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Bacteria AND essential genes

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https://www.readbyqxmd.com/read/28214450/in-silico-structural-and-functional-analysis-of-mesorhizobium-acc-deaminase
#1
Krishnendu Pramanik, Tithi Soren, Soumik Mitra, Tushar Kanti Maiti
Nodulation is one of the very important processes of legume plants as it is the initiating event of fixing nitrogen. Although ethylene has essential role in normal plant metabolism but it has also negative impact on plants particularly in nodule formation in legume plants. It is also produced due to a variety of biotic or abiotic stresses. 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase is a rhizobial enzyme which cleaves ACC (immediate precursor of ethylene) into α-ketobutyrate and ammonia. As a result, the level of ethylene from the plant cells is decreased and the negative impact of ethylene on nodule formation is reduced...
February 11, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28212413/scarless-deletion-of-up-to-seven-methyl-accepting-chemotaxis-genes-with-an-optimized-method-highlights-key-function-of-chem-in-salmonella-typhimurium
#2
Stefanie Hoffmann, Christiane Schmidt, Steffi Walter, Jennifer K Bender, Roman G Gerlach
Site-directed scarless mutagenesis is an essential tool of modern pathogenesis research. We describe an optimized two-step protocol for genome editing in Salmonella enterica serovar Typhimurium to enable multiple sequential mutagenesis steps in a single strain. The system is based on the λ Red recombinase-catalyzed integration of a selectable antibiotics resistance marker followed by replacement of this cassette. Markerless mutants are selected by expressing the meganuclease I-SceI which induces double-strand breaks in bacteria still harboring the resistance locus...
2017: PloS One
https://www.readbyqxmd.com/read/28208705/the-escherichia-coli-cog1738-member-yhhq-is-involved-in-7-cyanodeazaguanine-preq%C3%A2-transport
#3
Rémi Zallot, Yifeng Yuan, Valérie de Crécy-Lagard
Queuosine (Q) is a complex modification of the wobble base in tRNAs with GUN anticodons. The full Q biosynthesis pathway has been elucidated in Escherichia coli. FolE, QueD, QueE and QueC are involved in the conversion of guanosine triphosphate (GTP) to 7-cyano-7-deazaguanine (preQ₀), an intermediate of increasing interest for its central role in tRNA and DNA modification and secondary metabolism. QueF then reduces preQ₀ to 7-aminomethyl-7-deazaguanine (preQ₁). PreQ₁ is inserted into tRNAs by tRNA guanine(34) transglycosylase (TGT)...
February 8, 2017: Biomolecules
https://www.readbyqxmd.com/read/28207825/discovery-of-a-new-family-of-relaxases-in-firmicutes-bacteria
#4
Gayetri Ramachandran, Andrés Miguel-Arribas, David Abia, Praveen K Singh, Isidro Crespo, César Gago-Córdoba, Jian An Hao, Juan Roman Luque-Ortega, Carlos Alfonso, Ling J Wu, D Roeland Boer, Wilfried J J Meijer
Antibiotic resistance is a serious global problem. Antibiotic resistance genes (ARG), which are widespread in environmental bacteria, can be transferred to pathogenic bacteria via horizontal gene transfer (HGT). Gut microbiomes are especially apt for the emergence and dissemination of ARG. Conjugation is the HGT route that is predominantly responsible for the spread of ARG. Little is known about conjugative elements of Gram-positive bacteria, including those of the phylum Firmicutes, which are abundantly present in gut microbiomes...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28205635/deciphering-the-distance-to-antibiotic-resistance-for-the-pneumococcus-using-genome-sequencing-data
#5
Fredrick M Mobegi, Amelieke J H Cremers, Marien I de Jonge, Stephen D Bentley, Sacha A F T van Hijum, Aldert Zomer
Advances in genome sequencing technologies and genome-wide association studies (GWAS) have provided unprecedented insights into the molecular basis of microbial phenotypes and enabled the identification of the underlying genetic variants in real populations. However, utilization of genome sequencing in clinical phenotyping of bacteria is challenging due to the lack of reliable and accurate approaches. Here, we report a method for predicting microbial resistance patterns using genome sequencing data. We analyzed whole genome sequences of 1,680 Streptococcus pneumoniae isolates from four independent populations using GWAS and identified probable hotspots of genetic variation which correlate with phenotypes of resistance to essential classes of antibiotics...
