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https://www.readbyqxmd.com/read/29792173/impact-of-growth-ph-and-glucose-concentrations-on-the-cody-regulatory-network-in-streptococcus-salivarius
#1
Jianing Geng, Szu-Chuan Huang, Yueh-Ying Chen, Cheng-Hsun Chiu, Songnian Hu, Yi-Ywan M Chen
BACKGROUND: Streptococcus salivarius is an abundant isolate of the human oral microbiota. Since both pH and glucose availability fluctuate frequently in the oral cavity, the goal of this study was to investigate regulation by CodY, a conserved pleiotropic regulator of Gram positive bacteria, in response to these two signals. The chemostat culture system was employed to precisely control the growth parameters, and the transcriptomes of wild-type S. salivarius 57.I and its CodY-null derivative (ΔcodY) grown at pH 7 and 5...
May 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29784884/the-effector-gene-xopae-of-xanthomonas-euvesicatoria-85-10-is-part-of-an-operon-and-encodes-an-e3-ubiquitin-ligase
#2
Georgy Popov, Bharat Bhusan Majhi, Guido Sessa
The type III effector XopAE from the Xanthomonas euvesicatoria strain 85-10 ( Xe 85-10) was previously shown to inhibit plant immunity and enhance pathogen-induced disease symptoms. Evolutionary analysis of 60 xopAE alleles ( AEal ) revealed that the xopAE locus is conserved in multiple Xanthomonas species. The majority of xopAE alleles (55 out of 60) encodes a single ORF ( xopAE ), while in 5 alleles, including AEal 37 of the Xe 85-10 strain, a frame-shift splits the locus into two ORFs ( hpaF and a truncated xopAE )...
May 21, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29784781/c-4-sterol-demethylation-enzymes-distinguish-bacterial-and-eukaryotic-sterol-synthesis
#3
Alysha K Lee, Amy B Banta, Jeremy H Wei, David J Kiemle, Ju Feng, José-Luis Giner, Paula V Welander
Sterols are essential eukaryotic lipids that are required for a variety of physiological roles. The diagenetic products of sterol lipids, sterane hydrocarbons, are preserved in ancient sedimentary rocks and are utilized as geological biomarkers, indicating the presence of both eukaryotes and oxic environments throughout Earth's history. However, a few bacterial species are also known to produce sterols, bringing into question the significance of bacterial sterol synthesis for our interpretation of sterane biomarkers...
May 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29778819/detection-of-tem-and-ctx-m-genes-from-ciprofloxacin-resistant-proteus-mirabilis-and-escherichia-coli-isolated-on-urinary-tract-infections-utis
#4
Govindan Rajivgandhi, Muthuchamy Maruthupandy, Natesan Manoharan
The multidrug resistant Gram negative bacteria (MDRGNB) is an emerging burden and now represents a daily challenge for the management of antimicrobial therapy in healthcare settings. The present study was aimed to detect the prevalence of TEM and CTX-M type genes from GNB on urinary tract infection (UTIs). The ciprofloxacin resistant uropathogens were detected by HEXA UTI 5 disc diffusion method. The phenotypic detection of uropathogens producing extended spectrum beta lactamases (ESBLs) was confirmed by double disc combination (DDCT) and phenotype confirmation methods (PCT)...
May 17, 2018: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29778216/nitric-oxide-signalling-in-yeast
#5
Rika I Astuti, Ryo Nasuno, Hiroshi Takagi
Nitric oxide (NO) is a cellular signalling molecule widely conserved among organisms, including microorganisms such as bacteria, yeasts, and fungi, and higher eukaryotes such as plants and mammals. NO is mainly produced by the activities of NO synthase (NOS) or nitrite reductase (NIR). There are several NO detoxification systems, including NO dioxygenase (NOD) and S-nitrosoglutathione reductase (GSNOR). NO homeostasis, based on the balance between NO synthesis and degradation, is important for regulating its physiological functions, since an excess of NO causes nitrosative stress due to the high reactivity of NO and NO-derived compounds...
