Attenuation regulation of amino acid biosynthetic operons in proteobacteria: comparative genomics analysis

Vitreschak, Alexey G.

doi:10.1016/j.femsle.2004.04.005

Cited by 20 publications

(25 citation statements)

References 36 publications

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“…FywP has the same substrate specificity but is not closely related in sequence to the aromatic amino acid transporter AroP, hence the different names. LysP and HisP (formerly LysQ) were identified as lysine and histidine transporters, respectively, which was predicted previously based on regulatory sequences in their promoter regions (38,39). The predicted functions of AguD as an agmatine/putrescine exchanger (9) and ArcD1 and ArcD2 as arginine/ornithine exchangers (30) were also confirmed.…”

Section: Discussionsupporting

confidence: 71%

Cloning, Expression, and Functional Characterization of Secondary Amino Acid Transporters of Lactococcus lactis

2013

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Fourteen genes encoding putative secondary amino acid transporters were identified in the genomes of Lactococcus lactis subsp. cremoris strains MG1363 and SK11 and L. lactis subsp. lactis strains IL1403 and KF147, 12 of which were common to all four strains. Amino acid uptake in L. lactis cells overexpressing the genes revealed transporters specific for histidine, lysine, arginine, agmatine, putrescine, aromatic amino acids, acidic amino acids, serine, and branched-chain amino acids. Substrate specificities were demonstrated by inhibition profiles determined in the presence of excesses of the other amino acids. Four knockout mutants, lacking the lysine transporter LysP, the histidine transporter HisP (formerly LysQ), the acidic amino acid transporter AcaP (YlcA), or the aromatic amino acid transporter FywP (YsjA), were constructed. The LysP, HisP, and FywP deletion mutants showed drastically decreased rates of uptake of the corresponding substrates at low concentrations. The same was observed for the AcaP mutant with aspartate but not with glutamate. In rich M17 medium, the deletion of none of the transporters affected growth. In contrast, the deletion of the HisP, AcaP, and FywP transporters did affect growth in a defined medium with free amino acids as the sole amino acid source. HisP was essential at low histidine concentrations, and AcaP was essential in the absence of glutamine. FywP appeared to play a role in retaining intracellularly synthesized aromatic amino acids when these were not added to the medium. Finally, HisP, AcaP, and FywP did not play a role in the excretion of accumulated histidine, glutamate, or phenylalanine, respectively, indicating the involvement of other transporters.

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Section: Discussionsupporting

confidence: 71%

Cloning, Expression, and Functional Characterization of Secondary Amino Acid Transporters of Lactococcus lactis

2013

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“…This phenomenon is exploited by many bacteria to regulate the expression of amino acid biosynthesis genes (Yanofsky 2000;Vitreschak et al 2004;Merino et al 2008). This RNA-based regulatory strategy by premature termination of transcription, often called transcription attenuation (Henkin and Yanofsky 2002), relies on the selective formation of either of two mutually exclusive RNA secondary structures (the antiterminator and the terminator) in the nascent transcript.…”

Section: Application 2: Cotranscriptional Foldingmentioning

confidence: 99%

BarMap: RNA folding on dynamic energy landscapes

Hofacker¹,

Flamm²,

Heine³

et al. 2010

RNA

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Dynamical changes of RNA secondary structures play an important role in the function of many regulatory RNAs. Such kinetic effects, especially in time-variable and externally triggered systems, are usually investigated by means of extensive and expensive simulations of large sets of individual folding trajectories. Here we describe the theoretical foundations of a generic approach that not only allows the direct computation of approximate population densities but also reduces the efforts required to analyze the folding energy landscapes to a one-time preprocessing step. The basic idea is to consider the kinetics on individual landscapes and to model external triggers and environmental changes as small but discrete changes in the landscapes. A ''barmap'' links macrostates of temporally adjacent landscapes and defines the transfer of population densities from one ''snapshot'' to the next. Implemented in the BarMap software, this approach makes it feasible to study folding processes at the level of basins, saddle points, and barriers for many nonstationary scenarios, including temperature changes, cotranscriptional folding, refolding in consequence to degradation, and mechanically constrained kinetics, as in the case of the translocation of a polymer through a pore.

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“…We will define ( ) F ω assuming that ω is a hairpin and that ω is an arbitrary microstate, thus rendering definitions Eqs. (8)(9)(10)(11) complete.…”

Section: Shifting Of Rna-polymerase On Dna Strandmentioning

confidence: 99%

“…Presence of classic attenuation in these bacteria is corroborated partly by experiment [55,25] and partly by analyses of multiple alignments of native leader regions. Alignment data is available for actinobacteria [19] and proteobacteria [11]. (2) In silico mutations were introduced at a very limited number of positions only in the left box of antiterminators, which had a great impact on modeling result (ref.…”

Section: The Case Of Proteobacteriamentioning

confidence: 99%

“…the ribosome in case of classic attenuation or regulatory proteins, tRNAs and co-factors in other attenuation types [4,5,6,7,8,9]. Detailed evidence on attenuation is available for gamma-proteobacteria and Firmicutes [10,11,12,13,14,15]. Regulations of novel type on the level of transcription and translation were proposed to involve T-boxes [16,12], recently discovered riboswitches [17,18,7,8], hypothetical regulatory LEU-element [19] as well as other elements, e.g.…”

Section: Introductionmentioning

confidence: 99%

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Modeling Classic Attenuation Regulation of Gene Expression in Bacteria

Lyubetsky

Пирогов

Rubanov

et al. 2007

J. Bioinform. Comput. Biol.

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A model is proposed primarily for the classical RNA attenuation regulation of gene expression through premature transcription termination. The model is based on the concept of the RNA secondary structure macrostate within the regulatory region between the ribosome and RNApolymerase, on hypothetical equation describing deceleration of RNA-polymerase by a macrostate and on views of transcription and translation initiation and elongation, under different values of the four basic model parameters which were varied. A special effort was made to select adequate model parameters. We first discuss kinetics of RNA folding and define the concept of the macrostate as a specific parentheses structure used to construct a conventional set of hairpins. The originally developed software that realizes the proposed model offers functionality to fully model RNA secondary folding kinetics. Its performance is compared to that of a public server described in [1]. We then describe the delay in RNA-polymerase shifting to the next base or its premature termination caused by an RNA secondary structure or, herefrom, a macrostate. In this description, essential concepts are the basic and excited states of the polymerase first introduced in [2]: the polymerase shifting to the next base can occur only in the basic state, and its detachment from DNA strand -only in excited state. As to the authors' knowledge, such a model incorporating the above mentioned attenuation characteristics is not published elsewhere. The model was implemented in an application with command line interface for running in batch mode in Windows and Linux environments, as well as a public web server [3]. The model was tested with a conventional Monte-Carlo procedure. In these simulations, the estimate of correlation between the premature transcription termination probability p and concentration c of charged amino acyl-tRNA was obtained as function p(c) for many regulatory regions in many bacterial genomes, as well as for local mutations in these regions.

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Attenuation regulation of amino acid biosynthetic operons in proteobacteria: comparative genomics analysis

Cited by 20 publications

References 36 publications

Cloning, Expression, and Functional Characterization of Secondary Amino Acid Transporters of Lactococcus lactis

Cloning, Expression, and Functional Characterization of Secondary Amino Acid Transporters of Lactococcus lactis

BarMap: RNA folding on dynamic energy landscapes

Modeling Classic Attenuation Regulation of Gene Expression in Bacteria

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