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https://www.readbyqxmd.com/read/29614781/exploiting-a-phage-bacterium-interaction-system-as-a-molecular-switch-to-decipher-macromolecular-interactions-in-the-living-cell
#1
Éva Viola Surányi, Rita Hírmondó, Kinga Nyíri, Szilvia Tarjányi, Bianka Kőhegyi, Judit Tóth, Beáta G Vértessy
Pathogenicity islands of Staphylococcus aureus are under the strong control of helper phages, where regulation is communicated at the gene expression level via a family of specific repressor proteins. The repressor proteins are crucial to phage-host interactions and, based on their protein characteristics, may also be exploited as versatile molecular tools. The Stl repressor from this protein family has been recently investigated and although the binding site of Stl on DNA was recently discovered, there is a lack of knowledge on the specific protein segments involved in this interaction...
April 1, 2018: Viruses
https://www.readbyqxmd.com/read/29529243/single-target-regulators-form-a-minor-group-of-transcription-factors-in-escherichia-coli-k-12
#2
Tomohiro Shimada, Hiroshi Ogasawara, Akira Ishihama
The identification of regulatory targets of all TFs is critical for understanding the entire network of the genome regulation. The lac regulon of Escherichia coli K-12 W3110 is composed of the lacZYA operon and its repressor lacI gene, and has long been recognized as the seminal model of transcription regulation in bacteria with only one highly preferred target. After the Genomic SELEX screening in vitro of more than 200 transcription factors (TFs) from E. coli K-12, however, we found that most TFs regulate multiple target genes...
February 26, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29529037/relatively-slow-stochastic-gene-state-switching-in-the-presence-of-positive-feedback-significantly-broadens-the-region-of-bimodality-through-stabilizing-the-uninduced-phenotypic-state
#3
Hao Ge, Pingping Wu, Hong Qian, Sunney Xiaoliang Xie
Within an isogenic population, even in the same extracellular environment, individual cells can exhibit various phenotypic states. The exact role of stochastic gene-state switching regulating the transition among these phenotypic states in a single cell is not fully understood, especially in the presence of positive feedback. Recent high-precision single-cell measurements showed that, at least in bacteria, switching in gene states is slow relative to the typical rates of active transcription and translation...
March 12, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29453395/the-genes-of-the-sulphoquinovose-catabolism-in-escherichia-coli-are-also-associated-with-a-previously-unknown-pathway-of-lactose-degradation
#4
Anna Kaznadzey, Pavel Shelyakin, Evgeniya Belousova, Aleksandra Eremina, Uliana Shvyreva, Darya Bykova, Vera Emelianenko, Anastasiya Korosteleva, Maria Tutukina, Mikhail S Gelfand
Comparative genomics analysis of conserved gene cassettes demonstrated resemblance between a recently described cassette of genes involved in sulphoquinovose degradation in Escherichia coli K-12 MG1655 and a Bacilli cassette linked with lactose degradation. Six genes from both cassettes had similar functions related to carbohydrate metabolism, namely, hydrolase, aldolase, kinase, isomerase, transporter, and transcription factor. The Escherichia coli sulphoglycolysis cassette was thus predicted to be associated with lactose degradation...
February 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29335877/development-of-cyclic-amp-receptor-protein-based-artificial-transcription-factor-for-intensifying-gene-expression
#5
Peng Zhao, Wenjuan Wang, Pingfang Tian
Vector-dependent gene overexpression typically relies on an efficient operon and sufficient RNA polymerases (RNAPs). The lac (lactose) operon is a paradigm of transcription control, and cyclic AMP receptor protein (CRP) is a global regulator capable of recruiting RNAPs. However, the gap between lac operon and CRP has not been well bridged. In this work, CRP was fused to lac repressor protein (lacI) to form an artificial transcription factor (ATF) with the expectation that when LacI acted on the lacO-positioned upstream of gene of interest, the LacI-tethered CRP would trap RNAPs and thus improve the expression of PuuC, an aldehyde dehydrogenase catalyzing 3-hydroxypropionaldehyde (3-HPA) to 3-hydroxypropionic acid (3-HP) in Klebsiella pneumoniae...
February 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29335514/monitoring-single-cell-gene-regulation-under-dynamically-controllable-conditions-with-integrated-microfluidics-and-software
#6
Matthias Kaiser, Florian Jug, Thomas Julou, Siddharth Deshpande, Thomas Pfohl, Olin K Silander, Gene Myers, Erik van Nimwegen
Much is still not understood about how gene regulatory interactions control cell fate decisions in single cells, in part due to the difficulty of directly observing gene regulatory processes in vivo. We introduce here a novel integrated setup consisting of a microfluidic chip and accompanying analysis software that enable long-term quantitative tracking of growth and gene expression in single cells. The dual-input Mother Machine (DIMM) chip enables controlled and continuous variation of external conditions, allowing direct observation of gene regulatory responses to changing conditions in single cells...