2018: Advances in Microbial Physiology
https://www.readbyqxmd.com/read/29778215/anaerobic-bacterial-response-to-nitrosative-stress
#6
Jeffrey A Cole
This chapter provides an overview of current knowledge of how anaerobic bacteria protect themselves against nitrosative stress. Nitric oxide (NO) is the primary source of this stress. Aerobically its removal is an oxidative process, whereas reduction is required anaerobically. Mechanisms required to protect aerobic and anaerobic bacteria are therefore different. Several themes recur in the review. First, how gene expression is regulated often provides clues to the physiological function of the gene products...
2018: Advances in Microbial Physiology
https://www.readbyqxmd.com/read/29765362/tachyplesin-causes-membrane-instability-that-kills-multidrug-resistant-bacteria-by-inhibiting-the-3-ketoacyl-carrier-protein-reductase-fabg
#7
Cunbao Liu, Jialong Qi, Bin Shan, Yanbing Ma
Tachyplesin is a type of cationic β-hairpin antimicrobial peptide discovered in horseshoe crab approximately 30 years ago that is well known for both its potential antimicrobial activities against multidrug-resistant bacteria and its cytotoxicity to mammalian cells. Though its physical interactions with artificial membranes have been well studied, details of its physiological mechanism of action the physiological consequences of its action remain limited. By using the DNA-binding fluorescent dye propidium iodide to monitor membrane integrity, confocal microscopy to assess the intracellular location of FITC-tagged tachyplesin, and RNA sequencing of the differentially expressed genes in four Gram-negative bacteria ( Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae , and Pseudomonas aeruginosa ) treated with lethal or sublethal concentrations of tachyplesin, we found that compared with levofloxacin-treated bacteria, tachyplesin-treated bacteria showed significant effects on the pathways underlying unsaturated fatty acid biosynthesis...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29764950/cagy-dependent-regulation-of-type-iv-secretion-in-helicobacter-pylori-is-associated-with-alterations-in-integrin-binding
#8
Emma C Skoog, Vasilios A Morikis, Miriam E Martin, Greg A Foster, Lucy P Cai, Lori M Hansen, Beibei Li, Jennifer A Gaddy, Scott I Simon, Jay V Solnick
Strains of Helicobacter pylori that cause ulcer or gastric cancer typically express a type IV secretion system (T4SS) encoded by the cag pathogenicity island ( cag PAI). CagY is an ortholog of VirB10 that, unlike other VirB10 orthologs, has a large middle repeat region (MRR) with extensive repetitive sequence motifs, which undergo CD4+ T cell-dependent recombination during infection of mice. Recombination in the CagY MRR reduces T4SS function, diminishes the host inflammatory response, and enables the bacteria to colonize at a higher density...
May 15, 2018: MBio
https://www.readbyqxmd.com/read/29764946/comparative-genomics-reveals-the-core-gene-toolbox-for-the-fungus-insect-symbiosis
#9
Yan Wang, Matt Stata, Wei Wang, Jason E Stajich, Merlin M White, Jean-Marc Moncalvo
Modern genomics has shed light on many entomopathogenic fungi and expanded our knowledge widely; however, little is known about the genomic features of the insect-commensal fungi. Harpellales are obligate commensals living in the digestive tracts of disease-bearing insects (black flies, midges, and mosquitoes). In this study, we produced and annotated whole-genome sequences of nine Harpellales taxa and conducted the first comparative analyses to infer the genomic diversity within the members of the Harpellales...
May 15, 2018: MBio
https://www.readbyqxmd.com/read/29760498/hierarchical-mechanism-of-amino-acid-sensing-by-the-t-box-riboswitch
#10
Krishna C Suddala, Javier Cabello-Villegas, Malgorzata Michnicka, Collin Marshall, Edward P Nikonowicz, Nils G Walter
In Gram-positive bacteria, T-box riboswitches control gene expression to maintain the cellular pools of aminoacylated tRNAs essential for protein biosynthesis. Co-transcriptional binding of an uncharged tRNA to the riboswitch stabilizes an antiterminator, allowing transcription read-through, whereas an aminoacylated tRNA does not. Recent structural studies have resolved two contact points between tRNA and Stem-I in the 5' half of the T-box riboswitch, but little is known about the mechanism empowering transcriptional control by a small, distal aminoacyl modification...
