scholarly journals Biochemical Features and Functional Implications of the RNA-Based T-Box Regulatory Mechanism

2009 ◽  
Vol 73 (1) ◽  
pp. 36-61 ◽  
Author(s):  
Ana Gutiérrez-Preciado ◽  
Tina M. Henkin ◽  
Frank J. Grundy ◽  
Charles Yanofsky ◽  
Enrique Merino
Keyword(s):  
Amino Acid ◽  
Regulatory Mechanism ◽  
Regulatory Elements ◽  
Trna Synthetase ◽  
Cell Physiology ◽  
T Box ◽  
Expression Of Genes ◽  
Functional Implications ◽  
Genes Encoding ◽  
Attenuation Mechanism

SUMMARY The T-box mechanism is a common regulatory strategy used for modulating the expression of genes of amino acid metabolism-related operons in gram-positive bacteria, especially members of the Firmicutes. T-box regulation is usually based on a transcription attenuation mechanism in which an interaction between a specific uncharged tRNA and the 5′ region of the transcript stabilizes an antiterminator structure in preference to a terminator structure, thereby preventing transcription termination. Although single T-box regulatory elements are common, double or triple T-box arrangements are also observed, expanding the regulatory range of these elements. In the present study, we predict the functional implications of T-box regulation in genes encoding aminoacyl-tRNA synthetases, proteins of amino acid biosynthetic pathways, transporters, and regulatory proteins. We also consider the global impact of the use of this regulatory mechanism on cell physiology. Novel biochemical relationships between regulated genes and their corresponding metabolic pathways were revealed. Some of the genes identified, such as the quorum-sensing gene luxS, in members of the Lactobacillaceae were not previously predicted to be regulated by the T-box mechanism. Our analyses also predict an imbalance in tRNA sensing during the regulation of operons containing multiple aminoacyl-tRNA synthetase genes or biosynthetic genes involved in pathways common to more than one amino acid. Based on the distribution of T-box regulatory elements, we propose that this regulatory mechanism originated in a common ancestor of members of the Firmicutes, Chloroflexi, Deinococcus-Thermus group, and Actinobacteria and was transferred into the Deltaproteobacteria by horizontal gene transfer.

Phytochrome signal-transduction: characterization of pathways and isolation of mutants

1995 ◽  
Vol 350 (1331) ◽  
pp. 67-74 ◽  
Keyword(s):  
Gene Expression ◽  
Signal Transduction ◽  
Red Light ◽  
Signal Transduction Pathway ◽  
Regulatory Elements ◽  
Signal Transduction Pathways ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Regulated Gene Expression ◽  
Dependent Pathway

The study of phytochrome signalling has yielded a wealth of data describing both the perception of light by the receptor, and the terminal steps in phytochrome-regulated gene expression by a number of transcription factors. We are now focusing on establishing the intervening steps linking phytochrome photoactivation to gene expression, and the regulation and interactions of these signalling pathways. Recent work has utilized both a pharmacological approach in phototrophic soybean suspension cultures and microinjection techniques in tomato to establish three distinct phytochrome signal-transduction pathways: (i) a calcium-dependent pathway that regulates the expression of genes encoding the chlorophyll a/b binding protein ( CAB ) and other components of photosystem II; (ii) a cGMP-dependent pathway that regulates the expression of the gene encoding chalcone synthase ( CHS ) and the production of anthocyanin pigments; and (iii) a pathway dependent upon both calcium and cGMP that regulates the expression of genes encoding components of photosystem I and is necessary for the production of mature chloroplasts. To study the components and the regulation of phytochrome signal-transduction pathways, mutants with altered photomorphogenic responses have been isolated by a number of laboratories. However, with several possible exceptions, little real progress has been made towards the isolation of mutants in positive regulatory elements of the phytochrome signal-transduction pathway. We have characterized a novel phytochrome A (phyA)-mediated far-red light (FR) response in Arabidopsis seedlings which we are currently using to screen for specific phyA signal-transduction mutants.

