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Bacteria AND essential genes

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https://www.readbyqxmd.com/read/28936208/cas9-nickase-assisted-rna-repression-enables-stable-and-efficient-manipulation-of-essential-metabolic-genes-in-clostridium-cellulolyticum
#1
Tao Xu, Yongchao Li, Zhili He, Joy D Van Nostrand, Jizhong Zhou
Essential gene functions remain largely underexplored in bacteria. Clostridium cellulolyticum is a promising candidate for consolidated bioprocessing; however, its genetic manipulation to reduce the formation of less-valuable acetate is technically challenging due to the essentiality of acetate-producing genes. Here we developed a Cas9 nickase-assisted chromosome-based RNA repression to stably manipulate essential genes in C. cellulolyticum. Our plasmid-based expression of antisense RNA (asRNA) molecules targeting the phosphotransacetylase (pta) gene successfully reduced the enzymatic activity by 35% in cellobiose-grown cells, metabolically decreased the acetate titer by 15 and 52% in wildtype transformants on cellulose and xylan, respectively...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28934382/complete-genome-analysis-of-lactobacillus-fermentum-sk152-from-kimchi-reveals-genes-associated-with-its-antimicrobial-activity
#2
DongAhn Yoo, Bernadette B Bagon, Valerie Diane V Valeriano, Ju Kyoung Oh, Heebal Kim, Seoae Cho, Dae-Kyung Kang
Research findings on probiotics highlight their importance in repressing harmful bacteria, leading to more extensive research on their potential applications. We analysed the genome of Lactobacillus fermentum SK152, which was isolated from the Korean traditional fermented vegetable dish kimchi, to determine the genetic makeup and genetic factors responsible for the antimicrobial activity of L. fermentum SK152 and performed a comparative genome analysis with other L. fermentum strains. The genome of L. fermentum SK152 was found to comprise a complete circular chromosome of 2092 273 bp, with an estimated GC content of 51...
October 2, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28933646/visualizing-trna-dependent-mistranslation-in-human-cells
#3
Jeremy T Lant, Matthew D Berg, Daniel Hw Sze, Kyle S Hoffman, Ibukunoluwa C Akinpelu, Matthew Turk, Ilka U Heinemann, Martin L Duennwald, Christopher J Brandl, Patrick O'Donoghue
High-fidelity translation and a strictly accurate proteome were originally assumed as essential to life and cellular viability. Yet recent studies in bacteria and eukaryotic model organisms suggest that proteome-wide mistranslation can provide selective advantages and is tolerated in the cell at higher levels than previously thought (one error in 6.9 × 10(-4) in yeast) with a limited impact on phenotype. Previously, we selected a tRNA(Pro) containing a single mutation that induces mistranslation with alanine at proline codons in yeast...
September 21, 2017: RNA Biology
https://www.readbyqxmd.com/read/28932674/propulsion-and-chemotaxis-in-bacteria-driven-microswimmers
#4
Jiang Zhuang, Byung-Wook Park, Metin Sitti
Despite the large body of experimental work recently on biohybrid microsystems, few studies have focused on theoretical modeling of such systems, which is essential to understand their underlying functioning mechanisms and hence design them optimally for a given application task. Therefore, this study focuses on developing a mathematical model to describe the 3D motion and chemotaxis of a type of widely studied biohybrid microswimmer, where spherical microbeads are driven by multiple attached bacteria. The model is developed based on the biophysical observations of the experimental system and is validated by comparing the model simulation with experimental 3D swimming trajectories and other motility characteristics, including mean squared displacement, speed, diffusivity, and turn angle...
September 2017: Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
https://www.readbyqxmd.com/read/28929086/role-of-two-cell-wall-amidases-in-septal-junction-and-nanopore-formation-in-the-multicellular-cyanobacterium-anabaena-sp-pcc-7120
#5
Jan Bornikoel, Alejandro Carrión, Qing Fan, Enrique Flores, Karl Forchhammer, Vicente Mariscal, Conrad W Mullineaux, Rebeca Perez, Nadine Silber, C Peter Wolk, Iris Maldener
Filamentous cyanobacteria have developed a strategy to perform incompatible processes in one filament by differentiating specialized cell types, N2-fixing heterocysts and CO2-fixing, photosynthetic, vegetative cells. These bacteria can be considered true multicellular organisms with cells exchanging metabolites and signaling molecules via septal junctions, involving the SepJ and FraCD proteins. Previously, it was shown that the cell wall lytic N-acetylmuramyl-L-alanine amidase, AmiC2, is essential for cell-cell communication in Nostoc punctiforme...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28925547/biogeographic-conservation-of-the-cytosine-epigenome-in-the-globally-important-marine-nitrogen-fixing-cyanobacterium-trichodesmium
#6
Nathan G Walworth, David A Hutchins, Egor Dolzhenko, Michael D Lee, Feixue Fu, Andrew D Smith, Eric A Webb
Cytosine methylation has been shown to regulate essential cellular processes and impact biological adaptation. Despite its evolutionary importance, only a handful of bacterial, genome-wide cytosine studies have been conducted, with none for marine bacteria. Here, we examine the genome-wide, C(5) -Methyl-cytosine (m5C) methylome and its correlation to global transcription in the marine nitrogen-fixing cyanobacterium Trichodesmium. We characterize genome-wide methylation and highlight conserved motifs across 3 Trichodesmium isolates and 2 Trichodesmium metagenomes, thereby identifying highly conserved, novel genomic signatures of potential gene regulation in Trichodesmium...
