NORMAL GENOMIC

• Vindal V, Ranjan S, Ranjan A
• In silico analysis and characterization of GntR family of regulators fromMycobacterium tuberculosis.
• Tuberculosis (Edinb). 2007; 87: 242-7
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• The genome of Mycobacterium tuberculosis contains a large number ofhypothetical and poorly characterized proteins including the proteinsbelonging to the GntR family. The regulators of this family show aconserved N-terminal DNA-binding domain but have a highly diverseC-terminal domain involved in the effector-binding and/or oligomerization.This heterogeneity has led to a further classification of this family intovarious subfamilies. The sequence analysis of the M. tuberculosis genomerevealed that five genes encode for FadR-like regulators, one gene forHutC-like regulator and one for YtrA-like regulator. This classificationwas also consistent with specific secondary structural features known tobe associated with FadR, HutC and YtrA subfamilies. Out of the fiveFadR-like regulators three of the regulators were further subclassifiedinto FadR group and two of them into the VanR group. InterestinglyRv3060c, a FadR-like regulator, was shown to have an unusual size whichled us to demonstrate it as a product of a gene duplication and fusionevent. Thus this study extends the genome annotation of M. tuberculosisand provides important leads for initiating experimental characterizationof these proteins, which in turn will enrich our knowledge of their rolein cellular physiology.

• Vindal V, Suma K, Ranjan A
• GntR family of regulators in Mycobacterium smegmatis: a sequence andstructure based characterization.
• BMC Genomics. 2007; 8: 289-289
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• BACKGROUND: Mycobacterium smegmatis is fast growing non-pathogenicmycobacteria. This organism has been widely used as a model organism tostudy the biology of other virulent and extremely slow growing specieslike Mycobacterium tuberculosis. Based on the homology of the N-terminalDNA binding domain, the recently sequenced genome of M. smegmatis has beenshown to possess several putative GntR regulators. A strikingcharacteristic feature of this family of regulators is that they possess aconserved N-terminal DNA binding domain and a diverse C-terminal domaininvolved in the effector binding and/or oligomerization. Since thephysiological role of these regulators is critically dependent uponeffector binding and operator sites, we have analysed and classified theseregulators into their specific subfamilies and identified their potentialbinding sites. RESULTS: The sequence analysis of M. smegmatis putativeGntRs has revealed that FadR, HutC, MocR and the YtrA-like regulators areencoded by 45, 8, 8 and 1 genes respectively. Further out of 45 FadR-likeregulators, 19 were classified into the FadR group and 26 into the VanRgroup. All these proteins showed similar secondary structural elementsspecific to their respective subfamilies except MSMEG_3959, which showedadditional secondary structural elements. Using the reciprocal BLASTsearches, we further identified the orthologs of these regulators inBacillus subtilis and other mycobacteria. Since the expression of manyregulators is auto-regulatory, we have identified potential operator sitesfor a number of these GntR regulators by analyzing the upstream sequences.CONCLUSION: This study helps in extending the annotation of M. smegmatisGntR proteins. It identifies the GntR regulators of M. smegmatis thatcould serve as a model for studying orthologous regulators from virulentas well as other saprophytic mycobacteria. This study also sheds somelight on the nucleotide preferences in the target-motifs of GntRs thusproviding important leads for initiating the experimental characterizationof these proteins, construction of the gene regulatory network for theseregulators and an understanding of the influence of these proteins on thephysiology of the mycobacteria.