January 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29166860/msaabcr-operon-is-involved-in-persister-cell-formation-in-staphylococcus-aureus
#7
Gyan S Sahukhal, Shanti Pandey, Mohamed O Elasri
BACKGROUND: Persister cells comprise a phenotypic variant that shows extreme antibiotic tolerance resulting in treatment failures of bacterial infections. While this phenomenon has posed a great threat in public health, mechanisms underlying their formation in Staphylococcus aureus remain largely unknown. Increasing evidences of the presence of persister cells in recalcitrant infections underscores the great urgency to unravel the mechanism by which these cells develop. Previously, we characterized msaABCR operon that plays roles in regulation of virulence, biofilm development and antibiotic resistance...
November 22, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28686609/self-consistent-theory-of-transcriptional-control-in-complex-regulatory-architectures
#8
Jasper Landman, Robert C Brewster, Franz M Weinert, Rob Phillips, Willem K Kegel
Individual regulatory proteins are typically charged with the simultaneous regulation of a battery of different genes. As a result, when one of these proteins is limiting, competitive effects have a significant impact on the transcriptional response of the regulated genes. Here we present a general framework for the analysis of any generic regulatory architecture that accounts for the competitive effects of the regulatory environment by isolating these effects into an effective concentration parameter. These predictions are formulated using the grand-canonical ensemble of statistical mechanics and the fold-change in gene expression is predicted as a function of the number of transcription factors, the strength of interactions between the transcription factors and their DNA binding sites, and the effective concentration of the transcription factor...
2017: PloS One
https://www.readbyqxmd.com/read/28683812/mechano-growth-factor-a-splice-variant-of-igf-1-promotes-neurogenesis-in-the-aging-mouse-brain
#9
Jason J Tang, Jewel L Podratz, Miranda Lange, Heidi J Scrable, Mi-Hyeon Jang, Anthony J Windebank
Mechano growth factor (MGF) is a splice variant of IGF-1 first described in skeletal muscle. MGF induces muscle cell proliferation in response to muscle stress and injury. In control mice we found endogenous expression of MGF in neurogenic areas of the brain and these levels declined with age. To better understand the role of MGF in the brain, we used transgenic mice that constitutively overexpressed MGF from birth. MGF overexpression significantly increased the number of BrdU+ proliferative cells in the dentate gyrus (DG) of the hippocampus and subventricular zone (SVG)...
July 7, 2017: Molecular Brain
https://www.readbyqxmd.com/read/28651524/insights-into-the-geobacillus-stearothermophilus-species-based-on-phylogenomic-principles
#10
COMPARATIVE STUDY
S A Burgess, S H Flint, D Lindsay, M P Cox, P J Biggs
BACKGROUND: The genus Geobacillus comprises bacteria that are Gram positive, thermophilic spore-formers, which are found in a variety of environments from hot-springs, cool soils, to food manufacturing plants, including dairy manufacturing plants. Despite considerable interest in the use of Geobacillus spp. for biotechnological applications, the taxonomy of this genus is unclear, in part because of differences in DNA-DNA hybridization (DDH) similarity values between studies. In addition, it is also difficult to use phenotypic characteristics to define a bacterial species...
June 26, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28639170/bistability-and-asynchrony-in-a-boolean-model-of-the-l-arabinose-operon-in-escherichia-coli
#11
Andy Jenkins, Matthew Macauley
The lactose operon in Escherichia coli was the first known gene regulatory network, and it is frequently used as a prototype for new modeling paradigms. Historically, many of these modeling frameworks use differential equations. More recently, Stigler and Veliz-Cuba proposed a Boolean model that captures the bistability of the system and all of the biological steady states. In this paper, we model the well-known arabinose operon in E. coli with a Boolean network. This has several complex features not found in the lac operon, such as a protein that is both an activator and repressor, a DNA looping mechanism for gene repression, and the lack of inducer exclusion by glucose...
June 21, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28494968/bistability-and-nonmonotonic-induction-of-the-lac-operon-in-the-natural-lactose-uptake-system
#12
Dominique Zander, Daniel Samaga, Ronny Straube, Katja Bettenbrock
The Escherichia coli lac operon is regulated by a positive feedback loop whose potential to generate an all-or-none response in single cells has been a paradigm for bistable gene expression. However, so far bistable lac induction has only been observed using gratuitous inducers, raising the question about the biological relevance of bistable lac induction in the natural setting with lactose as the inducer. In fact, the existing experimental evidence points to a graded rather than an all-or-none response in the natural lactose uptake system...
May 9, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28463205/aggregation-for-computing-multi-modal-stationary-distributions-in-1-d-gene-regulatory-networks
#13
Neslihan Avcu, Nihal Pekergin, Ferhan Pekergin, Cuneyt Guzelis
This paper proposes aggregation-based, three-stage algorithms to overcome the numerical problems encountered in computing stationary distributions and mean first passage times for multi-modal birth-death processes of large state space sizes. The considered birth-death processes which are defined by Chemical Master Equations are used in modeling stochastic behavior of gene regulatory networks. Computing stationary probabilities for a multi-modal distribution from Chemical Master Equations is subject to have numerical problems due to the probability values running out of the representation range of the standard programming languages with the increasing size of the state space...
