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Trp operon

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https://www.readbyqxmd.com/read/27665603/exploring-alternative-rna-structure-sets-using-mc-flashfold-and-db2cm
#1
Paul Dallaire, François Major
We created an accelerated version of MC-Fold called MC-Flashfold that allows us to compute large numbers of competing secondary structures including noncanonical base pairs. We visualize the base pairs in these sets using high quality intuitive dot plots and arc plots. Our new tools allow us to explore RNA dynamics by visualizing the competing structures in free energy bands. Here we describe how to use these tools to generate dot plots that reveal the postulated anti-terminator stem in the E. coli trp operon leader sequence...
2016: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27531515/nonribosomal-peptide-synthetase-with-a-unique-iterative-alternative-optional-mechanism-catalyzes-amonabactin-synthesis-in-aeromonas
#2
Qassim Esmaeel, Mickael Chevalier, Gabrielle Chataigné, Rathinasamy Subashkumar, Philippe Jacques, Valérie Leclère
Based on the exploration of data generated by genome sequencing, a bioinformatics approach has been chosen to identify the biosynthetic pathway of the siderophores produced by Aeromonas species. The amonabactins, considered as a virulence factor, represent a family of four variants of catechol peptidic siderophores containing Dhb, Lys, Gly, and an aromatic residue either Trp or Phe in a D-configuration. The synthesis operon is constituted of seven genes named amoCEBFAGH and is iron-regulated. The cluster includes genes encoding proteins involved in the synthesis and incorporation of the Dhb monomer, and genes encoding specific nonribosomal peptide synthetases, which are responsible for the building of the peptidic moiety...
October 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27446814/was-the-chlamydial-adaptative-strategy-to-tryptophan-starvation-an-early-determinant-of-plastid-endosymbiosis
#3
Ugo Cenci, Mathieu Ducatez, Derifa Kadouche, Christophe Colleoni, Steven G Ball
Chlamydiales were recently proposed to have sheltered the future cyanobacterial ancestor of plastids in a common inclusion. The intracellular pathogens are thought to have donated those critical transporters that triggered the efflux of photosynthetic carbon and the consequent onset of symbiosis. Chlamydiales are also suspected to have encoded glycogen metabolism TTS (Type Three Secretion) effectors responsible for photosynthetic carbon assimilation in the eukaryotic cytosol. We now review the reasons underlying other chlamydial lateral gene transfers evidenced in the descendants of plastid endosymbiosis...
2016: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/27400720/tryptophan-codon-dependent-transcription-in-chlamydia-pneumoniae-during-gamma-interferon-mediated-tryptophan-limitation
#4
Scot P Ouellette, Kelsey J Rueden, Elizabeth A Rucks
In evolving to an obligate intracellular niche, Chlamydia has streamlined its genome by eliminating superfluous genes as it relies on the host cell for a variety of nutritional needs like amino acids. However, Chlamydia can experience amino acid starvation when the human host cell in which the bacteria reside is exposed to interferon gamma (IFN-γ), which leads to a tryptophan (Trp)-limiting environment via induction of the enzyme indoleamine-2,3-dioxygenase (IDO). The stringent response is used to respond to amino acid starvation in most bacteria but is missing from Chlamydia Thus, how Chlamydia, a Trp auxotroph, responds to Trp starvation in the absence of a stringent response is an intriguing question...
September 2016: Infection and Immunity
https://www.readbyqxmd.com/read/26882169/inter-protein-sequence-co-evolution-predicts-known-physical-interactions-in-bacterial-ribosomes-and-the-trp-operon
#5
Christoph Feinauer, Hendrik Szurmant, Martin Weigt, Andrea Pagnani
Interaction between proteins is a fundamental mechanism that underlies virtually all biological processes. Many important interactions are conserved across a large variety of species. The need to maintain interaction leads to a high degree of co-evolution between residues in the interface between partner proteins. The inference of protein-protein interaction networks from the rapidly growing sequence databases is one of the most formidable tasks in systems biology today. We propose here a novel approach based on the Direct-Coupling Analysis of the co-evolution between inter-protein residue pairs...
