| Structural highlights
Function
[RS8_ECOLI] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity).[HAMAP-Rule:MF_01302_B] Protein S8 is a translational repressor protein, it controls the translation of the spc operon by binding to its mRNA.[HAMAP-Rule:MF_01302_B] [RS13_ECOLI] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA.[1] In the E.coli 70S ribosome in the initiation state (PubMed:12809609) was modeled to contact the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; bridge B1a is broken in the model with bound EF-G, while the protein-protein contacts between S13 and L5 in B1b change (PubMed:12809609). The 23S rRNA contact site in bridge B1a is modeled to differ in different ribosomal states (PubMed:16272117), contacting alternately S13 or S19. In the two 3.5 angstroms resolved ribosome structures (PubMed:12859903) the contacts between L5, S13 and S19 bridge B1b are different, confirming the dynamic nature of this interaction. Bridge B1a is not visible in the crystallized ribosomes due to 23S rRNA disorder.[2] Contacts the tRNAs in the A and P sites.[3] The C-terminal tail plays a role in the affinity of the 30S P site for different tRNAs.[4] [RS5_ECOLI] With S4 and S12 plays an important role in translational accuracy. Many suppressors of streptomycin-dependent mutants of protein S12 are found in this protein, some but not all of which decrease translational accuracy (ram, ribosomal ambiguity mutations).[5] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body.[6] The physical location of this protein suggests it may also play a role in mRNA unwinding by the ribosome, possibly by forming part of a processivity clamp.[7] [RS9_ECOLI] The C-terminal tail plays a role in the affinity of the 30S P site for different tRNAs. Mutations that decrease this affinity are suppressed in the 70S ribosome.[8] [RS11_ECOLI] Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01310] [RS4_ECOLI] One of two assembly initiator proteins for the 30S subunit, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit.[9] [10] [11] With S5 and S12 plays an important role in translational accuracy; many suppressors of streptomycin-dependent mutants of protein S12 are found in this protein, some but not all of which decrease translational accuracy (ram, ribosomal ambiguity mutations).[12] [13] [14] Plays a role in mRNA unwinding by the ribosome, possibly by forming part of a processivity clamp.[15] [16] [17] Protein S4 is also a translational repressor protein, it controls the translation of the alpha-operon (which codes for S13, S11, S4, RNA polymerase alpha subunit, and L17) by binding to its mRNA.[18] [19] [20] Also functions as a rho-dependent antiterminator of rRNA transcription, increasing the synthesis of rRNA under conditions of excess protein, allowing a more rapid return to homeostasis. Binds directly to RNA polymerase.[21] [22] [23] [RS19_ECOLI] In the E.coli 70S ribosome in the initiation state (PubMed:12809609) it has been modeled to contact the 23S rRNA of the 50S subunit forming part of bridge B1a; this bridge is broken in the model with bound EF-G. The 23S rRNA contact site in bridge B1a is modeled to differ in different ribosomal states (PubMed:12859903), contacting alternately S13 or S19. In the 3.5 angstroms resolved ribosome structures (PubMed:16272117) the contacts between L5, S13 and S19 bridge B1b are different, confirming the dynamic nature of this interaction. Bridge B1a is not visible in the crystallized ribosomes due to 23S rRNA disorder.[HAMAP-Rule:MF_00531] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. Contacts the A site tRNA.[HAMAP-Rule:MF_00531] [RS14_ECOLI] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site.[HAMAP-Rule:MF_00537] [RS17_ECOLI] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. Also plays a role in translational accuracy; neamine-resistant ribosomes show reduced neamine-induced misreading in vitro.[HAMAP-Rule:MF_01345] [RS16_ECOLI] In addition to being a ribosomal protein, S16 also has a cation-dependent endonuclease activity.[24] In-frame fusions with the ribosome maturation factor rimM suppress mutations in the latter (probably due to increased rimM expression) and are found in translationally active 70S ribosomes.[25] [RS10_ECOLI] Involved in the binding of tRNA to the ribosomes.[HAMAP-Rule:MF_00508] [RS6_ECOLI] Binds together with S18 to 16S ribosomal RNA.[HAMAP-Rule:MF_00360] [RS20_ECOLI] Binds directly to 16S ribosomal RNA.