May 14, 2018: Nature Communications
https://www.readbyqxmd.com/read/29758858/treated-and-untreated-wastewater-effluents-alter-river-sediment-bacterial-communities-involved-in-nitrogen-and-sulphur-cycling
#11
Miren Martínez-Santos, Anders Lanzén, Jessica Unda-Calvo, Iker Martín, Carlos Garbisu, Estilita Ruiz-Romera
Studying the dynamics of nitrogen and sulphur cycling bacteria in river surface sediments is essential to better understand their contribution to global biogeochemical cycles. Evaporitic rocks settled at the headwater of the Deba River catchment (northern Spain) lead to high values of sulphate concentration in its waters. Besides, the discharge of effluents from untreated and treated residual (urban and industrial) wastewaters increases the concentration of metals, nutrients and organic compounds in its mid- and low-water courses...
August 15, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29758131/the-outer-membrane-omp85-like-protein-p39-influences-metabolic-homeostasis-in-mature-arabidopsis-thaliana
#12
Yi-Ching Hsueh, Kerstin Nicolaisen, Lucia E Gross, Joachim Nöthen, Nicolas Schauer, Lea Vojta, Franziska Ertel, Ina Koch, Roman Ladig, Hrvoje Fulgosi, Alisdair R Fernie, Enrico Schleiff
Omp85 proteins form a large membrane protein family found in bacteria and eukaryotes. Omp85 proteins are composed of a C-terminal β-barrel-shaped membrane domain and one, or more, N-terminal polypeptide-transport-associated (POTRA) domain(s). However, Arabidopsis thaliana contains two genes coding for Omp85 proteins without POTRA domain. One gene is designated P39, according to the molecular weight of the encoded protein. The protein is targeted to plastids and it was established that p39 shows electrophysiological properties similar to the other Omp85 family members, particularly to the one designated Toc75V/Oep80...
May 14, 2018: Plant Biology
https://www.readbyqxmd.com/read/29757649/functional-annotation-of-proteins-encoded-by-the-minimal-bacterial-genome-based-on-secondary-structure-element-alignment
#13
Zhiyuan Yang, Stephen Kwok-Wing Tsui
In synthetic biology, one of key focuses is building a minimal artificial cell which can provide basic chassis for functional study. Recently, the J. Craig Venter Institute published the latest version of the minimal bacterial genome JCVI-syn3.0, which only encoded 438 essential proteins. However, among them functions of 149 proteins remain unknown because of the lack of effective annotation method. Here, we report a secondary structure element alignment method called SSEalign based on an effective training dataset extracting from various bacterial genomes...
May 14, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29755805/analysis-of-bacterial-diversity-in-different-heavy-oil-wells-of-a-reservoir-in-south-oman-with-alkaline-ph
#14
Biji Shibulal, Saif N Al-Bahry, Yahya M Al-Wahaibi, Abdulkadir E Elshafie, Ali S Al-Bemani, Sanket J Joshi
The identification of potential hydrocarbon utilizing bacteria is an essential requirement in microbial enhanced oil recovery (MEOR). Molecular approaches like proteomic and genomic characterization of the isolates are replacing the traditional method of identification with systemic classification. Genotypic profiling of the isolates includes fingerprint or pattern-based technique and sequence-based technique. Understanding community structure and dynamics is essential for studying diversity profiles and is challenging in the case of microbial analysis...