• Brinkman AB, Ettema TJ, de Vos WM, van der Oost J
• The Lrp family of transcriptional regulators.
• Mol Microbiol. 2003; 48: 287-94
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• Genome analysis has revealed that members of the Lrp family oftranscriptional regulators are widely distributed among prokaryotes, bothbacteria and archaea. The archetype Leucine-responsive Regulatory Proteinfrom Escherichia coli is a global regulator involved in modulating avariety of metabolic functions, including the catabolism and anabolism ofamino acids as well as pili synthesis. Most Lrp homologues, however,appear to act as specific regulators of amino acid metabolism-relatedgenes. Like most prokaryotic transcriptional regulators, Lrp-likeregulators consist of a DNA-binding domain and a ligand-binding domain.The crystal structure of the Pyrococcus furiosus LrpA revealed anN-terminal domain with a common helix-turn-helix fold, and a C-terminaldomain with a typical alphabeta-sandwich fold. The latter regulatorydomain constitutes a novel ligand-binding site and has been designatedRAM. Database analysis reveals that the RAM domain is present in manyprokaryotic genomes, potentially encoding (1) Lrp-homologues, when fusedto a DNA-binding domain (2) enzymes, when fused as a potential regulatorydomain to a catalytic domain, and (3) stand-alone RAM modules with unknownfunction. The architecture of Lrp regulators with two distinct domainsthat harbour the regulatory (effector-binding) site and the active(DNA-binding) site, and their separation by a flexible hinge region,suggests a general allosteric switch of Lrp-like regulators.

• Fukami-Kobayashi K, Tateno Y, Nishikawa K
• Parallel evolution of ligand specificity between LacI/GalR familyrepressors and periplasmic sugar-binding proteins.
• Mol Biol Evol. 2003; 20: 267-77
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• The bacterial LacI/GalR family repressors such as lactose operon repressor(LacI), purine nucleotide synthesis repressor (PurR), and trehalose operonrepressor (TreR) consist of not only the N-terminal helix-turn-helixDNA-binding domain but also the C-terminal ligand-binding domain that isstructurally homologous to periplasmic sugar-binding proteins. Thesestructural features imply that the repressor family evolved by acquiringthe DNA-binding domain in the N-terminal of an ancestral periplasmicbinding protein (PBP). Phylogenetic analysis of the LacI/GalR familyrepressors and their PBP homologues revealed that the acquisition of theDNA-binding domain occurred first in the family, and ligand specificitythen evolved. The phylogenetic tree also indicates that the acquisitionoccurred only once before the divergence of the major lineages ofeubacteria, and that the LacI/GalR and the PBP families have sinceundergone extensive gene duplication/loss independently along theevolutionary lineages. Multiple alignments of the repressors and PBPsfurthermore revealed that repressors and PBPs with the same ligandspecificity have the same or similar residues in their binding sites. Thisresult, together with the phylogenetic relationship, demonstrates that therepressors and the PBPs individually acquired the same ligand specificityby homoplasious replacement, even though their genes are encoded in thesame operon.

• Rigali S, Derouaux A, Giannotta F, Dusart J
• Subdivision of the helix-turn-helix GntR family of bacterial regulators inthe FadR, HutC, MocR, and YtrA subfamilies.
• J Biol Chem. 2002; 277: 12507-15
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• Haydon and Guest (Haydon, D. J, and Guest, J. R. (1991) FEMS Microbiol.Lett. 63, 291-295) first described the helix-turn-helix GntR family ofbacterial regulators. They presented them as transcription factors sharinga similar N-terminal DNA-binding (d-b) domain, but they observednear-maximal divergence in the C-terminal effector-binding andoligomerization (E-b/O) domain. To elucidate this C-terminalheterogeneity, structural, phylogenetic, and functional analyses wereperformed on a family that now comprises about 270 members. Ourcomparative study first focused on the C-terminal E-b/O domains and nexton DNA-binding domains and palindromic operator sequences, has classifiedthe GntR members into four subfamilies that we called FadR, HutC, MocR,and YtrA. Among these subfamilies a degree of similarity of about 55% wasobserved throughout the entire sequence. Structure/function associationswere highlighted although they were not absolutely stringent. Theconsensus sequences deduced for the DNA-binding domain were slightlydifferent for each subfamily, suggesting that fusion between the D-b andE-b/O domains have occurred separately, with each subfamily having its ownD-b domain ancestor. Moreover, the compilation of the known or predictedpalindromic cis-acting elements has highlighted different operatorsequences according to our subfamily subdivision. The observed C-terminalE-b/O domain heterogeneity was therefore reflected on the DNA-bindingdomain and on the cis-acting elements, suggesting the existence of a tightlink between the three regions involved in the regulating process.