[HAMAP-Rule:MF_00500] [RSGA_ECOLI] One of at least 4 proteins (Era, RbfA, RimM and RsgA/YjeQ) that assist in the late maturation steps of the functional core of the 30S ribosomal subunit (PubMed:18223068, PubMed:21102555, PubMed:21303937, PubMed:25904134, PubMed:27382067). Binds the 30S subunit contacting the head, platform, and rRNA helix 44, which may assist the last maturation stages (PubMed:21788480, PubMed:21960487). Removes RbfA from mature, but not immature 30S ribosomes in a GTP-dependent manner; 95% removal in the presence of GTP, 90% removal in GMP-PNP and 65% removal in the presence of GDP (PubMed:21102555, PubMed:25904134). Circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover (PubMed:12220175). Dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96-fold increase in kcat) ribosomes (PubMed:14973029). Mature 30S ribosomes stimulate intrinsic GTPase more than do immature 30S ribosomes (PubMed:25904134). Ribosome-associated GTPase activity is stimulated by RbfA (PubMed:21102555). The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin (PubMed:15466596) streptomycin and spectinomycin (PubMed:15828870). This inhibition is not due to competition for binding sites on the 30S or 70S ribosome (PubMed:15828870).[26] [27] [28] [29] [30] [31] [32] [33] [RS12_ECOLI] With S4 and S5 plays an important role in translational accuracy.[HAMAP-Rule:MF_00403_B] Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity).[HAMAP-Rule:MF_00403_B] Cryo-EM studies suggest that S12 contacts the EF-Tu bound tRNA in the A-site during codon-recognition. This contact is most likely broken as the aminoacyl-tRNA moves into the peptidyl transferase center in the 50S subunit.[HAMAP-Rule:MF_00403_B] [RS15_ECOLI] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_01343] In the E.coli 70S ribosome it has been modeled (PubMed:12809609) to contact the 23S rRNA of the 50S subunit forming part of bridge B4. In the two 3.5 A resolved ribosome structures (PubMed:16272117) there are minor differences between side-chain conformations.[HAMAP-Rule:MF_01343] [RS18_ECOLI] Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit.[HAMAP-Rule:MF_00270] [RS7_ECOLI] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, where it has been shown to contact mRNA. Has been shown to contact tRNA in both the P and E sites; it probably blocks exit of the E site tRNA.[34] Protein S7 is also a translational repressor protein; it regulates the expression of the str operon members to different degrees by binding to its mRNA.[35]
Publication Abstract from PubMed
During 30S ribosomal subunit biogenesis, assembly factors are believed to prevent accumulation of misfolded intermediate states of low free energy that slowly convert into mature 30S subunits, namely, kinetically trapped particles. Among the assembly factors, the circularly permuted GTPase, RsgA, plays a crucial role in the maturation of the 30S decoding center. Here, directed hydroxyl radical probing and single particle cryo-EM are employed to elucidate RsgA's mechanism of action. Our results show that RsgA destabilizes the 30S structure, including late binding r-proteins, providing a structural basis for avoiding kinetically trapped assembly intermediates. Moreover, RsgA exploits its distinct GTPase pocket and specific interactions with the 30S to coordinate GTPase activation with the maturation state of the 30S subunit. This coordination validates the architecture of the decoding center and facilitates the timely release of RsgA to control the progression of 30S biogenesis.
RsgA couples the maturation state of the 30S ribosomal decoding center to activation of its GTPase pocket.,Lopez-Alonso JP, Kaminishi T, Kikuchi T, Hirata Y, Iturrioz I, Dhimole N, Schedlbauer A, Hase Y, Goto S, Kurita D, Muto A, Zhou S, Naoe C, Mills DJ, Gil-Carton D, Takemoto C, Himeno H, Fucini P, Connell SR Nucleic Acids Res. 2017 May 8. doi: 10.1093/nar/gkx324. PMID:28482099[36]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Hoang L, Fredrick K, Noller HF. Creating ribosomes with an all-RNA 30S subunit P site. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12439-43. Epub 2004 Aug 12. PMID:15308780 doi:10.1073/pnas.0405227101
- ↑ Hoang L, Fredrick K, Noller HF. Creating ribosomes with an all-RNA 30S subunit P site. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12439-43. Epub 2004 Aug 12. PMID:15308780 doi:10.1073/pnas.0405227101
- ↑ Hoang L, Fredrick K, Noller HF. Creating ribosomes with an all-RNA 30S subunit P site. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12439-43. Epub 2004 Aug 12. PMID:15308780 doi:10.1073/pnas.0405227101
- ↑ Hoang L, Fredrick K, Noller HF. Creating ribosomes with an all-RNA 30S subunit P site. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12439-43. Epub 2004 Aug 12. PMID:15308780 doi:10.1073/pnas.0405227101
- ↑ Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042
- ↑ Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042
- ↑ Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042
- ↑ Hoang L, Fredrick K, Noller HF. Creating ribosomes with an all-RNA 30S subunit P site. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12439-43. Epub 2004 Aug 12. PMID:15308780 doi:10.1073/pnas.0405227101