February 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28203245/small-rnas-derived-from-the-t-dna-of-agrobacterium-rhizogenes-in-hairy-roots-of-phaseolus-vulgaris
#6
Pablo Peláez, Alejandrina Hernández-López, Georgina Estrada-Navarrete, Federico Sanchez
Agrobacterium rhizogenes is a pathogenic bacteria that causes hairy root disease by transferring bacterial DNA into the plant genome. It is an essential tool for industry and research due to its capacity to produce genetically modified roots and whole organisms. Here, we identified and characterized small RNAs generated from the transfer DNA (T-DNA) of A. rhizogenes in hairy roots of common bean (Phaseolus vulgaris). Distinct abundant A. rhizogenes T-DNA-derived small RNAs (ArT-sRNAs) belonging to several oncogenes were detected in hairy roots using high-throughput sequencing...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28203231/error-prone-dnae2-balances-the-genome-mutation-rates-in-myxococcus-xanthus-dk1622
#7
Ran Peng, Jiang-He Chen, Wan-Wan Feng, Zheng Zhang, Jun Yin, Ze-Shuo Li, Yue-Zhong Li
dnaE is an alpha subunit of the tripartite protein complex of DNA polymerase III that is responsible for the replication of bacterial genome. The dnaE gene is often duplicated in many bacteria, and the duplicated dnaE gene was reported dispensable for cell survivals and error-prone in DNA replication in a mystery. In this study, we found that all sequenced myxobacterial genomes possessed two dnaE genes. The duplicate dnaE genes were both highly conserved but evolved divergently, suggesting their importance in myxobacteria...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28202315/mycobacterium-tuberculosis-chorismate-mutase-a-potential-target-for-tb
#8
REVIEW
Manjulatha Khanapur, Mallika Alvala, Maddela Prabhakar, K Shiva Kumar, R K Edwin, P S V K Sri Saranya, Raj Kumar Patel, Gopalakrishnan Bulusu, P Misra, Manojit Pal
Mycobacterium tuberculosis chorismate mutase (MtbCM) catalyzes the rearrangement of chorismate to prephenate in the shikimate biosynthetic pathway to form the essential amino acids, phenylalanine and tyrosine. Two genes encoding chorismate mutase have been identified in Mtb. The secretory form,∗MtbCM (encoded by Rv1885c) is assumed to play a key role in pathogenesis of tuberculosis. Also, the inhibition of MtbCM may hinder the supply of nutrients to the organism. Indeed, the existence of chorismate mutase (CM) in bacteria, fungi and higher plants but not in human and low sequence homology among known CM makes it an interesting target for the discovery of anti-tubercular agents...
February 4, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28201991/plasmid-diversity-and-phylogenetic-consistency-in-the-lyme-disease-agent-borrelia-burgdorferi
#9
Sherwood R Casjens, Eddie B Gilcrease, Marija Vujadinovic, Emmanuel F Mongodin, Benjamin J Luft, Steven E Schutzer, Claire M Fraser, Wei-Gang Qiu
BACKGROUND: Bacteria from the genus Borrelia are known to harbor numerous linear and circular plasmids. We report here a comparative analysis of the nucleotide sequences of 236 plasmids present in fourteen independent isolates of the Lyme disease agent B. burgdorferi. RESULTS: We have sequenced the genomes of 14 B. burgdorferi sensu stricto isolates that carry a total of 236 plasmids. These individual isolates carry between seven and 23 plasmids. Their chromosomes, the cp26 and cp32 circular plasmids, as well as the lp54 linear plasmid, are quite evolutionarily stable; however, the remaining plasmids have undergone numerous non-homologous and often duplicative recombination events...
February 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28198411/the-secondary-resistome-of-multidrug-resistant-klebsiella-pneumoniae
#10
Bimal Jana, Amy K Cain, William T Doerrler, Christine J Boinett, Maria C Fookes, Julian Parkhill, Luca Guardabassi
Klebsiella pneumoniae causes severe lung and bloodstream infections that are difficult to treat due to multidrug resistance. We hypothesized that antimicrobial resistance can be reversed by targeting chromosomal non-essential genes that are not responsible for acquired resistance but essential for resistant bacteria under therapeutic concentrations of antimicrobials. Conditional essentiality of individual genes to antimicrobial resistance was evaluated in an epidemic multidrug-resistant clone of K. pneumoniae (ST258)...
