⊟Summary[edit | edit source]
- pan ID?: SAUPAN002664000
- symbol?: prfB
- synonym:
- description?: peptide chain release factor 2
- peptide chain release factor 2
- peptide chain release factor 2 (RF-2)
- peptide chain release factor RF2
- pseudogene
descriptions from strain specific annotations:
- strand?: +
- coordinates?: 3161633..3162743
- synteny block?: BlockID0018990
- occurrence?: in 100% of 34 strains
prfB : peptide chain release factor 2 [1]
Ribosomal peptide release has not been extensively characterized in firmicutes and functions are therefore extrapolated from foundational studies in E. coli and pseudomonas. Peptide chain release factor 2 (RF-2) is a "class 1" release factor required for the release of completed peptides from the ribosome at stop codons UGA and UAA. RF-2 requires post-translational methylation by PrmC at glutamine-252 for proper function. After promoting release of peptides from UGA/UAA stop codons, RF-2 needs to be dissociated from the ribosome by "class 2" RF-3, particularly if the stop codon is UGA, before it can act on another ribosome. It also has a role in proofreading following peptidyl transfer, a role that is not associated with RF-1. Finally, RF-2 has a highly atypical coding sequence of 1,111 bp that is rarely annotated correctly. After leucine-24, the coding sequence has an in-frame "UGA" stop codon resulting in ribosomal pausing. Full-length RF-2 is generated by a high-frequency ribosomal frameshift and, since UGA-terminated peptides can only be released by RF-2, provides a negative feedback regulation for full-length RF-2. Indeed, placing the coding sequence all in-frame without the programmed frameshift is lethal in firmicutes.
⊟Orthologs[edit | edit source]
⊟Genome Viewer[edit | edit source]
| COL | |
| N315 | |
| NCTC8325 | |
| Newman | |
| USA300_FPR3757 |
⊟Alignments[edit | edit source]
- alignment of orthologues: CLUSTAL format alignment by MAFFT L-INS-i (v7.307)
COL MELSEIKRNIDKYNQDLTQIRGSLDLENKETNIQEYEEMMAEPNFWDNQTKAQDIIDKNN
N315 ---------------------------------------MAEPNFWDNQTKAQDIIDKNN
NCTC8325 ------------------------------------------------------------
Newman --------------------------------------MMAEPNFWDNQTKAQDIIDKNN
COL ALKAIVNGYKTLQAEVDDMDATWDLLQEEFDEEMKEDLEQEVINFKAKVDEYELQLLLDG
N315 ALKAIVNGYKTLQAEVDDMDATWDLLQEEFDEEMKEDLEQEVINFKAKVDEYELQLLLDG
NCTC8325 ------------------MDATWDLLQEEFDEEMKEDLEQEVINFKAKVDEYELQLLLDG
Newman ALKAIVNGYKTLQAEVDDMDATWDLLQEEFDEEMKEDLEQEVINFKAKVDEYELQLLLDG
******************************************
COL PHDANNAILELHPGAGGTESQDWANMLFRMYQRYCEKKGFKVETVDYLPGDEAGIKSVTL
N315 PHDANNAILELHPGAGGTESQDWANMLFRMYQRYCEKKGFKVETVDYLPGDEAGIKSVTL
NCTC8325 PHDANNAILELHPGAGGTESQDWANMLFRMYQRYCEKKGFKVETVDYLPGDEAGIKSVTL
Newman PHDANNAILELHPGAGGTESQDWANMLFRMYQRYCEKKGFKVETVDYLPGDEAGIKSVTL
************************************************************
COL LIKGHNAYGYLKAEKGVHRLVRISPFDSSGRRHTSFASCDVIPDFNNDEIEIEINPDDIT
N315 LIKGHNAYGYLKAEKGVHRLVRISPFDSSGRRHTSFASCDVIPDFNNDEIEIEINPDDIT
NCTC8325 LIKGHNAYGYLKAEKGVHRLVRISPFDSSGRRHTSFASCDVIPDFNNDEIEIEINPDDIT
Newman LIKGHNAYGYLKAEKGVHRLVRISPFDSSGRRHTSFASCDVIPDFNNDEIEIEINPDDIT
************************************************************
COL VDTFRASGAGGQHINKTESAIRITHHPSGIVVNNQNERSQIKNREAAMKMLKSKLYQLKL
N315 VDTFRASGAGGQHINKTESAIRITHHPSGIVVNNQNERSQIKNREAAMKMLKSKLYQLKL
NCTC8325 VDTFRASGAGGQHINKTESAIRITHHPSGIVVNNQNERSQIKNREAAMKMLKSKLYQLKL
Newman VDTFRASGAGGQHINKTESAIRITHHPSGIVVNNQNERSQIKNREAAMKMLKSKLYQLKL
************************************************************
COL EEQAREMAEIRGEQKEIGWGSQIRSYVFHPYSMVKDHRTNEETGKVDAVMDGDIGPFIES
N315 EEQAREMAEIRGEQKEIGWGSQIRSYVFHPYSMVKDHRTNEETGKVDAVMDGDIGPFIES
NCTC8325 EEQAREMAEIRGEQKEIGWGSQIRSYVFHPYSMVKDHRTNEETGKVDAVMDGDIGPFIES
Newman EEQAREMAEIRGEQKEIGWGSQIRSYVFHPYSMVKDHRTNEETGKVDAVMDGDIGPFIES
************************************************************
COL YLRQTMSHD
N315 YLRQTMSHD
NCTC8325 YLRQTMSHD
Newman YLRQTMSHD
*********
- ↑ Alexandros D Petropoulos, Megan E McDonald, Rachel Green, Hani S Zaher
Distinct roles for release factor 1 and release factor 2 in translational quality control.
J Biol Chem: 2014, 289(25);17589-96
[PubMed:24798339] [WorldCat.org] [DOI] (I p)Cassidy R Prince, Isabella N Lin, Heather A Feaga
The evolution and functional significance of the programmed ribosomal frameshift in prfB.
bioRxiv: 2024;
[PubMed:39386688] [WorldCat.org] [DOI] (I e)