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https://www.readbyqxmd.com/read/29337088/cross-regulatory-network-in-pseudomonas-aeruginosa-biofilm-genes-and-tio2-anatase-induced-molecular-perturbations-in-key-proteins-unraveled-by-a-systems-biology-approach
#1
Rani Anupama, S Sajitha Lulu, Amitava Mukherjee, Subramanian Babu
A systems biology approach was used to study all the biofilm related genes of P. aeruginosa PAO1, and the interaction of titanium dioxide (TiO2) anatase with biofilm related proteins. Among the 71 genes, the interactions of all the nodal pairs were extracted by STRING 10.5 database. The inter-relationship among these genes was predicted by constructing complete PPI network and visualized in Cytoscape v 3.4.0. Total number of nodes of the network was found to be 335 and edges were 795. The network was further investigated for its clusters and the best cluster was further analyzed for the hub proteins which significantly contribute in cross-regulation of the biofilm related process...
January 11, 2018: Gene
https://www.readbyqxmd.com/read/29244728/transcriptome-analysis-of-paraburkholderia-phymatum-under-nitrogen-starvation-and-during-symbiosis-with-phaseolus-vulgaris
#2
Martina Lardi, Yilei Liu, Gabriela Purtschert, Samanta Bolzan de Campos, Gabriella Pessi
Paraburkholderia phymatum belongs to the β-subclass of proteobacteria. It has recently been shown to be able to nodulate and fix nitrogen in symbiosis with several mimosoid and papilionoid legumes. In contrast to the symbiosis of legumes with α-proteobacteria, very little is known about the molecular determinants underlying the successful establishment of this mutualistic relationship with β-proteobacteria. In this study, we performed an RNA-sequencing (RNA-seq) analysis of free-living P. phymatum growing under nitrogen-replete and -limited conditions, the latter partially mimicking the situation in nitrogen-deprived soils...
December 15, 2017: Genes
https://www.readbyqxmd.com/read/29177086/broad-scale-redistribution-of-mrna-abundance-and-transcriptional-machinery-in-response-to-growth-rate-in-salmonella-enterica-serovar-typhimurium
#3
Andrew D S Cameron, Shane C Dillon, Carsten Kröger, Laurens Beran, Charles J Dorman
We have investigated the connection between the four-dimensional architecture of the bacterial nucleoid and the organism's global gene expression programme. By localizing the transcription machinery and the transcriptional outputs across the genome of the model bacterium Salmonella enterica serovar Typhimurium at different stages of the growth cycle, a surprising disconnection between gene dosage and transcriptional output was revealed. During exponential growth, gene output occurred chiefly in the Ori (origin), Ter (terminus) and NSL (non-structured left) domains, whereas the Left macrodomain remained transcriptionally quiescent at all stages of growth...
October 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29091182/quinolone-resistant-gyrase-mutants-demonstrate-decreased-susceptibility-to-triclosan
#4
Mark A Webber, Michelle M C Buckner, Liam S Redgrave, Gyles Ifill, Lesley A Mitchenall, Carly Webb, Robyn Iddles, Anthony Maxwell, Laura J V Piddock
Objectives: Cross-resistance between antibiotics and biocides is a potentially important driver of MDR. A relationship between susceptibility of Salmonella to quinolones and triclosan has been observed. This study aimed to: (i) investigate the mechanism underpinning this; (ii) determine whether the phenotype is conserved in Escherichia coli; and (iii) evaluate the potential for triclosan to select for quinolone resistance. Methods: WT E. coli, Salmonella enterica serovar Typhimurium and gyrA mutants were used...
October 1, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29067482/sigma-factor-rpon-employs-a-dual-transcriptional-regulation-for-controlling-twitching-motility-and-biofilm-formation-in-lysobacter-enzymogenes-oh11
#5
Sen Han, Danyu Shen, Yun Zhao, Dan Xu, Jing Liu, Shan-Ho Chou, Fengquan Liu, Guoliang Qian
Lysobacter is a Gram-negative genus comprising a group of environmental bacteria with abilities to produce abundant novel antibiotics, as well as adopting a unique type IV pilus (T4P)-mediated twitching motility (TM) that remains poorly understood. Here, we employ L. enzymogenes OH11 exhibiting significant antifungal activity as a working model to address this issue. Via mutating the 28 potential sigma factors in strain OH11, we have identified one protein RpoNOH11 (sigma 54) that is indispensable for T4P formation and TM...
