze differences in the mRNA expression in seeds 12 h after germination. Using the reference genome of the "indica type" rice from GenBank, we created a chip with 386,000 high density DNA probes designed to target chromosome 3...
October 2017: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
https://www.readbyqxmd.com/read/29158600/crispr-cas9-library-screening-for-drug-target-discovery
#18
REVIEW
Morito Kurata, Kouhei Yamamoto, Branden S Moriarity, Masanobu Kitagawa, David A Largaespada
CRISPR/Cas9-based tools have rapidly developed in recent years. These include CRISPR-based gene activation (CRISPRa) or inhibition (CRISPRi), for which there are libraries. CRISPR libraries for loss of function have been widely used to identify new biological mechanisms, such as drug resistance and cell survival signals. CRISPRa is highly useful in screening for gain of functions, and CRISPRi is a more powerful tool than RNA interference (RNAi) libraries in screening for loss of functions. Positive selection using a CRISPR library can detect survival cells with specific conditions, such as drug treatment, and it can easily clarify drug resistance mechanisms...
November 20, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/29154530/atg101-single-stranded-antisense-rna-loaded-triangular-dna-nanoparticles-control-human-pulmonary-endothelial-growth-via-regulation-of-cell-macroautophagy
#19
Juan Du, Zhi Xu, Qian Liu, Yu Yang, Hang Qian, Mingdong Hu, Ye Fan, Qi Li, Wei Yao, Hongli Li, Guisheng Qian, Binfeng He, Deshan Zhou, Chengde Mao, Guansong Wang
Autophagy plays a key role in pulmonary vascular remodeling (PVR) via regulation of apoptosis and hyperproliferation of pulmonary arterial endothelial cells (PAECs), which are the subject of increased attention. ATG101 is an essential gene for the initiation of autophagy. While the structure of ATG101 has been well characterized, its exact biological function in autophagy is still unknown. In this study, an ATG101 single-stranded antisense RNA-loaded DNA triangular nanoparticle (ssATG101-TNP) is constructed to knock down ATG101 gene expression...
November 20, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29149435/equine-herpesvirus-type-1-orf51-encoding-ul11-as-an-essential-gene-for-replication-in-cultured-cells
#20
Yassien Badr, Ayaka Okada, Rania Abo-Sakaya, Emad Beshir, Kenji Ohya, Hideto Fukushi
Equine herpesvirus type 1 (EHV-1) UL11 is a 74-amino-acid tegument protein encoded by ORF51 of the EHV-1 genome. EHV-1 UL11 was previously reported by other researchers using the RacL22 and RacH strains to be nonessential for viral replication in cultured cells. Here, we constructed UL11 mutant viruses including a UL11 null mutant and three C-terminal truncated mutants, for further characterization of EHV-1 UL11 using bacterial artificial chromosome (BAC) technology based on the neuropathogenic strain Ab4p...
November 17, 2017: Archives of Virology
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