Previous updates


Release R26 (December 2012):

  1. Eleven new CDSs have been annotated (See de Souza et al., 2011; Kelkar et al., 2011):
    • Rv0078B • Rv2548A • Rv3190A
    • Rv0397A • Rv2468A
    • Rv0530A • Rv3032A
    • Rv1366A • Rv3098A
    • Rv2237A • Rv3136A
  2. Seven new ncRNAs have been annotated (See Arnvig et al., 2011; Pelly et al., 2012):
    • MTS0858 • MTS1338 • MTS2975
    • ncrMT1234 • MTS2823
    • MTS1082 • ncrMT3949
  3. Thirty-three corrections have been made to the genome sequence, affecting the amino acid sequence of 15 CDS:
    • Rv0082 • Rv1925 • Rv3011c
    • Rv0204c • Rv1979c • Rv3144c
    • Rv0355c • Rv2048c • Rv3919c
    • Rv0442c • Rv2101
    • Rv0473 • Rv2896c • Rv1783 (Rv1784)


Release R25 (April 2012):

  1. Two new genes have been annotated - Rv2395A and Rv2395B.
  2. A total of 2828 proteins have now been indentified by proteomics studies, of which, 183 previously did not have proteomics annotation in TubercuList.
  3. Links to 44 protein structures in the Protein Data Bank have been added. The structures of 4 proteins are reported for the first time.
  4. Gene essentiality predictions based on transposon mutagenesis and deep-sequencing from the publication by Griffin et al., 2011 have been added.

Quick Search has been modified to correct problems encountered when there are multiple matches to a search term.


Release 24 (December 2011): In total, 2298 genes have been updated with information from the current literature. Some of the notable changes in this release are: 1) One new gene has been annotated - Rv0691A, mycofactocin precursor protein; 2) 18 genes have been updated with characterization of mutant strains; 3) The functional category of 13 genes has been changed - Rv0428c, Rv0730, Rv0919, Rv2011c, Rv2036, Rv2170, Rv2669, Rv2701c, Rv2775, Rv2851c, Rv2867c, Rv3027c, Rv3168; 4) Links to 151 protein structures in the Protein data Bank have been added. The structures of 44 proteins are reported for the first time.; 5) Results from the publication by de Souza et al., 2011 have been added. This provides proteomic evidence for 2163 proteins, of which 387 did not previously have proteomic annotation in TubercuList.


Release 23 (September 2011): 281 genes have been updated with information from the current literature on regulation, function, proteomics, and mutants. Some of the notable changes in this release are: 1) Members of the putative regulons of MoaR1, SigC, SigF, SigK, and Crp have been annotated; 2) 51 gene names have been added, 46 of which are for possible toxin-antitoxin genes; 3) The coordinates of Rv1909c have been modified, making it 3 amino acids shorter; 4) The existing annotation in the Operon field has been reviewed and updated to more accurately reflect the experimental data.


Release 22 (May 2011): 1608 genes have been updated to include information gleaned from the current literature on regulation, function, proteomics and mutants. This includes results of proteomic studies, providing evidence for 533 proteins for which there was previously no proteomic annotation. Also, Rv0061 has been replaced by Rv0061c, and the coordinates of Rv1248c have been changed making it 17 amino acids longer.


Release 21 (August 2010): 207 genes have been updated to include information gleaned from the current literature on regulation, function, proteomics and mutants. This includes annotation of the putative regulons of SigE, Rv1404 and Mce3R. Also, 2 putative small regulatory RNAs have been added and the start position of Rv0981 has been changed. There are 19 new 3D structures for 11 proteins, and among these, the structures of 5 proteins are solved for the first time (glgB, Rv1496, Rv2228c, leuD, hsaA). We now also provide links for Mycobacterium smegmatis orthologs to the new SmegmaList website.


Release 20 (June 2010): 235 genes have been updated to include information gleaned from the current literature on regulation, function, and mutants. This includes annotation of the putative regulons of Cmr, RelA, DosR, and several RNA polymerase sigma factors. Also, 12 putative small regulatory RNAs have been added. There are 23 new 3D structures for 15 proteins, and among these, the structures of 13 proteins are solved for the first time (esxG, esxH, Rv0371c, Rv0603, sigL, rslA, ompA, argJ, pncA, rbsK, ddlA, birA, cdd).


Release 19 (April 2010): 474 genes have been updated to include information gleaned from the current literature on function, expression, localization, and mutants. One new gene has been added, Rv3879A, and the coordinates of Rv2240c have been changed making the predicted protein 69 amino acids shorter. Also annotated are regions that may be genomic islands, 32 genes presumed to be in the Zur regulon, and 144 proteins that are predicted to be located in the outer membrane. There are 10 new 3D structures for 7 proteins, and among these, the structures of 4 proteins are solved for the first time (cysA3, bfrA, murE, pdhC).