September 19, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28925527/one-gene-two-proteins-coordinated-production-of-a-copper-chaperone-by-differential-transcript-formation-and-translational-frameshifting-in-escherichia-coli
#7
Steffen Lorenz Drees, Birgit Klinkert, Stefan Helling, Dominik Fabian Beyer, Katrin Marcus, Franz Narberhaus, Mathias Lübben
Programmed ribosomal frameshifting (PRF) is a translational anomaly causing the ribosome to shift into an alternative reading frame. PRFs are common in viral genomes, using a single nucleotide sequence to code for two proteins in overlapping frames. In bacteria and eukaryota, PRFs are less frequent. We report on a PRF in the copper detoxification system of Escherichia coli where a metallochaperone is generated out of the first 69 amino acids and a C-terminal out-of-frame glycine of the gene copA. copA besides codes for the P1B -ATPase CopA, a membrane-integral protein and principal interaction target of the chaperone...
September 19, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28920507/navigating-the-structure-function-evolutionary-relationship-of-csaa-chaperone-in-archaea
#8
Archana Sharma, Shikha Rani, Manisha Goel
CsaA is a protein involved in the post-translational translocation of proteins across the cytoplasmic membrane. It is considered to be a functional homolog of SecB which participates in the Sec-dependent translocation pathway in an analogous manner. CsaA has also been reported to act as a molecular chaperone, preventing aggregation of unfolded proteins. It is essentially a prokaryotic protein which is absent in eukaryotes, but found extensively in bacteria and earlier thought to be widely present in archaea...
September 18, 2017: Critical Reviews in Microbiology
https://www.readbyqxmd.com/read/28911105/a-novel-nucleoid-associated-protein-coordinates-chromosome-replication-and-chromosome-partition
#9
James A Taylor, Gaël Panis, Patrick H Viollier, Gregory T Marczynski
We searched for regulators of chromosome replication in the cell cycle model Caulobacter crescentus and found a novel DNA-binding protein (GapR) that selectively aids the initiation of chromosome replication and the initial steps of chromosome partitioning. The protein binds the chromosome origin of replication (Cori) and has higher-affinity binding to mutated Cori-DNA that increases Cori-plasmid replication in vivo. gapR gene expression is essential for normal rapid growth and sufficient GapR levels are required for the correct timing of chromosome replication...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28904640/short-term-dietary-methionine-supplementation-affects-one-carbon-metabolism-and-dna-methylation-in-the-mouse-gut-and-leads-to-altered-microbiome-profiles-barrier-function-gene-expression-and-histomorphology
#10
Isabelle R Miousse, Rupak Pathak, Sarita Garg, Charles M Skinner, Stepan Melnyk, Oleksandra Pavliv, Howard Hendrickson, Reid D Landes, Annie Lumen, Alan J Tackett, Nicolaas E P Deutz, Martin Hauer-Jensen, Igor Koturbash
BACKGROUND: Methionine, a central molecule in one-carbon metabolism, is an essential amino acid required for normal growth and development. Despite its importance to biological systems, methionine is toxic when administered at supra-physiological levels. The aim of this study was to investigate the effects of short-term methionine dietary modulation on the proximal jejunum, the section of the gut specifically responsible for amino acid absorption, in a mouse model. Eight-week-old CBA/J male mice were fed methionine-adequate (MAD; 6...