February 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28197855/soil-microbial-community-responses-to-contamination-with-silver-aluminium-oxide-and-silicon-dioxide-nanoparticles
#11
C F McGee, S Storey, N Clipson, E Doyle
Soil microorganisms are key contributors to nutrient cycling and are essential for the maintenance of healthy soils and sustainable agriculture. Although the antimicrobial effects of a broad range of nanoparticulate substances have been characterised in vitro, little is known about the impact of these compounds on microbial communities in environments such as soil. In this study, the effect of three widely used nanoparticulates (silver, silicon dioxide and aluminium oxide) on bacterial and fungal communities in an agricultural pastureland soil was examined in a microcosm-based experiment using a combination of enzyme analysis, molecular fingerprinting and amplicon sequencing...
February 14, 2017: Ecotoxicology
https://www.readbyqxmd.com/read/28196402/pimelic-acid-the-first-precursor-of-the-bacillus-subtilis-biotin-synthesis-pathway-exists-as-the-free-acid-and-is-assembled-by-fatty-acid-synthesis
#12
Miglena Manandhar, John E Cronan
Biotin synthetic pathways are readily separated into two stages, synthesis of the seven carbon α, ω-dicarboxylic acid pimelate moiety and assembly of the fused heterocyclic rings. The biotin pathway genes responsible for pimelate moiety synthesis vary widely among bacteria whereas the ring synthesis genes are highly conserved. Bacillus subtilis seems to have redundant genes, bioI and bioW, for generation of the pimelate intermediate. Largely consistent with previous genetic studies we found that deletion of bioW caused a biotin auxotrophic phenotype whereas deletion of bioI did not...
February 14, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28193635/a-redox-responsive-transcription-factor-is-critical-for-pathogenesis-and-aerobic-growth-of-listeria-monocytogenes
#13
Aaron T Whiteley, Brittany R Ruhland, Mauna B Edrozo, Michelle L Reniere
Bacterial pathogens have evolved sophisticated mechanisms to sense and adapt to redox stress in nature and within the host. However, deciphering the redox environment encountered by intracellular pathogens in the mammalian cytosol is challenging and remains poorly understood. In this study, we assessed the contributions of the two redox-responsive, Spx-family transcriptional regulators to the virulence of Listeria monocytogenes, a Gram-positive facultative intracellular pathogen. Spx-family proteins are highly conserved in Firmicutes and L...
February 13, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28189107/c-elegans-and-its-bacterial-diet-as-a-model-for-systems-level-understanding-of-host-microbiota-interactions
#14
REVIEW
Jingyan Zhang, Amy D Holdorf, Albertha Jm Walhout
Resident microbes of the human body, particularly the gut microbiota, provide essential functions for the host, and, therefore, have important roles in human health as well as mitigating disease. It is difficult to study the mechanisms by which the microbiota affect human health, especially at a systems-level, due to heterogeneity of human genomes, the complexity and heterogeneity of the gut microbiota, the challenge of growing these bacteria in the laboratory, and the lack of bacterial genetics in most microbiotal species...
February 8, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28185613/development-of-quantitative-real-time-pcr-assays-for-postmortem-detection-of-mycobacterium-spp-common-in-zebrafish-danio-rerio-research-colonies
#15
Danielle M Meritet Donna M Mulrooney Michael L Kent And Christiane V Löhr
Mycobacterium spp. infections are common in zebrafish kept in research facilities. These comorbidities can substantiallymodulate the responses of these fish to external and internal stimuli. Therefore, diagnostic tests to detect Mycobacterium spp.infections in zebrafish colonies prove essential. Here, we outline the development of quantitative simplex real-time PCRassays to detect the 3 Mycobacterium species most commonly identified in laboratory zebrafish. The assays targeted the heatshock protein 65 gene of M...
