June 26, 2005

Mycoplasma genitalium

[Biology_] I was searching the net for any microarray data for mycoplasma genitalium. I found anything but... Here is a list of some useful links.

Cell Cycle Regulated Yeast Genes Spellman's yeast microarray paper and data.

SMD : Microarray Resources : Databases

EBI Databases - ArrayExpress Home Ebi microarray data. Contains some yeast.

ExpressDB Database of E.coli and yeast microarray data.

microarray data List of microarray data sources.

Expasy 191 out of 486 swiss-prot matches to M.G. are "hypothetical" proteins, i.e. we don't have a clue what they are doing...

PDB Query Result Only three M.G. proteins are found in PDB.

Swiss-Prot taxonomic query: Mycoplasma genitalium List of all genes in M.G. with descriptions. Only can get the first 100 for some reason...

the Gene Ontology website: Tries to organize gene functions.

2can Bioinformatics Educational Resource: Home Page great site that includes bioinformatics tutorials and a section on protein function.

Proteomics - Transcription Factors: some info on protein function

Saccharomyces cerevisiae

Genome Browser Need to figure out how to use this.

Genome Sizes:
E. coli 4,639,221 4,377 4,290 of these genes encode proteins; the rest RNAs
Mycoplasma genitalium 580,073 483 three of the smallest true organisms
Ureaplasma urealyticum 751,719 652
Mycoplasma pneumoniae 816,394 680
Saccharomyces cerevisiae 12,495,682 5,770 Budding yeast. A eukaryote.

Mycoplasma genitalium Background

Entrez PubMed: " The minimal gene complement of Mycoplasma genitalium.

Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, Bult CJ, Kerlavage AR, Sutton G, Kelley JM, et al.

Institute for Genomic Research, Rockville, MD 20850, USA.

The complete nucleotide sequence (580,070 base pairs) of the Mycoplasma genitalium genome, the smallest known genome of any free-living organism, has been determined by whole-genome random sequencing and assembly. A total of only 470 predicted coding regions were identified that include genes required for DNA replication, transcription and translation, DNA repair, cellular transport, and energy metabolism. Comparison of this genome to that of Haemophilus influenzae suggests that differences in genome content are reflected as profound differences in physiology and metabolic capacity between these two organisms.

PMID: 7569993 [PubMed - indexed for MEDLINE]

Mycoplasma genitalium G-37 Information TIGR did the sequencing of MG, this is its homepage.

The DNA sequences of the complete genomes of seven mycoplasmas have been determined, including

* Mycoplasma genitalium has 580,073 base pairs of DNA encoding 517 genes (480 for proteins; the rest for RNAs).
* Mycoplasma urealyticum has 751,719 base pairs of DNA encoding 651 genes (613 for proteins; 39 for RNAs).
* Mycoplasma pneumoniae has 816,394 base pairs of DNA encoding 679 genes.

How many genes does it take to make an organism?
The scientists at The Institute for Genomic Research (TIGR) who determined the Mycoplasma genitalium sequence followed this work by systematically destroying its genes (by mutating them with insertions) to see which ones are essential to life and which are dispensable. Of the 480 protein-encoding genes, they conclude that only 265–350 of them are essential to life.

Genome Sizes Here is a page that has the sizes of the smallest genomes.

NCBI HomePage The site that I found the complete genome of mycoplasma genitalium.

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