GeConT 2: gene context analysis for orthologous proteins, conserved domains and metabolic pathways

Martinez-Guerrero, Cristian E.; Ciria, Ricardo; Abreu‐Goodger, Cei; Moreno–Hagelsieb, Gabriel; Merino, Enrique

doi:10.1093/nar/gkn330

Cited by 42 publications

(34 citation statements)

References 37 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The criteria for concluding that adjacent genes are within the same operon were described previously by Janga et al and Salgado et al (65,89). The genomic contexts of the significant matches identified were further analyzed using our Web GeConT server (19,72). Our findings are organized according to the type of gene or genes that were identified downstream of a T-box element, as described in the following sections.…”

Section: General Features Of T-box Riboswitch Rnamentioning

confidence: 99%

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

Gutiérrez-Preciado

Henkin

Grundy

et al. 2009

Microbiol Mol Biol Rev

140

230

View full text Add to dashboard Cite

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.

show abstract

Section: General Features Of T-box Riboswitch Rnamentioning

confidence: 99%

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

Gutiérrez-Preciado

Henkin

Grundy

et al. 2009

Microbiol Mol Biol Rev

140

230

View full text Add to dashboard Cite

show abstract

“…By default, a predicted riboswitch sequence needs to be present in at least five non-redundant genomes to qualify as a genuine riboswitch. Once a prediction is made, genomic context of the discovered riboswitches is analyzed with an associated gene context tool (GeConT) [55, 56]. Thus, unlike Riboswitch Finder, a discovered riboswitch is placed into context of any neighboring transcriptional terminator and open reading frames, allowing tentative prediction of regulatory mechanism and functional assignment of detected riboswitches.…”

Section: Riboswitch Identification Tools Based On Folding Energy Amentioning

confidence: 99%

Computational analysis of riboswitch-based regulation

Sun

Rodionov

2014

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanism

View full text Add to dashboard Cite

Advances in computational analysis of riboswitches in the last decade have contributed greatly to our understanding of riboswitch regulatory roles and mechanisms. Riboswitches were originally discovered as part of sequence analysis of the 5′-untranslated region of mRNAs in the hope of finding novel gene regulatory sites, and the existence of structural RNAs appeared to be a spurious phenomenon. As more riboswitches were discovered, they illustrated diversity and adaptability of these RNA regulatory sequences. The fact that a chemically monotonous molecule like RNA can discern a wide range of substrates and exert a variety of regulatory mechanisms was subsequently demonstrated in diverse genomes and has hastened the development of sophisticated algorithms for their analysis and prediction. In this review, we focus on some of the computational tools for riboswitch detection and secondary structure prediction. The study of this simple yet efficient form of gene regulation promises to provide a more complete picture of a world that RNA once dominated and allows rational design of artificial riboswitches. This article is part of a Special Issue entitled: Riboswitches.

show abstract

“…Such queries, commonly performed by geneticists and phylogeneticists require tools of a different nature, able to provide promptly up to date syntenies in human-readable form. Several web services have been developed for this purpose such as GeConT2 [4], PSAT [5] and GCView [6]. Unfortunately, syntenies produced by these tools are pre-calculated and therefore often outdated.…”

Section: Introductionmentioning

confidence: 99%

“…Indeed, with over 2000 sequenced micro-organisms often responding to exotic genus names, keeping a mental track of all the lineages is a daunting task. To my knowledge, with the exception of GeCont2 [4] which offers partial access to phyla, none of the afore mentioned synteny tools allows organism selection on the basis of taxonomy. The SyntTax web service described here aims to assist the analysis of synteny by providing an organized tree exposing the full lineage of every completely sequenced prokaryote in the National Center for Biotechnology Information (NCBI) repository.…”

Section: Introductionmentioning

confidence: 99%

SyntTax: a web server linking synteny to prokaryotic taxonomy

2013

View full text Add to dashboard Cite

BackgroundThe study of the conservation of gene order or synteny constitutes a powerful methodology to assess the orthology of genomic regions and to predict functional relationships between genes. The exponential growth of microbial genomic databases is expected to improve synteny predictions significantly. Paradoxically, this genomic data plethora, without information on organisms relatedness, could impair the performance of synteny analysis programs.ResultsIn this work, I present SyntTax, a synteny web service designed to take full advantage of the large amount or archaeal and bacterial genomes by linking them through taxonomic relationships. SyntTax incorporates a full hierarchical taxonomic tree allowing intuitive access to all completely sequenced prokaryotes. Single or multiple organisms can be chosen on the basis of their lineage by selecting the corresponding rank nodes in the tree. The synteny methodology is built upon our previously described Absynte algorithm with several additional improvements.ConclusionsSyntTax aims to produce robust syntenies by providing prompt access to the taxonomic relationships connecting all completely sequenced microbial genomes. The reduction in redundancy offered by lineage selection presents the benefit of increasing accuracy while reducing computation time. This web tool was used to resolve successfully several conserved complex gene clusters described in the literature. In addition, particular features of SyntTax permit the confirmation of the involvement of the four components constituting the E. coli YgjD multiprotein complex responsible for tRNA modification. By analyzing the clustering evolution of alternative gene fusions, new proteins potentially interacting with this complex could be proposed. The web service is available at http://archaea.u-psud.fr/SyntTax.

show abstract

GeConT 2: gene context analysis for orthologous proteins, conserved domains and metabolic pathways

Cited by 42 publications

References 37 publications

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

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

Computational analysis of riboswitch-based regulation

SyntTax: a web server linking synteny to prokaryotic taxonomy

Contact Info

Product

Resources

About