October 24, 2017: Current Genetics
https://www.readbyqxmd.com/read/29033900/weak-organic-acids-decrease-borrelia-burgdorferi-cytoplasmic-ph-eliciting-an-acid-stress-response-and-impacting-rpon-and-rpos-dependent-gene-expression
#6
Daniel P Dulebohn, Crystal L Richards, Hua Su, Kevin A Lawrence, Frank C Gherardini
The spirochete Borrelia burgdorferi survives in its tick vector, Ixodes scapularis, or within various hosts. To transition between and survive in these distinct niches, B. burgdorferi changes its gene expression in response to environmental cues, both biochemical and physiological. Exposure of B. burgdorferi to weak monocarboxylic organic acids, including those detected in the blood meal of fed ticks, decreased the cytoplasmic pH of B. burgdorferi in vitro. A decrease in the cytoplasmic pH induced the expression of genes encoding enzymes that have been shown to restore pH homeostasis in other bacteria...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29018429/d-ribose-interferes-with-quorum-sensing-to-inhibit-biofilm-formation-of-lactobacillus-paraplantarum-l-zs9
#7
Lei Liu, Ruiyun Wu, Jinlan Zhang, Nan Shang, Pinglan Li
Biofilms help bacteria survive under adverse conditions, and the quorum sensing (QS) system plays an important role in regulating their activities. Quorum sensing inhibitors (QSIs) have great potential to inhibit pathogenic biofilm formation and are considered possible replacements for antibiotics; however, further investigation is required to understand the mechanisms of action of QSIs and to avoid inhibitory effects on beneficial bacteria. Lactobacillus paraplantarum L-ZS9, isolated from fermented sausage, is a bacteriocin-producing bacteria that shows potential to be a probiotic starter...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28974743/targeting-the-alternative-sigma-factor-rpon-to-combat-virulence-in-pseudomonas-aeruginosa
#8
Megan G Lloyd, Benjamin R Lundgren, Clayton W Hall, Luke B-P Gagnon, Thien-Fah Mah, Jennifer F Moffat, Christopher T Nomura
Pseudomonas aeruginosa is a Gram-negative, opportunistic pathogen that infects immunocompromised and cystic fibrosis patients. Treatment is difficult due to antibiotic resistance, and new antimicrobials are needed to treat infections. The alternative sigma factor 54 (σ(54), RpoN), regulates many virulence-associated genes. Thus, we evaluated inhibition of virulence in P. aeruginosa by a designed peptide (RpoN molecular roadblock, RpoN*) which binds specifically to RpoN consensus promoters. We expected that RpoN* binding to its consensus promoter sites would repress gene expression and thus virulence by blocking RpoN and/or other transcription factors...
October 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28968917/fleq-regulates-both-the-type-vi-secretion-system-and-flagella-in-pseudomonas-putida
#9
Yuzhou Wang, Ye Li, Jianli Wang, Xiaoyuan Wang
Based on the analysis of sodium dodecyl sulfate-polyacrylamide gel electrophoresis and mass spectrometry, flagellin FliC and a key member of the type VI secretion system Hcp1 were found to be secreted from Pseudomonas putida KT2442 cells in the late exponential phase, but in the early exponential phase only FliC was secreted. Relevant genes fleQ and rpoN were then individually deleted in P. putida KT2442, and the expression and transcription of fliC and hcp1 in these mutant strains were analyzed. In both △fleQ and △rpoN mutant cells, Hcp1 but not FliC was secreted in the late exponential phase, and it was secreted even in the early exponential phase...
October 2, 2017: Biotechnology and Applied Biochemistry
https://www.readbyqxmd.com/read/28924127/recurrent-painful-ophthalmoplegic-neuropathy-with-residual-mydriasis-in-an-adult-should-it-be-classified-as-ophthalmoplegic-migraine
#10
Yuya Kobayashi, Yasufumi Kondo, Kana Uchibori, Jun Tsuyuzaki
Recurrent painful ophthalmoplegic neuropathy (RPON) is a rare condition that manifests as headache and ophthalmoplegia. It typically occurs in children. Although migraine or neuropathy have been suggested as etiologies, the precise etiology remains unclear. In the International Classification of Headache Disorders 3rd edition-beta version (ICHD3β) (code 13.9), RPON was categorized into painful cranial neuropathies and other facial pains. We encountered a 48-year-old woman who had diplopia and right ptosis...
