ntr: transcriptional attenuation

[gocentral]

Hello,

I am requesting 3 new terms on behalf of colleague Dan Haft:

new term 1 name: transcriptional attenuation def: Regulation of transcription through variation in where transcription termination occurs. parent: new term 3 relationship to parent: isa

new term 2 name: ribosome-mediated transcriptional attenuation def: A type of transcriptional regulation at the level of early termination. This process can occur only in prokaryotes, where transcription of an operon into messenger RNA and translation of that mRNA into polypeptides occur simultaneously. The general principle is that alternative mRNA secondary structures occur under different physiological conditions such as high vs. low availability of a particular amino acid. One set of conditions favors early termination of transcription. In the classic example of the trp biosynthesis operon, translation of the gene for a short, trp-containing polypeptide called the trp operon leader peptide pauses either at a trp codon (if tryptophan is scarce) or the stop codon (if trp is readily available). In the former situation transcription continues, but in the latter a Rho-independent terminator forms and reduces, or "attenuates," expression of the tryptophan biosynthesis genes. Although the polypeptides encoded by leader peptide genes appear not to be stable once their translation is complete, it is suggested by recent studies that their nascent polypeptide chains interact specifically with ribosomes, specific uncharged tRNAs, or other cellular components to inhibit release at the stop codon and improve the function of transcriptional attenuation as a regulatory switch. parent: new term 1 relationship: isa synonym: (exact) "leader peptide-mediated transcriptional attenuation"

new term 3 name: regulation of transcription termination def: Any process that modulates the frequency, rate, extent, or location of transcription termination. parent: transcription termination GO:0006353 relationship to parent: regulates (are we using this yet?) parent: regulation of transcription GO:0045449 relatinship to parent: isa

Def refs: Dan looking at Genes IV, Lewin, plus a bit of me looking at other terms.

We are aware of other types of transcription attenuation, namely anisense-mediated transcription attenuation, but we are not prepared to request that term at this time, but this structure allows its insertion when we are ready.

Thanks, Michelle

Reported by: mlgwinn

Original Ticket: "geneontology/ontology-requests/2714":https://sourceforge.net/p/geneontology/ontology-requests/2714

[gocentral]

Logged In: YES user_id=436423

Hi Michelle,

This all looks fine ... and leads me to ask a favor. Did you or Dan happen to find anything that might help us with a definition for the existing term 'translational attenuation' (GO:0009386)?

Thanks, midori

Original comment by: mah11

[gocentral]

Logged In: YES user_id=482944

I don't have anything on hand, but I'll ask Dan and get back to you. Michelle

Original comment by: mlgwinn

[gocentral]

Logged In: YES user_id=482944

Hi Midori,

"I got the following from Dan: Good references for translational attenuation are PMID: 15805513 (prokaryotic) and PMID: 15694341 (eukaryotic). Translational attentuation is a regulatory mechanism analogous to ribosome-mediated transcriptional attenuation. The system requires the presence of a short ORF, called a leader peptide, encoded in the mRNA upstream of the ribosome-binding site and start codon of the gene whose translation is to be regulated. Certain conditions, such as presence of the antibiotic tetracycline in bacteria or amino acid starvation, may cause slowing or stalling of the ribosome translating the leader peptide. The stalled ribosome masks a region of the mRNA and affects which of two alternative mRNA folded structures will form, therefore controlling whether or not a ribosome will bind and initiate translation of the downstream gene. Translational attenuation is analogous to ribosome-mediated transcriptional attenuation, in which mRNA remodeling caused by ribosome stalling regulates transcriptional termination rather than translational initiation. "

Is this ok as a defintion - or is it too long?

Michelle

Original comment by: mlgwinn

[gocentral]

Logged In: YES user_id=436423

Well, it's not short, but there doesn't seem to be much extraneous matter, so it'll have to do. Thanks to you and Dan!

m

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> gomidori

Original comment by: mah11

[gocentral]

Logged In: YES user_id=436423

added regulation of transcription termination GO:0031554 transcriptional attenuation GO:0031555 ribosome-mediated transcriptional attenuation GO:0031556

... and the def for GO:0009386

note- nope, we haven't started using 'regulates' yet ...

Original comment by: mah11

[gocentral]

• milestone: --> TermGenie
• status: open --> closed-accepted

Original comment by: mah11