2017: Genes & Nutrition
https://www.readbyqxmd.com/read/28900025/psp-stress-response-proteins-form-a-complex-with-mislocalized-secretins-in-the-yersinia-enterocolitica-cytoplasmic-membrane
#11
Disha Srivastava, Amal Moumene, Josué Flores-Kim, Andrew J Darwin
The bacterial phage shock protein system (Psp) is a conserved extracytoplasmic stress response that is essential for the virulence of some pathogens, including Yersinia enterocolitica It is induced by events that can compromise inner membrane (IM) integrity, including the mislocalization of outer membrane pore-forming proteins called secretins. In the absence of the Psp system, secretin mislocalization permeabilizes the IM and causes rapid cell death. The Psp proteins PspB and PspC form an integral IM complex with two independent roles...
September 12, 2017: MBio
https://www.readbyqxmd.com/read/28900021/another-brick-in-the-wall-a-rhamnan-polysaccharide-trapped-inside-peptidoglycan-of-lactococcus-lactis
#12
Irina Sadovskaya, Evgeny Vinogradov, Pascal Courtin, Julija Armalyte, Mickael Meyrand, Efstathios Giaouris, Simon Palussière, Sylviane Furlan, Christine Péchoux, Stuart Ainsworth, Jennifer Mahony, Douwe van Sinderen, Saulius Kulakauskas, Yann Guérardel, Marie-Pierre Chapot-Chartier
Polysaccharides are ubiquitous components of the Gram-positive bacterial cell wall. In Lactococcus lactis, a polysaccharide pellicle (PSP) forms a layer at the cell surface. The PSP structure varies among lactococcal strains; in L. lactis MG1363, the PSP is composed of repeating hexasaccharide phosphate units. Here, we report the presence of an additional neutral polysaccharide in L. lactis MG1363 that is a rhamnan composed of α-l-Rha trisaccharide repeating units. This rhamnan is still present in mutants devoid of the PSP, indicating that its synthesis can occur independently of PSP synthesis...
September 12, 2017: MBio
https://www.readbyqxmd.com/read/28898292/the-effect-of-age-on-the-intestinal-mucus-thickness-microbiota-composition-and-immunity-in-relation-to-sex-in-mice
#13
Marlies Elderman, Bruno Sovran, Floor Hugenholtz, Katrine Graversen, Myrte Huijskes, Eva Houtsma, Clara Belzer, Mark Boekschoten, Paul de Vos, Jan Dekker, Jerry Wells, Marijke Faas
A mucus layer covers and protects the intestinal epithelial cells from direct contact with microbes. This mucus layer not only prevents inflammation but also plays an essential role in microbiota colonization, indicating the complex interplay between mucus composition-microbiota and intestinal health. However, it is unknown whether the mucus layer is influenced by age or sex and whether this contributes to reported differences in intestinal diseases in males and females or with ageing. Therefore, in this study we investigated the effect of age on mucus thickness, intestinal microbiota composition and immune composition in relation to sex...
2017: PloS One
https://www.readbyqxmd.com/read/28894204/novel-arsenic-transforming-bacteria-and-the-diversity-of-their-arsenic-related-genes-and-enzymes-arising-from-arsenic-polluted-freshwater-sediment
#14
Maria L S Suhadolnik, Ana P C Salgado, Larissa L S Scholte, Lucas Bleicher, Patrícia S Costa, Mariana P Reis, Marcela F Dias, Marcelo P Ávila, Francisco A R Barbosa, Edmar Chartone-Souza, Andréa M A Nascimento
Bacteria are essential in arsenic cycling. However, few studies have addressed 16S rRNA and arsenic-related functional gene diversity in long-term arsenic-contaminated tropical sediment. Here, using culture-based, metagenomic and computational approaches, we describe the diversity of bacteria, genes and enzymes involved in AsIII and AsV transformation in freshwater sediment and in anaerobic AsIII- and AsV-enrichment cultures (ECs). The taxonomic profile reveals significant differences among the communities...
September 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28892254/transcriptional-regulation-of-ectoine-catabolism-in-response-to-multiple-metabolic-and-environmental-cues
#15
Annina Schulz, Lucas Hermann, Sven-Andreas Freibert, Tobias Bönig, Tamara Hoffmann, Ramona Riclea, Jeroen S Dickschat, Johann Heider, Erhard Bremer
Ectoine and hydroxyectoine are effective microbial osmostress protectants, but can also serve as versatile nutrients for bacteria. We have studied the genetic regulation of ectoine and hydroxyectoine import and catabolism in the marine Roseobacter species Ruegeria pomeroyi and identified three transcriptional regulators involved in these processes: the GabR/MocR-type repressor EnuR, the feast and famine-type regulator AsnC, and the two-component system NtrYX. The corresponding genes are widely associated with ectoine and hydroxyectoine uptake and catabolic gene clusters (enuR, asnC), and with microorganisms predicted to consume ectoines (ntrYX)...