February 9, 2017: Journal of the American Association for Laboratory Animal Science: JAALAS
https://www.readbyqxmd.com/read/28181569/long-term-nitrogen-fertilization-decreased-the-abundance-of-inorganic-phosphate-solubilizing-bacteria-in-an-alkaline-soil
#16
Bang-Xiao Zheng, Xiu-Li Hao, Kai Ding, Guo-Wei Zhou, Qing-Lin Chen, Jia-Bao Zhang, Yong-Guan Zhu
Inorganic phosphate solubilizing bacteria (iPSB) are essential to facilitate phosphorus (P) mobilization in alkaline soil, however, the phylogenetic structure of iPSB communities remains poorly characterized. Thus, we use a reference iPSB database to analyze the distribution of iPSB communities based on 16S rRNA gene illumina sequencing. Additionally, a noval pqqC primer was developed to quantify iPSB abundance. In our study, an alkaline soil with 27-year fertilization treatment was selected. The percentage of iPSB was 1...
February 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28179109/mechanisms-of-defense-against-products-of-cysteine-catabolism-in-the-nematode-caenorhabditis-elegans
#17
Leonid Livshits, Arijit Kumar Chatterjee, Netanel Karbian, Rachel Abergel, Zohar Abergel, Einav Gross
Cysteine catabolism presents cells with a double-edged sword. On the one hand, cysteine degradation provides cells with essential molecules such as taurine and sulfide. The formation of sulfide in cells is thought to regulate important and diverse physiological processes including blood circulation, synaptic activity and inflammation. On the other hand, the catabolism of cysteine by gut microbiota can release high levels of sulfide that may underlie the development or relapse of ulcerative colitis, an inflammatory bowel disease affecting millions of people worldwide...
February 4, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28177216/bacterioferritin-structure-dynamics-and-protein-protein-interactions-at-play-in-iron-storage-and-mobilization
#18
Mario Rivera
Despite its essentiality to life, iron presents significant challenges to cells: the exceedingly low solubility of Fe(3+) limits its bioavailability, and the reactivity of Fe(2+) toward H2O2 is a source of the toxic hydroxyl radical (HO(•)). Consequently, cellular levels of free iron are highly regulated to ensure sufficiency while preventing iron-induced toxicity. Relatively little is known about the fate of iron in the bacterial cytosol or how cells balance the need for relatively high cytosolic iron concentrations with the potential toxicity of the nutrient...
February 8, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28174314/a-ferredoxin-and-f420h2-dependent-electron-bifurcating-heterodisulfide-reductase-with-homologs-in-the-domains-bacteria-and-archaea
#19
Zhen Yan, Mingyu Wang, James G Ferry
: Heterodisulfide reductases (Hdr) of the HdrABC class are ancient enzymes and a component of the anaerobic core belonging to the prokaryotic common ancestor. The ancient origin is consistent with the widespread occurrence of genes encoding putative HdrABC homologs in metabolically diverse prokaryotes predicting diverse physiological functions; however, only one HdrABC has been characterized and that was from a narrow metabolic group of obligate CO2-reducing methanogenic anaerobes (methanogens) from the domain Archaea Here we report the biochemical characterization of an HdrABC homolog (HdrA2B2C2) from the acetate-utilizing methanogen Methanosarcina acetivorans with unusual properties structurally and functionally distinct from the only other HdrABC characterized...
February 7, 2017: MBio
https://www.readbyqxmd.com/read/28174266/low-escape-rate-genome-safeguards-with-minimal-molecular-perturbation-of-saccharomyces-cerevisiae
#20
Neta Agmon, Zuojian Tang, Kun Yang, Ben Sutter, Shigehito Ikushima, Yizhi Cai, Katrina Caravelli, James A Martin, Xiaoji Sun, Woo Jin Choi, Allen Zhang, Giovanni Stracquadanio, Haiping Hao, Benjamin P Tu, David Fenyo, Joel S Bader, Jef D Boeke
As the use of synthetic biology both in industry and in academia grows, there is an increasing need to ensure biocontainment. There is growing interest in engineering bacterial- and yeast-based safeguard (SG) strains. First-generation SGs were based on metabolic auxotrophy; however, the risk of cross-feeding and the cost of growth-controlling nutrients led researchers to look for other avenues. Recent strategies include bacteria engineered to be dependent on nonnatural amino acids and yeast SG strains that have both transcriptional- and recombinational-based biocontainment...
February 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
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