SEA-PHAGES | Ribosomal Modulation Factor

Link to this post \| posted 19 Jul, 2019 18:05
cdshaffer	Ribosome Modulation Factors (RMF) were originally described as a set of proteins that appear to be involved in ribosome dimerization activity during the stationary phase of bacterial growth. See this JBchem article. According to this uniprot entry they have also been shown to hinder translation initiation. Phage Gilgamesh (see phage in PECAAN for all the details) gene 51 (46895-47104) is a 70 aa long protein which aligns by HHPRED to the v (lowercase v not the capital V) chain of crystal 6H4N and to the A chain of crystal 2JRM. Both these chains were annotated as "Ribosome Modulation Factor". Both HHPRED alignments are in the high 80-90% coverage, 99% probability and an e scores of around e-11. HHpred also aligns to the Pfam entry for ribosome modulation factor, with about the same coverage and e values. I see no reason to modify the current term used and would stick with "Ribosome Modulation Factor" and it is generic enough to cover how phage might be using these proteins differently than the host but the function is still likely to have something to do with modulating ribosome activity. Edited 19 Jul, 2019 19:57

Link to this post | posted 19 Jul, 2019 18:05

Ribosome Modulation Factors (RMF) were originally described as a set of proteins that appear to be involved in ribosome dimerization activity during the stationary phase of bacterial growth. See this JBchem article. According to this uniprot entry they have also been shown to hinder translation initiation.

Phage Gilgamesh (see phage in PECAAN for all the details) gene 51 (46895-47104) is a 70 aa long protein which aligns by HHPRED to the v (lowercase v not the capital V) chain of crystal 6H4N and to the A chain of crystal 2JRM. Both these chains were annotated as "Ribosome Modulation Factor". Both HHPRED alignments are in the high 80-90% coverage, 99% probability and an e scores of around e-11.

HHpred also aligns to the Pfam entry for ribosome modulation factor, with about the same coverage and e values.

I see no reason to modify the current term used and would stick with "Ribosome Modulation Factor" and it is generic enough to cover how phage might be using these proteins differently than the host but the function is still likely to have something to do with modulating ribosome activity.

Edited 19 Jul, 2019 19:57

Link to this post \| posted 13 May, 2021 15:14
kbutela	Hi all- I am working with phage Fitzgerald and wanted to follow up on Chris' proposal to add ribosome modulation factor to the approved functions database. Fitzgerald gp 14 (11299-11517) is 73 aa in length but is in a different pham than Gilgamesh gp 51. However, it aligns to the A chain of crystal structure 2JRM and 4V8G_CV, both of which are annotated as ribosome modulation factor in HHPred. Alignments are 98% probability with 60-70% coverage. I did an alignment of several BLAST results from this gene with the Escherichia coli RMF (see attached). There are 4 conserved residues that match up with the findings from E. coli RMF and other gammaproteobacteria (https://www.frontiersin.org/articles/10.3389/fmolb.2021.661691/full). Gilgamesh gp51 is annotated as ribosome modulation factor, but this function isn't on the approved list yet. Is this an okay term to use, or do we need more evidence? Edited 13 May, 2021 15:14 62Kb

Link to this post | posted 13 May, 2021 15:14

kbutela

Hi all-

I am working with phage Fitzgerald and wanted to follow up on Chris' proposal to add ribosome modulation factor to the approved functions database. Fitzgerald gp 14 (11299-11517) is 73 aa in length but is in a different pham than Gilgamesh gp 51. However, it aligns to the A chain of crystal structure 2JRM and 4V8G_CV, both of which are annotated as ribosome modulation factor in HHPred. Alignments are 98% probability with 60-70% coverage. I did an alignment of several BLAST results from this gene with the Escherichia coli RMF (see attached). There are 4 conserved residues that match up with the findings from E. coli RMF and other gammaproteobacteria (https://www.frontiersin.org/articles/10.3389/fmolb.2021.661691/full).

Gilgamesh gp51 is annotated as ribosome modulation factor, but this function isn't on the approved list yet. Is this an okay term to use, or do we need more evidence?

Edited 13 May, 2021 15:14

Link to this post \| posted 20 Dec, 2023 22:16
rlb6	Has "ribosome modulation factor" been given any consideration as an official function? Belphegor gp13 (10420-10245)MIPRDQQPMPTPAEAIEAYKAGQVSRPGAGNPYAGRRVLGSVWALGNREAQRDAYTEFRRREAERRE 68AA, same pham as Fitzgerald. Beckie Bortz 52Kb

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Ribosomal Modulation Factor