October 15, 2017: Internal Medicine
https://www.readbyqxmd.com/read/28635589/regulation-of-escherichia-coli-pathogenesis-by-alternative-sigma-factor-n
#11
James T Riordan, Avishek Mitra
σ(N) (also σ(54)) is an alternative sigma factor subunit of the RNA polymerase complex that regulates the expression of genes from many different ontological groups. It is broadly conserved in the Eubacteria with major roles in nitrogen metabolism, membrane biogenesis, and motility. σ(N) is encoded as the first gene of a five-gene operon including rpoN (σ(N)), ptsN, hpf, rapZ, and npr that has been genetically retained among species of Escherichia, Shigella, and Salmonella. In an increasing number of bacteria, σ(N) has been implicated in the control of genes essential to pathogenic behavior, including those involved in adherence, secretion, immune subversion, biofilm formation, toxin production, and resistance to both antimicrobials and biological stressors...
June 2017: EcoSal Plus
https://www.readbyqxmd.com/read/28553272/rpon-promotes-pseudomonas-aeruginosa-survival-in-the-presence-of-tobramycin
#12
Darija Viducic, Keiji Murakami, Takashi Amoh, Tsuneko Ono, Yoichiro Miyake
Pseudomonas aeruginosa has developed diverse strategies to respond and adapt to antibiotic stress. Among the factors that modulate survival in the presence of antibiotics, alternative sigma factors play an important role. Here, we demonstrate that the alternative sigma factor RpoN (σ(54)) promotes survival in the presence of tobramycin. The tobramycin-sensitive phenotype of logarithmic phase ΔrpoN mutant cells is suppressed by the loss of the alternative sigma factor RpoS. Transcriptional analysis indicated that RpoN positively regulates the expression of RsmA, an RNA-binding protein, in the P...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28500044/rpon-%C3%AF-54-is-required-for-floc-formation-but-not-for-extracellular-polysaccharide-biosynthesis-in-a-floc-forming-aquincola-tertiaricarbonis-strain
#13
Dianzhen Yu, Ming Xia, Liping Zhang, Yulong Song, You Duan, Tong Yuan, Minjie Yao, Liyou Wu, Chunyuan Tian, Zhenbin Wu, Xiangzhen Li, Jizhong Zhou, Dongru Qiu
Some bacteria are capable of forming flocs, in which bacterial cells become self-flocculated by secreted extracellular polysaccharides and other biopolymers. The floc-forming bacteria play a central role in activated sludge, which has been widely utilized for the treatment of municipal sewage and industrial wastewater. Here, we use a floc-forming bacterium, Aquincolatertiaricarbonis RN12, as a model to explore the biosynthesis of extracellular polysaccharides and the regulation of floc formation. A large gene cluster for exopolysaccharide biosynthesis and a gene encoding the alternative sigma factor RpoN1, one of the four paralogues, have been identified in floc formation-deficient mutants generated by transposon mutagenesis, and the gene functions have been further confirmed by genetic complementation analyses...
July 15, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28497290/medium-chain-length-polyhydroxyalkanoates-synthesis-by-pseudomonas-putida-kt2440-rela-spot-mutant-bioprocess-characterization-and-transcriptome-analysis
#14
Justyna Mozejko-Ciesielska, Dorota Dabrowska, Agnieszka Szalewska-Palasz, Slawomir Ciesielski
Pseudomonas putida KT2440 is a model bacteria used commonly for medium-chain-length polyhydroxyalkanoates (mcl-PHAs) production using various substrates. However, despite many studies conducted on P. putida KT2440 strain, the molecular mechanisms of leading to mcl-PHAs synthesis in reaction to environmental stimuli are still not clear. The rearrangement of the metabolism in response to environmental stress could be controlled by stringent response that modulates the transcription of many genes in order to promote survival under nutritional deprivation conditions...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28473604/recurrent-painful-ophthalmoplegic-neuropathy
#15
Cleo Huang, Maria Amasanti, Ben Lovell, Tim Young
Recurrent painful ophthalmologic neuropathy (RPON), previously termed ophthalmoplegic migraine, is characterised by repeated attacks of one or more ocular cranial nerve palsies with ipsilateral headache. Its cause remains unclear; it is currently thought to be neuropathic in origin, but there is debate in the literature. In documented cases, a third cranial nerve palsy is by far the most common. Here we present a case of RPON involveing the fourth and sixth cranial nervesonly. Thorough investigation, including MR scan of brain and lumbar puncture, found no alternative explanation...
