Glycine binds the transcriptional accessory protein GcvR to disrupt a GcvA/GcvR interaction and allow GcvA-mediated activation of the Escherichia coli gcvTHP operon

Heil, Gary L.; Stauffer, Lorraine T.; Stauffer, George V.

doi:10.1099/00221287-148-7-2203

Cited by 36 publications

(33 citation statements)

References 44 publications

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“…Again, this is an unusual situation because in most instances LysR-type regulated systems are very simple and involve a single regulatory component, the activator, which is able to directly sense the effector and to regulate transcription. In some systems, an additional regulatory protein has been shown to modulate the activity of the activator by binding to it and thus preventing its function (23). However, to our knowledge, this is the first report of a LysR-type activator that requires an auxiliary protein to activate transcription.…”

Section: Discussionmentioning

confidence: 76%

Regulation of Tetralin Biodegradation and Identification of Genes Essential for Expression of thn Operons

et al. 2004

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The tetralin biodegradation genes of Sphingomonas macrogolitabida strain TFA are clustered in two closely linked and divergent operons. To analyze expression of both operons under different growth conditions, transcriptional and translational gene fusions of the first genes of each operon to lacZ have been constructed in plasmids unable to replicate in Sphingomonas and integrated by recombination into the genome of strain TFA. Expression analysis indicated that the transcription of both genes is induced in similar ways by the presence of tetralin. Gene expression in both operons is also subjected to overimposed catabolic repression. Two additional genes named thnR and thnY have been identified downstream of thnCA3A4 genes. ThnR is similar to LysR-type regulators, and mutational analysis indicated that ThnR is strictly required for expression of the thn operons. Unlike other LysR-type regulators, ThnR does not repress its own synthesis. In fact, ThnR activates its own expression, since thnR is cotranscribed with the thnCA3A4 genes. ThnY is similar to the ferredoxin reductase components of dioxygenase systems and shows the fer2 domain, binding a Cys 4 [2Fe-2S] iron sulfur center, and the FAD-binding domain, common to those reductases. However, it lacks the NADbinding domain. Intriguingly, ThnY has a regulatory role, since it is also strictly required for expression of the thn operons. Given the similarity of ThnY to reductases and the possibility of its being present in the two redox states, it is tempting to speculate that ThnY is a regulatory component connecting expression of the thn operons to the physiological status of the cell.The organic solvent tetralin (1,2,3,4-tetrahydronaphthalene) is a bicyclic molecule composed of an aromatic and an alicyclic moiety, which share two carbon atoms. Tetralin is widely used as a degreasing agent and solvent for fats, resins, and waxes, as a substitute for turpentine in paints, lacquers, and shoe polishes, and also in the petrochemical industry in connection with coal liquefaction (19). A concentration of tetralin higher than 100 M inhibits bacterial growth (44). Its toxicity is partly due to its lipophilic character, which results in its accumulation in the cell membranes, thus leading to changes in their structure and function (46,47). In addition, tetralin also forms toxic hydroperoxides in the cell (17).A few bacterial strains which are able to aerobically grow on tetralin as the only carbon and energy source have been isolated (44). By the identification of accumulated intermediates, several reports suggest that some bacteria, such as Pseudomonas stutzeri AS39 (43), initially hydroxylate and further oxidize the alicyclic ring whereas others, such as Corynebacterium sp. strain C125 (45), initially dioxygenate the aromatic ring, thus indicating that aerobic metabolism of tetralin can be performed in different ways. Metabolism of tetralin has been best characterized in Sphingomonas macrogolitabida strain TFA. Biodegradation of tetralin by the strain TFA involves initial...

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Section: Discussionmentioning

confidence: 76%

Regulation of Tetralin Biodegradation and Identification of Genes Essential for Expression of thn Operons

et al. 2004

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“…GcvB is activated by the glycine cleavage system regulator, GcvA, under glycine-rich conditions (40). This interaction is dependent upon Lrp binding and is negatively regulated by GcvR when glycine is limiting (41). Using quantitative PCR, we measured relative expression levels of gcvB in wild-type, ΔgcvA, and Δlrp, with and without glycine addition (Fig.…”