September 11, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28890713/bad-phages-in-good-bacteria-role-of-the-mysterious-orf63-of-%C3%AE-and-shiga-toxin-converting-%C3%AE-24b-bacteriophages
#16
Aleksandra Dydecka, Sylwia Bloch, Ali Rizvi, Shaili Perez, Bozena Nejman-Falenczyk, Gracja Topka, Tomasz Gasior, Agnieszka Necel, Grzegorz Wegrzyn, Logan W Donaldson, Alicja Wegrzyn
Lambdoid bacteriophages form a group of viruses that shares a common schema of genome organization and lifecycle. Some of them can play crucial roles in creating the pathogenic profiles of Escherichia coli strains. For example, Shiga toxin-producing E. coli (STEC) acquired stx genes, encoding Shiga toxins, via lambdoid prophages (Stx phages). The results obtained so far present the evidence for the relation between the exo-xis region of the phage genome and lambdoid phage development, however molecular mechanisms of activities of the exo-xis genes' products are still unknown...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28888882/genome-wide-sequence-transposon-insertion-sites-and-analyze-the-essential-genes-of-brucella-melitensis
#17
Yanyan De, Congyue Dong, Yanyang Cao, Xiaolei Wang, Xiaowen Yang, Ning Wang, Cunrui Zhang, Zhen Wang, Yanli Lyu, Qingmin Wu
A transposon mutant library of B. melitensis NI including 32,640 transposon mutants was established. By sequencing the transposon insertion sites, 10,832 mutants were successfully defined for their insertion sites. Analysis of the mutants with defined transposon insertion sites (DTIS) indicated that the insertions were well spread through the two genomes. In addition, 948 genes with no detectable transposon insertions were taken as the candidate for identification of essential genes. In comparison with the Bacterial Database of Essential Genes and by using comparative genomics analysis, 183 potential essential genes of B...
September 6, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28878025/gallbladder-derived-surfactant-protein-d-regulates-gut-commensal-bacteria-for-maintaining-intestinal-homeostasis
#18
Hana Sarashina-Kida, Hideo Negishi, Junko Nishio, Wataru Suda, Yuki Nakajima, Mika Yasui-Kato, Keiko Iwaisako, Sujin Kang, Nobuyasu Endo, Hideyuki Yanai, Masataka Asagiri, Hiroshi Kida, Masahira Hattori, Atsushi Kumanogoh, Tadatsugu Taniguchi
The commensal microbiota within the gastrointestinal tract is essential in maintaining homeostasis. Indeed, dysregulation in the repertoire of microbiota can result in the development of intestinal immune-inflammatory diseases. Further, this immune regulation by gut microbiota is important systemically, impacting health and disease of organ systems beyond the local environment of the gut. What has not been explored is how distant organs might in turn shape the microbiota via microbe-targeted molecules. Here, we provide evidence that surfactant protein D (SP-D) synthesized in the gallbladder and delivered into intestinal lumen binds selectively to species of gut commensal bacteria...
September 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28875178/genetic-validation-of-leishmania-donovani-lysyl-trna-synthetase-shows-that-it-is-indispensable-for-parasite-growth-and-infectivity
#19
Sanya Chadha, N Arjunreddy Mallampudi, Debendra K Mohapatra, Rentala Madhubala
Leishmania donovani is a protozoan parasite that causes visceral leishmaniasis. Increasing resistance and severe side effects of existing drugs have led to the need to identify new chemotherapeutic targets. Aminoacyl-tRNA synthetases (aaRSs) are ubiquitous and are required for protein synthesis. aaRSs are known drug targets for bacterial and fungal pathogens. Here, we have characterized and evaluated the essentiality of L. donovani lysyl-tRNA synthetase (LdLysRS). Two different coding sequences for lysyl-tRNA synthetases are annotated in the Leishmania genome database...
July 2017: MSphere
https://www.readbyqxmd.com/read/28874412/isolation-of-a-membrane-protein-complex-for-type-vii-secretion-in-staphylococcus-aureus
#20
Khaled A Aly, Mark Anderson, Ryan Jay Ohr, Dominique Missiakas
The ESAT6-like secretion system (ESS) of Staphylococcus aureus promotes effector protein transport across the bacterial envelope. Genes in the ESS cluster are required for S. aureus establishment of persistent abscess lesions and the modulation of immune responses during blood stream infections. The biochemical functions of most of the ESS gene products, specifically the identity of secretion machine components, are however unknown. Earlier work demonstrated that deletion of essB, which encodes a membrane protein, abolishes S...
September 5, 2017: Journal of Bacteriology
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