2016: PloS One
https://www.readbyqxmd.com/read/26456832/trp-and-rhodopsin-transport-depends-on-dual-xport-er-chaperones-encoded-by-an-operon
#6
Zijing Chen, Hsiang-Chin Chen, Craig Montell
TRP channels and G protein-coupled receptors (GPCRs) play critical roles in sensory reception. However, the identities of the chaperones that assist GPCRs in translocating from the endoplasmic reticulum (ER) are limited, and TRP ER chaperones are virtually unknown. The one exception for TRPs is Drosophila XPORT. Here, we show that the xport locus is bicistronic and encodes unrelated transmembrane proteins, which enable the signaling proteins that initiate and culminate phototransduction, rhodopsin 1 (Rh1) and TRP, to traffic to the plasma membrane...
October 20, 2015: Cell Reports
https://www.readbyqxmd.com/read/26390211/detoxification-of-indole-by-an-indole-induced-flavoprotein-oxygenase-from-acinetobacter-baumannii
#7
Guang-Huey Lin, Hao-Ping Chen, Hung-Yu Shu
Indole, a derivative of the amino acid tryptophan, is a toxic signaling molecule, which can inhibit bacterial growth. To overcome indole-induced toxicity, many bacteria have developed enzymatic defense systems to convert indole to non-toxic, water-insoluble indigo. We previously demonstrated that, like other aromatic compound-degrading bacteria, Acinetobacter baumannii can also convert indole to indigo. However, no work has been published investigating this mechanism. Here, we have shown that the growth of wild-type A...
2015: PloS One
https://www.readbyqxmd.com/read/25889351/a-novel-strategy-to-analyze-l-tryptophan-through-allosteric-trp-repressor-based-on-rolling-circle-amplification
#8
Guojie Zhao, Tianyu Hu, Jun Li, Hua Wei, Hong Shang, Yifu Guan
Rolling circle amplification (RCA) has been considered as a powerful tool for nucleic acids detection. Here, a novel repressor-RCA-based method for L-tryptophan (L-Trp) detection was developed. This method utilizes the specific interaction between the RCA circular template and the Trp repressor protein (TrpR) involved in trp operon of Escherichia coli (E. coli). In the absence of L-Trp, the TrpR protein could not bind to the RCA template, and the RCA process can be continued. When L-Trp is present, the activated TrpR will bind to the operon sequence on the RCA template and inhibit the RCA reaction...
September 15, 2015: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/25886995/distribution-in-microbial-genomes-of-genes-similar-to-loda-and-goxa-which-encode-a-novel-family-of-quinoproteins-with-amino-acid-oxidase-activity
#9
Jonatan C Campillo-Brocal, María Dolores Chacón-Verdú, Patricia Lucas-Elío, Antonio Sánchez-Amat
BACKGROUND: L-Amino acid oxidases (LAOs) have been generally described as flavoproteins that oxidize amino acids releasing the corresponding ketoacid, ammonium and hydrogen peroxide. The generation of hydrogen peroxide gives to these enzymes antimicrobial characteristics. They are involved in processes such as biofilm development and microbial competition. LAOs are of great biotechnological interest in different applications such as the design of biosensors, biotransformations and biomedicine...
2015: BMC Genomics
https://www.readbyqxmd.com/read/25811953/the-tyrr-transcription-factor-regulates-the-divergent-akr-ipdc-operons-of-enterobacter-cloacae-uw5
#10
Thomas J D Coulson, Cheryl L Patten
The TyrR transcription factor regulates genes involved in the uptake and biosynthesis of aromatic amino acids in Enterobacteriaceae. Genes may be positively or negatively regulated depending on the presence or absence of each aromatic amino acid, all three of which function as cofactors for TyrR. In this report we detail the transcriptional control of two divergently transcribed genes, akr and ipdC, by TyrR, elucidated by promoter fusion expression assays and electrophoretic mobility shift assays to assess protein-DNA interactions...