Section: Resultsmentioning

confidence: 99%

Functional characterization of bacterial sRNAs using a network biology approach

Modi

Camacho

Kohanski

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

112

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Small RNAs (sRNAs) are important components of posttranscriptional regulation. These molecules are prevalent in bacterial and eukaryotic organisms, and involved in a variety of responses to environmental stresses. The functional characterization of sRNAs is challenging and requires highly focused and extensive experimental procedures. Here, using a network biology approach and a compendium of gene expression profiles, we predict functional roles and regulatory interactions for sRNAs in Escherichia coli. We experimentally validate predictions for three sRNAs in our inferred network: IsrA, GlmZ, and GcvB. Specifically, we validate a predicted role for IsrA and GlmZ in the SOS response, and we expand on current knowledge of the GcvB sRNA, demonstrating its broad role in the regulation of amino acid metabolism and transport. We also show, using the inferred network coupled with experiments, that GcvB and Lrp, a transcription factor, repress each other in a mutually inhibitory network. This work shows that a network-based approach can be used to identify the cellular function of sRNAs and characterize the relationship between sRNAs and transcription factors.microbiology | network inference | sRNA regulation S mall noncoding RNAs (sRNAs) are ubiquitous in all kingdoms of life. These molecules range in length from a few nucleotides to a few hundred nucleotides, and are involved in the regulation of a wide range of physiological processes (1-3). Bacterial sRNAs, some of which have been studied extensively (4), have been implicated in the regulation of bacterial stress responses, iron uptake, quorum sensing, virulence, and biofilm formation (5-8).The most widely studied class of bacterial sRNAs act as posttranscriptional regulators by base-pairing to target mRNAs. This interaction is facilitated by the Hfq protein, a bacterial Sm-like protein with chaperone function, which acts as a general cofactor in RNA interactions (9). Binding of an sRNA to its mRNA target can result in changes in translational efficiency as well as transcript instability, a process dependent on the RNase-E-including degradosome complex (10). To date, w80 sRNAs have been identified in Escherichia coli, 30 of which are Hfq-dependent. A number of these sRNAs have been well characterized, such as RyhB, which is known to regulate iron homeostasis (8).Small RNAs and their targets are being discovered and identified with greater efficiency (11-15); however, the functions of many sRNAs remain unknown. In the present study, we were interested in exploring the possibility of developing and using a network biology approach to elucidate sRNA functional roles. We applied a network inference algorithm to a compendium of E. coli microarray expression profiles to reconstruct an sRNA regulatory network. Functional enrichment of the resulting sRNA subnetworks confirmed known functions for some sRNAs and identified putative functions for others. We experimentally validated predicted functional roles for three sRNAs, and an indepth analysis of the inferred network led...

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“…We found that T. vaginalis has two H proteins, encoded by independent genes, both of which are effective substrates of the L protein ( Table 1). The H proteins in plants (2), mammals (6), Escherichia coli (19), and yeast (33) are encoded by a single gene. In some plants, tissue-specific alternative splicing results in two H proteins with or without an N-terminal extension of two amino acids (23,24).…”

Section: Discussionmentioning

confidence: 99%

Proteins of the Glycine Decarboxylase Complex in the Hydrogenosome ofTrichomonas vaginalis

et al. 2006

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Trichomonas vaginalis is a unicellular eukaryote that lacks mitochondria and contains a specialized organelle, the hydrogenosome, involved in carbohydrate metabolism and iron-sulfur cluster assembly. We report the identification of two glycine cleavage H proteins and a dihydrolipoamide dehydrogenase (L protein) of the glycine decarboxylase complex in T. vaginalis with predicted N-terminal hydrogenosomal presequences. Immunofluorescence analyses reveal that both H and L proteins are localized in hydrogenosomes, providing the first evidence for amino acid metabolism in this organelle. All three proteins were expressed in Escherichia coli and purified to homogeneity. The experimental K m of L protein for the two H proteins were 2.6 M and 3.7 M, consistent with both H proteins serving as substrates of L protein. Analyses using purified hydrogenosomes showed that endogenous H proteins exist as monomers and endogenous L protein as a homodimer in their native states. Phylogenetic analyses of L proteins revealed that the T. vaginalis homologue shares a common ancestry with dihydrolipoamide dehydrogenases from the firmicute bacteria, indicating its acquisition via a horizontal gene transfer event independent of the origins of mitochondria and hydrogenosomes.Hydrogenosomes are double membrane-bound organelles involved in iron-sulfur cluster assembly that produce molecular hydrogen and ATP via carbohydrate metabolism (30,40,41). These organelles were originally discovered in trichomonads and subsequently were detected in a variety of unrelated organisms, such as certain ciliates and fungi. Although the evolutionary origin(s) of hydrogenosomes is under debate, they appear to be polyphyletic, with ciliate hydrogenosomes being derived directly from mitochondria (3) and the origin of those in trichomonads and fungi less clear (11,17). Functional and phylogenetic data do, however, indicate that all hydrogenosomes are related to mitochondria (5,14,34,36,41).Trichomonas vaginalis is a deep-branching, microaerophilic, unicellular protist that lacks mitochondria and contains hydrogenosomes (30, 39). The lack of a genome in the hydrogenosomes of trichomonads precludes reconstruction of their ancestry directly as has been convincingly done for mitochondria (18). However, the phylogeny of genes that encode hydrogenosomal proteins, the hydrogenosomal targeting signals, and protein import machinery can provide indirect evidence for the evolutionary history of hydrogenosomes (4, 12, 43). Regardless of whether a protomitochondrion was modified to become a hydrogenosome or was lost during the adaptation of Trichomonas to anoxic environments, the absence of the tricarboxylic acid (TCA) cycle and many metabolic enzymes underscore the independent evolution of the T. vaginalis hydrogenosome as a unique organelle.Carbohydrates are the preferred source of nutrients for T. vaginalis; however, under conditions where carbohydrates are limiting, amino acids have been shown to sustain trichomonad growth and survival. Evidence of uptake of amino acids...

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Glycine binds the transcriptional accessory protein GcvR to disrupt a GcvA/GcvR interaction and allow GcvA-mediated activation of the Escherichia coli gcvTHP operon

Cited by 36 publications

References 44 publications

Regulation of Tetralin Biodegradation and Identification of Genes Essential for Expression of thn Operons

Regulation of Tetralin Biodegradation and Identification of Genes Essential for Expression of thn Operons

Functional characterization of bacterial sRNAs using a network biology approach

Proteins of the Glycine Decarboxylase Complex in the Hydrogenosome ofTrichomonas vaginalis

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