2018: Scientifica
https://www.readbyqxmd.com/read/29755426/comparative-genomics-and-mutational-analysis-reveals-a-novel-xoxf-utilizing-methylotroph-in-the-roseobacter-group-isolated-from-the-marine-environment
#15
Alexandra M Howat, John Vollmers, Martin Taubert, Carolina Grob, Joanna L Dixon, Jonathan D Todd, Yin Chen, Anne-Kristin Kaster, J C Murrell
The Roseobacter group comprises a significant group of marine bacteria which are involved in global carbon and sulfur cycles. Some members are methylotrophs, using one-carbon compounds as a carbon and energy source. It has recently been shown that methylotrophs generally require a rare earth element when using the methanol dehydrogenase enzyme XoxF for growth on methanol. Addition of lanthanum to methanol enrichments of coastal seawater facilitated the isolation of a novel methylotroph in the Roseobacter group: Marinibacterium anthonyi strain La 6...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29748556/regulatory-protein-srpa-controls-phage-infection-and-core-cellular-processes-in-pseudomonas-aeruginosa
#16
Jiajia You, Li Sun, Xiaojing Yang, Xuewei Pan, Zhiwei Huang, Xixi Zhang, Mengxin Gong, Zheng Fan, Lingyan Li, Xiaoli Cui, Zhaoyuan Jing, Shouguang Jin, Zhiming Rao, Weihui Wu, Hongjiang Yang
Our understanding of the molecular mechanisms behind bacteria-phage interactions remains limited. Here we report that a small protein, SrpA, controls core cellular processes in response to phage infection and environmental signals in Pseudomonas aeruginosa. We show that SrpA is essential for efficient genome replication of phage K5, and controls transcription by binding to a palindromic sequence upstream of the phage RNA polymerase gene. We identify potential SrpA-binding sites in 66 promoter regions across the P...
May 10, 2018: Nature Communications
https://www.readbyqxmd.com/read/29747692/low-abundant-bacteria-drive-compositional-changes-in-the-gut-microbiota-after-dietary-alteration
#17
Jacquelynn Benjamino, Stephen Lincoln, Ranjan Srivastava, Joerg Graf
BACKGROUND: As the importance of beneficial bacteria is better recognized, understanding the dynamics of symbioses becomes increasingly crucial. In many gut symbioses, it is essential to understand whether changes in host diet play a role in the persistence of the bacterial gut community. In this study, termites were fed six dietary sources and the microbial community was monitored over a 49-day period using 16S rRNA gene sequencing. A deep backpropagation artificial neural network (ANN) was used to learn how the six different lignocellulose food sources affected the temporal composition of the hindgut microbiota of the termite as well as taxon-taxon and taxon-substrate interactions...
May 10, 2018: Microbiome
https://www.readbyqxmd.com/read/29739247/glucuronoyl-esterases-diversity-properties-and-biotechnological-potential-a-review
#18
Rune Nygaard Monrad, Jens Eklöf, Kristian B R M Krogh, Peter Biely
Glucuronoyl esterases (GEs) belonging to the carbohydrate esterase family 15 (CE15) are involved in microbial degradation of lignocellulosic plant materials. GEs are capable of degrading complex polymers of lignin and hemicellulose cleaving ester bonds between glucuronic acid residues in xylan and lignin alcohols. GEs promote separation of lignin, hemicellulose and cellulose which is crucial for efficient utilization of biomass as an energy source and feedstock for further processing into products or chemicals...
May 8, 2018: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/29738683/argonaute-proteins-and-mechanisms-of-rna-interference-in-eukaryotes-and-prokaryotes
#19
REVIEW
A V Olina, A V Kulbachinskiy, A A Aravin, D M Esyunina
Noncoding RNAs play essential roles in genetic regulation in all organisms. In eukaryotic cells, many small noncoding RNAs act in complex with Argonaute proteins and regulate gene expression by recognizing complementary RNA targets. The complexes of Argonaute proteins with small RNAs also play a key role in silencing of mobile genetic elements and, in some cases, viruses. These processes are collectively called RNA interference. RNA interference is a powerful tool for specific gene silencing in both basic research and therapeutic applications...
May 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29736608/transcriptome-remodeling-of-pseudomonas-putida-kt2440-during-mcl-phas-synthesis-effect-of-different-carbon-sources-and-response-to-nitrogen-stress
#20
Justyna Mozejko-Ciesielska, Tomasz Pokoj, Slawomir Ciesielski
Bacterial response to environmental stimuli is essential for survival. In response to fluctuating environmental conditions, the physiological status of bacteria can change due to the actions of transcriptional regulatory machinery. The synthesis and accumulation of polyhydroxyalkanoates (PHAs) are one of the survival strategies in harsh environments. In this study, we used transcriptome analysis of Pseudomonas putida KT2440 to gain a genome-wide view of the mechanisms of environmental-friendly biopolymers accumulation under nitrogen-limiting conditions during conversion of metabolically different carbon sources (sodium gluconate and oleic acid)...
May 7, 2018: Journal of Industrial Microbiology & Biotechnology
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