2015: PloS One
https://www.readbyqxmd.com/read/25779640/cloning-of-toluene-4-monooxygenase-genes-and-application-of-two-phase-system-to-the-production-of-the-anticancer-agent-indirubin
#11
Lampet Wongsaroj, Ratiboot Sallabhan, James M Dubbs, Skorn Mongkolsuk, Suvit Loprasert
Indirubin is a strong inhibitor of several eukaryotic cell signaling pathways and shows promise as a treatment for myelocytic leukemia and Alzheimer's disease. The tmoABCDEF operon, encoding the components of a novel toluene 4-monooxygenase from the paint factory soil isolate, Pseudomonas sp. M4, was cloned and expressed in Escherichia coli. E. coli::pKSR12 expressing the tmo genes was used to develop a two-phase [dioctyl phthalate (DOP)/aqueous medium] culture system that was optimized to obtain maximal yields of indirubin from the starting substrate, indole...
August 2015: Molecular Biotechnology
https://www.readbyqxmd.com/read/25751035/four-rna-families-with-functional-transient-structures
#12
Jing Yun A Zhu, Irmtraud M Meyer
Protein-coding and non-coding RNA transcripts perform a wide variety of cellular functions in diverse organisms. Several of their functional roles are expressed and modulated via RNA structure. A given transcript, however, can have more than a single functional RNA structure throughout its life, a fact which has been previously overlooked. Transient RNA structures, for example, are only present during specific time intervals and cellular conditions. We here introduce four RNA families with transient RNA structures that play distinct and diverse functional roles...
2015: RNA Biology
https://www.readbyqxmd.com/read/25695834/substrate-dependent-activation-of-the-vibrio-cholerae-vexab-rnd-efflux-system-requires-vexr
#13
Dawn L Taylor, Vanessa M Ante, X Renee Bina, Mondraya F Howard, James E Bina
Vibrio cholerae encodes six resistance-nodulation-division (RND) efflux systems which function in antimicrobial resistance, virulence factor production, and intestinal colonization. Among the six RND efflux systems, VexAB exhibited broad substrate specificity and played a predominant role in intrinsic antimicrobial resistance. The VexAB system was encoded in an apparent three gene operon that included vexR; which encodes an uncharacterized TetR family regulator. In this work we examined the role of vexR in vexRAB expression...
2015: PloS One
https://www.readbyqxmd.com/read/25616795/anthranilate-deteriorates-the-structure-of-pseudomonas-aeruginosa-biofilms-and-antagonizes-the-biofilm-enhancing-indole-effect
#14
Soo-Kyoung Kim, Ha-Young Park, Joon-Hee Lee
Anthranilate and indole are alternative degradation products of tryptophan, depending on the bacterial species. While indole enhances the biofilm formation of Pseudomonas aeruginosa, we found that anthranilate, the tryptophan degradation product of P. aeruginosa, had an opposite effect on P. aeruginosa biofilm formation, in which anthranilate deteriorated the mushroom structure of biofilm. The anthranilate effect on biofilm formation was differentially exerted depending on the developmental stage and the presence of shear force...
April 2015: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/25605763/global-analysis-of-posttranscriptional-regulation-by-glmy-and-glmz-in-enterohemorrhagic-escherichia-coli-o157-h7
#15
Charley C Gruber, Vanessa Sperandio
Enterohemorrhagic Escherichia coli (EHEC) is a significant human pathogen and is the cause of bloody diarrhea and hemolytic-uremic syndrome. The virulence repertoire of EHEC includes the genes within the locus of enterocyte effacement (LEE) that are largely organized in five operons, LEE1 to LEE5, which encode a type III secretion system, several effectors, chaperones, and regulatory proteins. In addition, EHEC also encodes several non-LEE-encoded effectors and fimbrial operons. The virulence genes of this pathogen are under a large amount of posttranscriptional regulation...
