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TitleStructural basis of RfaH-mediated transcription-translation coupling.
Journal, issue, pagesNat Struct Mol Biol, Year 2024
Publish dateAug 8, 2024
AuthorsVadim Molodtsov / Chengyuan Wang / Jing Zhang / Jason T Kaelber / Gregor Blaha / Richard H Ebright /
PubMed AbstractThe NusG paralog RfaH mediates bacterial transcription-translation coupling in genes that contain a DNA sequence element, termed an ops site, required for pausing RNA polymerase (RNAP) and for ...The NusG paralog RfaH mediates bacterial transcription-translation coupling in genes that contain a DNA sequence element, termed an ops site, required for pausing RNA polymerase (RNAP) and for loading RfaH onto the paused RNAP. Here, we report cryo-electron microscopy structures of transcription-translation complexes (TTCs) containing Escherichia coli RfaH. The results show that RfaH bridges RNAP and the ribosome, with the RfaH N-terminal domain interacting with RNAP and the RfaH C-terminal domain interacting with the ribosome. The results show that the distribution of translational and orientational positions of RNAP relative to the ribosome in RfaH-coupled TTCs is more restricted than in NusG-coupled TTCs because of the more restricted flexibility of the RfaH interdomain linker. The results further suggest that the structural organization of RfaH-coupled TTCs in the 'loading state', in which RNAP and RfaH are located at the ops site during formation of the TTC, is the same as the structural organization of RfaH-coupled TTCs in the 'loaded state', in which RNAP and RfaH are located at positions downstream of the ops site during function of the TTC. The results define the structural organization of RfaH-containing TTCs and set the stage for analysis of functions of RfaH during translation initiation and transcription-translation coupling.
External linksNat Struct Mol Biol / PubMed:39117885
MethodsEM (single particle)
Resolution3.1 - 6.6 Å
Structure data

EMDB-42453, PDB-8upo:
Escherichia coli transcription-translation coupled complex class A (TTC-A) containing RfaH bound to ops signal, mRNA with a 21 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome
Method: EM (single particle) / Resolution: 5.5 Å

EMDB-42454, PDB-8upr:
Escherichia coli transcription-translation coupled complex class A (TTC-A) containing RfaH bound to ops signal, mRNA with a 21 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome
Method: EM (single particle) / Resolution: 5.3 Å

EMDB-42473, PDB-8uql:
Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH in loaded state, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-42474, PDB-8uqm:
Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH in loaded state, NusA, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome
Method: EM (single particle) / Resolution: 5.3 Å

EMDB-42477, PDB-8uqp:
Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-42479, PDB-8ur0:
Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, NusA, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-42492, PDB-8urh:
Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, mRNA with a 27 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome
Method: EM (single particle) / Resolution: 5.7 Å

EMDB-42493, PDB-8uri:
Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, NusA, mRNA with a 27 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome
Method: EM (single particle) / Resolution: 5.3 Å

EMDB-42503, PDB-8urx:
Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, mRNA with a 30 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome
Method: EM (single particle) / Resolution: 6.6 Å

EMDB-42504, PDB-8ury:
Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, NusA, mRNA with a 30 nt long spacer, and fMet-tRNA in E-site and P-site of the ribosome
Method: EM (single particle) / Resolution: 3.1 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

Source
  • escherichia coli (E. coli)
  • synthetic construct (others)
KeywordsTRANSCRIPTION / translation / RfaH / gene expression / regulation / ops / ribosome / coupling / expressome / NusA / RNA / RNA polymerase

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