Subsystem: Heat shock dnaK gene cluster extended

This subsystem's description is:

DnaK forms chaperone machinery with co-chaperones DnaJ and GrpE, which participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins. In some species (e.g., in Salmonella enterica) DnaK operon is apparently induced also inside host macrophages during infection (Takaya et al., 2004). See SS: “Protein chaperons” for details

This SS is a collection of poorly characterized genes, which tend to co-localize with the hrcA-dnaK-dnaJ-grpE genes in genomes of various microbial species, and, hence, might also be involved in heat/oxidative stress response. A stunning example – a large gene cluster preserved in many Firmicutes. Furthermore, co-expression of three of these hypothetical genes with the hrcA-dnaK-dnaJ-grpE operon has been experimentally demonstrated in B. subtilis (Homuth et al., 1997). In this SS they are annotated as:
Orf35 (yqeT): Ribosomal protein L11 methyltransferase (EC 2.1.1.-)
Orf28 (yqeU): Hypothetical protein DUF558, predicted RNA methyltransferase
Orf50 (yqeV): MiaB family protein, possibly involved in tRNA or rRNA modification

Although specific functions of these and other genes in conserved cluster with dnaK operon are currently unknown, it is noteworthy that many of them are predicted to be involved in various tRNA or rRNA modifications. Since many tRNA modifications are believed to improve reading frame maintenance (Urbonavicius et al., 2001), it is tempting to speculate that the role of these additional proteins is protecting ribosomal function (e.g. accuracy of translation) during heat shock and other stresses. Indeed, MiaB-like enzymes are specifically over-represented in certain thermophiles, such as Thermotoga maritima, Aquifex aeolicus and Methanococcus jannaschii, suggesting that they might additionally participate in some thermophile-specific nucleotide modifications (Anantharaman et al., 2001). MiaB is a bifunctional radical-S-adenosylmethionine enzyme, an isopentenyl-adenosine tRNA methylthiolase that assists in the prevention of frameshift mutations (Esberg et al., 1999; Pierrel et al., 2004). It's paralog (not actual MiaB) is often present in this gene cluster.

The hypothesis that these putative additional heat-shock-related proteins are potentially involvement in improving ribosomal function during stress is further supported by the fact that “GTP-binding protein LepA” is often co-localized with these “extended dnaK gene clusters”. This universally conserved protein has been recently shown to function as an additional elongation factor required for back-translocating posttranslocational ribosomes. LepA recognizes ribosomes after a defective translocation reaction and induces a back-translocation (giving EF-G a second chance to translocate the tRNAs correctly (Qin et al., 2006))

For more information, please check out the description and the additional notes tabs, below

DiagramFunctional RolesSubsystem SpreadsheetDescriptionAdditional Notes 

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