MycoperonDB aims to provide a computational model of Transcription units and Operons in Mycobacteria.
It allows users to search the Operon and Transcriptional unit context of
  • a regulatory motif or
  • a gene or ORF
How to use?
Go to SearchDB tab. Fill up the query text box on the page. Select the nature of query string eg. Motif, Gene name or ORFID. Select the genome of interest and hit submit button to search the database. If the user is not sure about the gene name then he/she can click the Browse Gene button to select the gene of interest from a popup window.

Search result

The MycoperonDB will return the the result of Database search back to the browser as table in HTML page. Each entry in result table is hyperlinked with a graphical display tool that represent the information in a graphical window. For example, if you are interested in operon context of Rv0002, MycoperonDB will show graphically all the genes which are part of same operon according to our in silico model.

Additional tools
The side panel of MycoperonDB page is linked to some of the related addional database sites and web tools.

How MycoperonDB was generated?
Methods: Genome sequences of all mycobacterial species have been collected from NCBI site.The ptt tables, which have genes along with their coordinates have also been taken from NCBI. The genome was analyzed to predict boundries of operon and transcriptional units.
To predict operon boundaries, we have done following analyses-
  • Orientation of genes,
  • Positions of predicted transcriptional terminators.
  • Intergenic distance between the genes,and
  • Conserved gene clusters among the cloesly related species
Verification of prediction
To verify our operon prediction, we collected information (literature search) on experimentally characterized operons. Our predictions tallied with the experimental results.


Glossary:

Regulator gene - a gene that codes for a repressor protein molecule. The repressor molecule binds to the operator and prevents RNA polymerase from binding to the promoter.

Promoter - a short sequence of DNA where RNA polymerase first attaches when a gene is to be transcribed.

Operator - a short sequence of DNA where the repressor binds, preventing RNA polymerase from attaching to the promoter.

Operon- clusters of genes, found in prokaryotes, that are transcribed as a single message, and regulated by the same gene expression machinery.

iniA - gene encoding a protein with a phosphopantetheine attachment site motif that is characteristic of acyl-carrier proteins iniB- gene encoding a protein with weak homology to alanine-glycine-rich cell wall structural proteins

IdeR-iron dependent regulator that modulates transcription of many genes including siderophore, iron storage genes, virulence genes etc.

EmbR- a transcriptional regulator, homologous to the OmpR class of transcriptional regulator that possess winged helix-turn-helix DNA binding motifs. It has shown to be phosphorylated by mycobacterial serine/threonine kinase PknH.

NusA-a key regulator of bacterial transcriptional elongation, pauses termination and antitermination. In M.tb it binds with BoxB-BoxA-BoxC antitermination sequences within the leader region of the rRNA operon with high affinity and specifity.

VirS-a regulator of AraC family on which the transcription of mymA operon is dependent.

devR- a transcriptional regulator that mediates the genetic response of Mycobacteria to oxygen limitation and nitric oxide exposure. It is a regulator of hypoxia-responsive genes. devR is co-transcribed along with devS,which encodes its cognate sensor kinase, and an upstream gene, Rv3134c. Rv3134c-devR-devS operon is transcribed from multiple promoters and is autoregulated

nat-all enzymes of this operon have a similar endogeous role to that of the nat enzyme(arylamine N-acetyltransferase) and are part of a pathway important for cell wall synthesis

Mce1R - a negative regulator that acts intracellularly to repress expression of the mce1 operon. It facilitates balanced temporal expression of the mce1 products required for organized granuloma formation, which is both protective to the host and necessary for the persistence of M. tuberculosis.

KasA- a key enzyme for mycolic acid biosynthesis, inhibition or depletion of which causes cell lysis

InhA-a fatty acid synthase II (FASII) enzyme, which when inhibited or inactivated, leads to mycobacterial cell lysis.

hmp- it encodes a protein which is homologous to flavohemoglobin in E.coli. The putative roles of flavohemoglobin are in oxygen diffusion, metabolism and protection of microorganisms from oxidative and nitrosative stress.

Rv1057-encodes the single seven bladed beta propeller of Mycobacterium tuberculosis

TrcR-a regulator that represses transcription of the intracellulaly expressed gene (Rv1057) encoding a seven bladed beta propeller. It binds to a 69-bp AT-rich sequence within the Rv1057 intergenic region and generates specific contacts on the same side of the DNA helix.

eis- eis gene of M. tuberculosis H37Rv has been shown to enhance the intracellular survival of Mycobacterium smegmatis, which does not contain eis, within macrophages

HflX- a GTP binding protein

HspX-(Rv2031c)- a major M. tuberculosis antigen recognized by the sera of a high proportion of TB patients and is induced under anoxic condition. If this gene is inactivated in M tuberculosis, the growth of Mycobacteria is severely attenuated in the macrophages.

OmpA-(Rv0899)-a porin like protein which can form pores in liposomes.

HbhA-(Rv0475)- It is present on the surface of virulent Mycobacteria but is not found in M. smegmatis.

Icl-(Rv0467)-an enzyme that converts isocitrate to succinate in the glyoxalate shunt.

NarG- a subunit of prokaryotic respiratory nitrate reductase that plays major role in respiration in the absence of oxygen.

KatG- (Rv1908)- a catalase peroxidase that degrades H2O2 and organic peroxides. It is the only enzyme with catalase activity in M.tuberculosis , and it also activates the prodrug INH to form a reactive species that inhibits mycolic acid biosynthesis.

AhpC-(Rv2428)-an alkyl hydroperoxide reductase which detoxifies organic hydroxyperoxides.

SodA-(Rv3846)- an iron factored superoxide dismutase that degrades superoxides, which are normal by-products of normal aerobic respiration and are also produced by the phagocytic respiratory burst enzyme. So it is important for the survival of the intracellular pathogens during infections.

SodC-(Rv0342)-Cu,Zn-factored superoxide dismutase that is responsible for a small part of total sod activity in M. tuberculosis.

SigA-(Rv2703)-essential principal sigma factor which is necessary for most mycobacterial house keeping gene transcription.

SigE-(Rv1221)-Sigma E is a member of the ECF(extracytoplasmic function) group of sigma factors that control the bacterial response to external stimuli.

MurA-it encodes an enzyme important for peptidoglycan synthesis.

SigH- It regulates major components of oxidative and heat stress responses.

HspR- a repressor of dnaK expression in M.tuberculosis