April 27, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28463103/a-conserved-hexanucleotide-motif-is-important-in-uv-inducible-promoters-in-sulfolobus-acidocaldarius
#14
Thuong Ngoc Le, Alexander Wagner, Sonja-Verena Albers
Upon DNA damage, Sulfolobales exhibit a global gene regulatory response resulting in the expression of DNA transfer and repair proteins and the repression of the cell division machinery. Because the archaeal DNA damage response is still poorly understood, we investigated the promoters of the highly induced ups operon. Ups pili are involved in cellular aggregation and DNA exchange between cells. With LacS reporter gene assays we identified a conserved, non-palindromic hexanucleotide motif upstream of the ups core promoter elements to be essential for promoter activity...
May 2017: Microbiology
https://www.readbyqxmd.com/read/28387245/design-and-application-of-a-lactulose-biosensor
#15
Jieyuan Wu, Peixia Jiang, Wei Chen, Dandan Xiong, Linglan Huang, Junying Jia, Yuanyuan Chen, Jian-Ming Jin, Shuang-Yan Tang
In this study the repressor of Escherichia coli lac operon, LacI, has been engineered for altered effector specificity. A LacI saturation mutagenesis library was subjected to Fluorescence Activated Cell Sorting (FACS) dual screening. Mutant LacI-L5 was selected and it is specifically induced by lactulose but not by other disaccharides tested (lactose, epilactose, maltose, sucrose, cellobiose and melibiose). LacI-L5 has been successfully used to construct a whole-cell lactulose biosensor which was then applied in directed evolution of cellobiose 2-epimerase (C2E) for elevated lactulose production...
April 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28382022/occlusion-of-the-ribosome-binding-site-connects-the-translational-initiation-frequency-mrna-stability-and-premature-transcription-termination
#16
Mette Eriksen, Kim Sneppen, Steen Pedersen, Namiko Mitarai
Protein production is controlled by ribosome binding to the messenger RNA (mRNA), quantified in part by the binding affinity between the ribosome and the ribosome binding sequence on the mRNA. Using the E. coli lac operon as model, Ringquist et al. (1992) found a more than 1,000-fold difference in protein yield when varying the Shine-Dalgarno sequence and its distance to the translation start site. Their proposed model accounted for this large variation by only a variation in the binding affinity and the subsequent initiation rate...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28193904/effector-overlap-between-the-lac-and-mel-operons-of-escherichia-coli-induction-of-the-mel-operon-with-%C3%AE-galactosides
#17
Atul Narang, Stefan Oehler
The lac (lactose) operon (which processes β-galactosides) and the mel (melibiose) operon (which processes α-galactosides) of Escherichia coli have a close historical connection. A number of shared substrates and effectors of the permeases and regulatory proteins have been reported over the years. Until now, β-thiogalactosides like TMG (methyl-β-d-thiogalactopyranoside) and IPTG (isopropyl-β-d-thiogalactopyranoside) have not generally been considered to be inducers of the mel operon. The same is true for β-galactosides such as lactose [β-d-galactopyranosyl-(1→4)-d-glucose], which is a substrate but is not itself an inducer of the lac operon...
May 1, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28113910/robust-reachability-of-boolean-control-networks
#18
Fangfei Li, Yang Tang
Boolean networks serve a powerful tool in analysis of genetic regulatory networks since it emphasizes the fundamental principles and establishes a nature framework for capturing the dynamics of regulation of cellular states. In this paper, the robust reachability of Boolean control networks is investigated by means of semi-tensor product. Necessary and sufficient conditions for the robust reachability of Boolean control networks are provided, in which control inputs relying on disturbances or not are considered, respectively...
May 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/27785540/construction-properties-and-application-of-the-pcb5-plasmid-a-novel-conjugative-shuttle-vector-with-a-cupriavidus-basilensis-origin-of-replication
#19
Sheng Wang, Mei-Nan Zhang, Na-Ling Bai, Hai-Tao Ding, Xu-Fen Zhu, Yu-Hua Zhao
Cupriavidus basilensis is a species with diverse metabolic capabilities, including degradation of xenobiotics and heavy metal resistance. Although the genomes of several strains of this species have been sequenced, no plasmid has yet been constructed for genetic engineering in this species. In this study, we identified a novel plasmid, designated pWS, from C. basilensis WS with a copy number of 1-3 per cell and a length of 2150 bp. pWS contained three protein-coding genes, among which only rep was required for plasmid replication...
February 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27783696/supercoiling-effects-on-short-range-dna-looping-in-e-coli
#20
Lauren S Mogil, Nicole A Becker, L James Maher
DNA-protein loops can be essential for gene regulation. The Escherichia coli lactose (lac) operon is controlled by DNA-protein loops that have been studied for decades. Here we adapt this model to test the hypothesis that negative superhelical strain facilitates the formation of short-range (6-8 DNA turns) repression loops in E. coli. The natural negative superhelicity of E. coli DNA is regulated by the interplay of gyrase and topoisomerase enzymes, adding or removing negative supercoils, respectively. Here, we measured quantitatively DNA looping in three different E...
2016: PloS One
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