April 2015: Infection and Immunity
https://www.readbyqxmd.com/read/25579595/characterization-of-trap-mediated-regulation-of-the-b-subtilis-trp-operon-using-in-vitro-transcription-and-transcriptional-reporter-fusions-in-vivo
#16
Natalie M McAdams, Paul Gollnick
In Bacillus subtilis, transcription of the tryptophan biosynthetic operon is regulated by an attenuation mechanism involving two alternative RNA secondary structures in the 5' leader region upstream of the structural genes. Regulation is accomplished, at least in part, by controlling which RNA structure forms during transcription of the operon. When intracellular tryptophan levels are high, the trp RNA-binding attenuation protein (TRAP) binds to the nascent trp mRNA to promote formation of a transcription terminator structure so as to induce transcription termination prior to the structural genes...
2015: Methods in Molecular Biology
https://www.readbyqxmd.com/read/25477200/unique-aspects-of-fiber-degradation-by-the-ruminal-ethanologen-ruminococcus-albus-7-revealed-by-physiological-and-transcriptomic-analysis
#17
Melissa R Christopherson, John A Dawson, David M Stevenson, Andrew C Cunningham, Shanti Bramhacharya, Paul J Weimer, Christina Kendziorski, Garret Suen
BACKGROUND: Bacteria in the genus Ruminococcus are ubiquitous members of the mammalian gastrointestinal tract. In particular, they are important in ruminants where they digest a wide range of plant cell wall polysaccharides. For example, Ruminococcus albus 7 is a primary cellulose degrader that produces acetate usable by its bovine host. Moreover, it is one of the few organisms that ferments cellulose to form ethanol at mesophilic temperatures in vitro. The mechanism of cellulose degradation by R...
2014: BMC Genomics
https://www.readbyqxmd.com/read/25402755/the-utility-of-simple-mathematical-models-in-understanding-gene-regulatory-dynamics
#18
REVIEW
Michael C Mackey, Moisés Santillán, Marta Tyran-Kamińska, Eduardo S Zeron
In this review, we survey work that has been carried out in the attempts of biomathematicians to understand the dynamic behaviour of simple bacterial operons starting with the initial work of the 1960's. We concentrate on the simplest of situations, discussing both repressible and inducible systems and then turning to concrete examples related to the biology of the lactose and tryptophan operons. We conclude with a brief discussion of the role of both extrinsic noise and so-called intrinsic noise in the form of translational and/or transcriptional bursting...
2015: In Silico Biology
https://www.readbyqxmd.com/read/25372495/the-specialized-hsp70-hsca-interdomain-linker-binds-to-its-nucleotide-binding-domain-and-stimulates-atp-hydrolysis-in-both-cis-and-trans-configurations
#19
T Reid Alderson, Jin Hae Kim, Kai Cai, Ronnie O Frederick, Marco Tonelli, John L Markley
Proteins from the isc operon of Escherichia coli constitute the machinery used to synthesize iron-sulfur (Fe-S) clusters for delivery to recipient apoproteins. Efficient and rapid [2Fe-2S] cluster transfer from the holo-scaffold protein IscU depends on ATP hydrolysis in the nucleotide-binding domain (NBD) of HscA, a specialized Hsp70-type molecular chaperone with low intrinsic ATPase activity (0.02 min(-1) at 25 °C, henceforth reported in units of min(-1)). HscB, an Hsp40-type cochaperone, binds to HscA and stimulates ATP hydrolysis to promote cluster transfer, yet while the interactions between HscA and HscB have been investigated, the role of HscA's interdomain linker in modulating ATPase activity has not been explored...
November 25, 2014: Biochemistry
https://www.readbyqxmd.com/read/25310980/molecular-basis-for-the-ribosome-functioning-as-an-l-tryptophan-sensor
#20
Lukas Bischoff, Otto Berninghausen, Roland Beckmann
Elevated levels of the free amino acid L-tryptophan (L-Trp) trigger expression of the tryptophanase tnaCAB operon in E. coli. Activation depends on tryptophan-dependent ribosomal stalling during translation of the upstream TnaC peptide. Here, we present a cryoelectron microscopy (cryo-EM) reconstruction at 3.8 Å resolution of a ribosome stalled by the TnaC peptide. Unexpectedly, we observe two L-Trp molecules in the ribosomal exit tunnel coordinated within composite hydrophobic pockets formed by the nascent TnaC peptide and the tunnel wall...
October 23, 2014: Cell Reports
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