August 2017: Practical Neurology
https://www.readbyqxmd.com/read/28439037/regulation-of-a-glycerol-induced-quinoprotein-alcohol-dehydrogenase-by-%C3%AF-54-and-a-luxr-type-regulator-in-azospirillum-brasilense-sp7
#16
Vijay Shankar Singh, Ashutosh Prakash Dubey, Ankush Gupta, Sudhir Singh, Bhupendra Narain Singh, Anil Kumar Tripathi
Azospirillum brasilense Sp7 uses glycerol as a carbon source for growth and nitrogen fixation. When grown in medium containing glycerol as a source of carbon, it upregulates the expression of a protein which was identified as quinoprotein alcohol dehydrogenase (ExaA). Inactivation of exaA adversely affects the growth of A. brasilense on glycerol. A determination of the transcription start site of exaA revealed an RpoN-dependent -12/-24 promoter consensus. The expression of an exaA::lacZ fusion was induced maximally by glycerol and was dependent on σ(54) Bioinformatic analysis of the sequence flanking the -12/-24 promoter revealed a 17-bp sequence motif with a dyad symmetry of 6 nucleotides upstream of the promoter, the disruption of which caused a drastic reduction in promoter activity...
July 1, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28419759/regulation-of-burkholderia%C3%A2-cenocepacia-biofilm-formation-by-rpon-and-the-c-di-gmp-effector-berb
#17
Mustafa Fazli, Morten Rybtke, Elisabeth Steiner, Elisabeth Weidel, Jens Berthelsen, Julie Groizeleau, Wu Bin, Boo Zhao Zhi, Zhang Yaming, Volkhard Kaever, Michael Givskov, Rolf W Hartmann, Leo Eberl, Tim Tolker-Nielsen
Knowledge about the molecular mechanisms that are involved in the regulation of biofilm formation is essential for the development of biofilm-control measures. It is well established that the nucleotide second messenger cyclic diguanosine monophosphate (c-di-GMP) is a positive regulator of biofilm formation in many bacteria, but more knowledge about c-di-GMP effectors is needed. We provide evidence that c-di-GMP, the alternative sigma factor RpoN (σ54), and the enhancer-binding protein BerB play a role in biofilm formation of Burkholderia cenocepacia by regulating the production of a biofilm-stabilizing exopolysaccharide...
August 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28412516/switching-between-nitrogen-and-glucose-limitation-unraveling-transcriptional-dynamics-in-escherichia-coli
#18
Michael Löffler, Joana Danica Simen, Jan Müller, Günter Jäger, Salaheddine Laghrami, Karin Schäferhoff, Andreas Freund, Ralf Takors
Transcriptional control under nitrogen and carbon-limitation conditions have been well analyzed for Escherichia coli. However, the transcriptional dynamics that underlie the shift in regulatory programs from nitrogen to carbon limitation is not well studied. In the present study, cells were cultivated at steady state under nitrogen (ammonia)-limited conditions then shifted to carbon (glucose) limitation to monitor changes in transcriptional dynamics. Nitrogen limitation was found to be dominated by sigma 54 (RpoN) and sigma 38 (RpoS), whereas the "housekeeping" sigma factor 70 (RpoD) and sigma 38 regulate cellular status under glucose limitation...
April 13, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28400753/the-helicobacter-pylori-j99-jhp0106-gene-under-the-control-of-the-csra-rpon-regulatory-system-modulates-flagella-formation-and-motility
#19
Cheng-Yen Kao, Jenn-Wei Chen, Shuying Wang, Bor-Shyang Sheu, Jiunn-Jong Wu
CsrA has been shown to positively control the expression of flagella-related genes, including flaA and flaB, through regulating expression of an alternative sigma factor RpoN in Helicobacter pylori J99. Here, we aimed to characterize the CsrA regulatory system by comparative transcriptomic analysis carried out with RNA-seq on strain J99 and a csrA mutant. Fifty-three genes in the csrA mutant were found to be differentially expressed compared with the wild-type. Among CsrA-regulated genes, jhp0106, with unclear function, was found located downstream of flaB in the J99 genome...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28373272/novel-dna-binding-and-regulatory-activities-for-%C3%AF-54-rpon-in-salmonella-enterica-serovar-typhimurium-14028s
#20
Ashley C Bono, Christine E Hartman, Sina Solaimanpour, Hao Tong, Steffen Porwollik, Michael McClelland, Jonathan G Frye, Jan Mrázek, Anna C Karls
The variable sigma (σ) subunit of the bacterial RNA polymerase (RNAP) holoenzyme, which is responsible for promoter specificity and open complex formation, plays a strategic role in the response to environmental changes. Salmonella enterica serovar Typhimurium utilizes the housekeeping σ(70) and five alternative sigma factors, including σ(54) The σ(54)-RNAP differs from other σ-RNAP holoenzymes in that it forms a stable closed complex with the promoter and requires ATP hydrolysis by an activated cognate bacterial enhancer binding protein (bEBP) to transition to an open complex and initiate transcription...
June 15, 2017: Journal of Bacteriology
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