scholarly journals Regulation of Expression of the Lactococcus lactis Histidine Operon

1999 ◽  
Vol 181 (7) ◽  
pp. 2026-2037 ◽  
Author(s):  
C. Delorme ◽  
S. D. Ehrlich ◽  
P. Renault
Keyword(s):  
Lactococcus Lactis ◽  
Dna Sequences ◽  
Trna Synthetase ◽  
Site Directed Mutagenesis ◽  
Regulation Of Transcription ◽  
Leader Region ◽  
Regulation Of Expression ◽  
T Box ◽  
Copy Numbers ◽  
Attenuation Mechanism

ABSTRACT In Lactococcus lactis, the his operon contains all the genes necessary for histidine biosynthesis. It is transcribed from a unique promoter, localized 300 bp upstream of the first gene. The region corresponding to the untranslated 5′ end of the transcript, named the his leader region, displays the typical features of the T box transcriptional attenuation mechanism which is involved in the regulation of many amino acid biosynthetic operons and tRNA synthetase genes in gram-positive bacteria. Here we describe the regulation of transcription of the his operon by the level of histidine in the growth medium. In the absence of histidine, two transcripts are present. One covers the entire operon, while the other stops at a terminator situated about 250 bp downstream of the transcription start point. DNA sequences implicated in regulation of the his operon were identified by transcriptional fusion with luciferase genes and site-directed mutagenesis. In addition to the previously defined sequences necessary for effective T-box-mediated regulation, new essential regions were identified. Eighteen percent of the positions of the hisleader region were found to differ in seven distantly related strains of L. lactis. Analysis of the variable positions supports the folding model of the central part of the his leader region. Lastly, in addition to the T-box-mediated regulation, the operon is regulated at the level of initiation of transcription, which is repressed in the presence of histidine. An operator site, necessary for full repression, overlaps the terminator involved in the T box attenuation mechanism. The functionality of the operator is altered on plasmids with low and high copy numbers, suggesting that supercoiling may play a role in the expression of the his operon. The extents of regulation at the levels of initiation and attenuation of transcription are 6- to 8-fold and 14-fold, respectively. Together, the two levels of control allow a 120-fold range of regulation of theL. lactis operon by histidine.

Aminoacyl-tRNA synthetase genes of Bacillus subtilis: organization and regulation

1999 ◽  
Vol 77 (4) ◽  
pp. 343-347 ◽  
Author(s):  
Martin Pelchat ◽  
Jacques Lapointe
Keyword(s):  
Bacillus Subtilis ◽  
Initiation Site ◽  
Trna Synthetase ◽  
Translation Initiation Site ◽  
Aminoacyl Trna Synthetase ◽  
Gene Encoding ◽  
T Box ◽  
Trna Synthetases ◽  
Genes Encoding ◽  
Mature Mrnas

In Bacillus subtilis, 14 of the 24 genes encoding aminoacyl-tRNA synthetases (aaRS) are regulated by tRNA-mediated antitermination in response to starvation for their cognate aminoacid. Their transcripts have an untranslated leader mRNA of about 300 nucleotides, including alternative and mutually exclusive terminator-antiterminator structures, just upstream from the translation initiation site. Following antitermination, some of these transcripts are cleaved leaving at the 5prime-end of the mature mRNAs, stable secondary structures that can protect them against degradation. Although most B. subtilis aaRS genes are expressed as monocistronic mRNAs, the gltX gene encoding the glutamyl-tRNA synthetase is cotranscribed with cysE and cysS encoding serine acetyl-transferase and cysteinyl-tRNA synthetase, respectively. Transcription of gltX is not controlled by a tRNA, but tRNACys-mediated antitermination regulates the elongation of transcription into cysE and cysS. The full-length gltX-cysE-cysS transcript is then cleaved into a monocistronic gltX mRNA and a cysE-cysS mRNA.Key words: regulation, aminoacyl-tRNA synthetase, T-Box, processing.