Release 18 (February 2010): 141 genes have been updated to include information gleaned from the current literature on function, expression, and protein structures. There are 14 new 3D structures for 9 proteins, and among these, the structures of 5 proteins are solved for the first time (Rv0674, pgi, ilvE, htdY, TB11.2). Also, information on knock-out mutants and their availability for sixteen genes has been incorporated in this release, courtesy of Prof Tanya Parish and Prof Yossef Av-Gay. An online form to catalogue Mtb knockout and mutant strains is now available on our website. Investigators are asked to submit published or unpublished Mtb knockout and mutant strains data they have generated in their laboratories on a simple, easy-to-complete form that can be found under the "TB Mutants" tab. This information will be publicly accessible and will benefit the entire research community by increasing communication and collaboration within the field. We encourage investigators to participate in this initiative. The following organizations have participated in development of this initiative: Tuberculist, NIAID/NIH, The Bill and Melinda Gates Foundation, and the Stop TB Partnership Working Group on New TB Drugs. We look forward to your participation. We now also provide Mycobacterium marinum orthologs with links to the new MarinoList website and Multiple Sequences Alignments between orthologous proteins (section Orthologs on the Gene Detail pages). Furthermore, a new Advanced Search option is proposed: Search by peptide motif by entering the standard aminoacid one letter code.


Release 17 (December 2009): 188 genes have been updated to include information gleaned from the current literature on function, mutants, expression, and protein structures. Thirty-seven genes associated with the type VII secretion systems have been updated and renamed according to the recent opinion article by Bitter et. al (PLoS Pathog, 2009), in order to provide these genes with a systematic nomenclature. Moreover, there are 8 new 3D structures for 2 proteins, and among these, the structure of 1 protein is solved for the first time (cyp125).


Release 16 (November 2009): 88 genes have been updated to include information gleaned from the current literature on function, mutants and expression. Several genes involved in the mycobacterial proteasomal degradation pathway have been annotated, including pafA, pup, and dop. Also, the translational start site of esxU has been changed, making the protein 20 amino acids shorter. Moreover, there are 65 new 3D structures for 33 proteins, and among these, the structures of 6 proteins are solved for the first time (gyrA, cyp124, acpS, Rv2714, rubB, Rv3529c). An initiative from the working group of Stop TB Partnership, NIH/NIAID, the Bill and Melinda Gates Foundation and the TubercuList website has propose TubercuList as a host for a complete catalogue of TB knock-outs and Transposon mutants together with the coordinates of the laboratories around the world. This initiative is publicly available through the website and investigators are able to complete the form on the front page of the website and contribute towards a complete catalogue of TB mutants.


Release 15 (September 2009): 135 genes have been updated to include information gleaned from the current literature on function, mutants, proteomics and expression. Nine recently identified small regulatory RNAs have been annotated (MTB000051 to MTB000059). One gene has been identified with new coordinates and new aminoacid sequence (mce1R). Moreover, there are 80 new 3D structures for 54 proteins, and among these, the structures of 11 proteins are solved for the first time (Rv0300, Rv0301, Rv0802c, echA6, Rv0956, purN, gcvH, garA, Rv1941, Rv2175c, mbtH). We now also provide direct links to protein family (PFAM) domains.


Release 14 (July 2009): 294 genes have been updated to include information gleaned from the current literature on function, mutants, regulation and expression. Proteomics data on 167 proteins has been amended. Also, predicted or confirmed members of the IdeR/Rv2711 regulon have been annotated. Moreover, there are 18 new 3D structures for 13 proteins, and among these, the structures of 11 proteins are solved for the first time (Rv0005, Rv0233, Rv0363c, Rv0429c, Rv1438, Rv1825, Rv1846c, Rv2726c, Rv2865, Rv2986c, Rv3357). We now also provide Mycobacterium smegmatis orthologs and Transmembrane predictions using HMM.


Release 13 (April 2009): One new ORF has been added, Rv1954A, part of the Rv1955, Rv1956, Rv1957 operon. Additional proteomics data on membrane proteins of over 850 proteins has been incorporated. Also, further entries have been updated to include information gleaned from the current literature on function, mutants, regulation and expression. In total, 897 genes have been updated. Moreover, there are 11 new 3D structures for 7 proteins, and among these, the structures of 5 proteins are solved for the first time (Rv0407, Rv0626, Rv0627, Rv1335, Rv1938). We now also provide Gene Ontology annotation and links to 3D Structure Viewer.


Release 12 (January 2009): One new gene has been added, a copper-binding metallothionein mymT (Rv0186A), and proteomics data on the identification and localization of over 1000 proteins has been incorporated. Also, approximately 190 additional entries have been updated to include information gleaned from the current literature on function, mutants, and expression. PDBids: 23 new structures for 14 genes between them 8 new genes without existing 3D structure: Rv0058, Rv1018c, Rv1207, Rv1336, Rv1340, Rv1657, Rv2976c, Rv3248c. Release of the new website tuberculist.epfl.ch


Release 11 (October 2008): Five new genes have been added (Rv2063A, Rv2142A, Rv2231A, Rv2231B, Rv2274A) and more than 400 entries have been updated with information gleaned from the current literature comprising information on function, mutants, and transcriptome. In addition, there are 34 new 3D structures for 15 genes, between them there are 8 genes that their structure has been solved for the first time (Rv0098, Rv0321, Rv1256c, Rv1568, Rv1612, Rv1689, Rv2780, Rv2919c).