scholarly journals PPARα via HNF4α regulates the expression of genes encoding hepatic amino acid catabolizing enzymes to maintain metabolic homeostasis

2015 ◽  
Vol 10 (2) ◽  
Author(s):  
Alejandra V. Contreras ◽  
Claudia Rangel-Escareño ◽  
Nimbe Torres ◽  
Gabriela Alemán-Escondrillas ◽  
Victor Ortiz ◽  
...  
Keyword(s):  
Amino Acid ◽  
Metabolic Homeostasis ◽  
Expression Of Genes ◽  
Genes Encoding

scholarly journals Selection and Characterization of Escherichia coliVariants Capable of Growth on an Otherwise Toxic Tryptophan Analogue

2001 ◽  
Vol 183 (18) ◽  
pp. 5414-5425 ◽  
Author(s):  
Jamie M. Bacher ◽  
Andrew D. Ellington
Keyword(s):  
Amino Acid ◽  
Unnatural Amino Acids ◽  
Trna Synthetase ◽  
Growth Patterns ◽  
Amino Acid Permease ◽  
Mass Spectral ◽  
Genes Encoding ◽  
Tryptophan Analogues ◽  
Tryptophan Uptake

ABSTRACT Escherichia coli isolates that were tolerant of incorporation of high proportions of 4-fluorotryptophan were evolved by serial growth. The resultant strain still preferred tryptophan for growth but showed improved growth relative to the parental strain on other tryptophan analogues. Evolved clones fully substituted fluorotryptophan for tryptophan in their proteomes within the limits of mass spectral and amino acid analyses. Of the genes sequenced, many genes were found to be unaltered in the evolved strain; however, three genes encoding enzymes involved in tryptophan uptake and utilization were altered: the aromatic amino acid permease (aroP) and tryptophanyl-tRNA synthetase (trpS) contained several amino acid substitutions, and the tyrosine repressor (tyrR) had a nonsense mutation. While kinetic analysis of the tryptophanyl-tRNA synthetase suggests discrimination against 4-fluorotryptophan, an analysis of the incorporation and growth patterns of the evolved bacteria suggest that other mutations also aid in the adaptation to the tryptophan analogue. These results suggest that the incorporation of unnatural amino acids into organismal proteomes may be possible but that extensive evolution may be required to reoptimize proteins and metabolism to accommodate such analogues.

Activation tagging in plants—generation of novel, gain-of-function mutations

2007 ◽  
Vol 58 (6) ◽  
pp. 490 ◽  
Author(s):  
Michael A. Ayliffe ◽  
Anthony J. Pryor
Keyword(s):  
Regulatory Element ◽  
Regulatory Elements ◽  
Activation Tagging ◽  
Regulatory Sequences ◽  
Gain Of Function ◽  
Diverse Range ◽  
Over Expression ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Mutant Phenotypes

Activation tagging is a mutagenesis strategy that generates dominant, gain-of-function mutations as a consequence of gene over-expression. These mutations cause a class of mutant previously unobtainable by conventional mutagenesis. Unlike most mutant phenotypes, which are generally a consequence of gene inactivation, activation tagged phenotypes arise from excess functional gene product. Gene over-expression mutations are obtained by randomly inserting regulatory sequences throughout the genome, using either high-throughput plant transformation or mobile transposable elements to distribute these regulatory elements. Since the sequence of the regulatory element vector is known, it acts as a molecular tag, making isolation of the over-expressed gene a relatively straightforward process using standard molecular biological techniques. Activation tagged phenotypes have been generated by the over-expression of genes encoding a diverse range of protein and RNA products that are involved in all aspects of plant biogenesis. This mutation approach has been used extensively in Arabidopsis and to a lesser extent in several other species. In this review we summarise activation tagging in plants and suggest that the development of this mutagenesis strategy in more plants of agronomic significance is highly desirable.

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