- ↑ Nowotny V, Nierhaus KH. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry. 1988 Sep 6;27(18):7051-5. PMID:2461734
- ↑ Torres M, Condon C, Balada JM, Squires C, Squires CL. Ribosomal protein S4 is a transcription factor with properties remarkably similar to NusA, a protein involved in both non-ribosomal and ribosomal RNA antitermination. EMBO J. 2001 Jul 16;20(14):3811-20. PMID:11447122 doi:10.1093/emboj/20.14.3811
- ↑ Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042
- ↑ Nowotny V, Nierhaus KH. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry. 1988 Sep 6;27(18):7051-5. PMID:2461734
- ↑ Torres M, Condon C, Balada JM, Squires C, Squires CL. Ribosomal protein S4 is a transcription factor with properties remarkably similar to NusA, a protein involved in both non-ribosomal and ribosomal RNA antitermination. EMBO J. 2001 Jul 16;20(14):3811-20. PMID:11447122 doi:10.1093/emboj/20.14.3811
- ↑ Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042
- ↑ Nowotny V, Nierhaus KH. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry. 1988 Sep 6;27(18):7051-5. PMID:2461734
- ↑ Torres M, Condon C, Balada JM, Squires C, Squires CL. Ribosomal protein S4 is a transcription factor with properties remarkably similar to NusA, a protein involved in both non-ribosomal and ribosomal RNA antitermination. EMBO J. 2001 Jul 16;20(14):3811-20. PMID:11447122 doi:10.1093/emboj/20.14.3811
- ↑ Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042
- ↑ Nowotny V, Nierhaus KH. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry. 1988 Sep 6;27(18):7051-5. PMID:2461734
- ↑ Torres M, Condon C, Balada JM, Squires C, Squires CL. Ribosomal protein S4 is a transcription factor with properties remarkably similar to NusA, a protein involved in both non-ribosomal and ribosomal RNA antitermination. EMBO J. 2001 Jul 16;20(14):3811-20. PMID:11447122 doi:10.1093/emboj/20.14.3811
- ↑ Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042
- ↑ Nowotny V, Nierhaus KH. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry. 1988 Sep 6;27(18):7051-5. PMID:2461734
- ↑ Torres M, Condon C, Balada JM, Squires C, Squires CL. Ribosomal protein S4 is a transcription factor with properties remarkably similar to NusA, a protein involved in both non-ribosomal and ribosomal RNA antitermination. EMBO J. 2001 Jul 16;20(14):3811-20. PMID:11447122 doi:10.1093/emboj/20.14.3811
- ↑ Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042
- ↑ Oberto J, Bonnefoy E, Mouray E, Pellegrini O, Wikstrom PM, Rouviere-Yaniv J. The Escherichia coli ribosomal protein S16 is an endonuclease. Mol Microbiol. 1996 Mar;19(6):1319-30. PMID:8730873
- ↑ Oberto J, Bonnefoy E, Mouray E, Pellegrini O, Wikstrom PM, Rouviere-Yaniv J. The Escherichia coli ribosomal protein S16 is an endonuclease. Mol Microbiol. 1996 Mar;19(6):1319-30. PMID:8730873
- ↑ Daigle DM, Rossi L, Berghuis AM, Aravind L, Koonin EV, Brown ED. YjeQ, an essential, conserved, uncharacterized protein from Escherichia coli, is an unusual GTPase with circularly permuted G-motifs and marked burst kinetics. Biochemistry. 2002 Sep 17;41(37):11109-17. PMID:12220175
- ↑ Daigle DM, Brown ED. Studies of the interaction of Escherichia coli YjeQ with the ribosome in vitro. J Bacteriol. 2004 Mar;186(5):1381-7. PMID:14973029
- ↑ Himeno H, Hanawa-Suetsugu K, Kimura T, Takagi K, Sugiyama W, Shirata S, Mikami T, Odagiri F, Osanai Y, Watanabe D, Goto S, Kalachnyuk L, Ushida C, Muto A. A novel GTPase activated by the small subunit of ribosome. Nucleic Acids Res. 2004 Oct 5;32(17):5303-9. Print 2004. PMID:15466596 doi:http://dx.doi.org/10.1093/nar/gkh861
- ↑ Campbell TL, Daigle DM, Brown ED. Characterization of the Bacillus subtilis GTPase YloQ and its role in ribosome function. Biochem J. 2005 Aug 1;389(Pt 3):843-52. PMID:15828870 doi:http://dx.doi.org/BJ20041873
- ↑ Goto S, Kato S, Kimura T, Muto A, Himeno H. RsgA releases RbfA from 30S ribosome during a late stage of ribosome biosynthesis. EMBO J. 2011 Jan 5;30(1):104-14. doi: 10.1038/emboj.2010.291. Epub 2010 Nov 23. PMID:21102555 doi:http://dx.doi.org/10.1038/emboj.2010.291
- ↑ Jeganathan A, Razi A, Thurlow B, Ortega J. The C-terminal helix in the YjeQ zinc-finger domain catalyzes the release of RbfA during 30S ribosome subunit assembly. RNA. 2015 Jun;21(6):1203-16. doi: 10.1261/rna.049171.114. Epub 2015 Apr 22. PMID:25904134 doi:http://dx.doi.org/10.1261/rna.049171.114
- ↑ Campbell TL, Brown ED. Genetic interaction screens with ordered overexpression and deletion clone sets implicate the Escherichia coli GTPase YjeQ in late ribosome biogenesis. J Bacteriol. 2008 Apr;190(7):2537-45. Epub 2008 Jan 25. PMID:18223068 doi:http://dx.doi.org/JB.01744-07
- ↑ Thurlow B, Davis JH, Leong V, F Moraes T, Williamson JR, Ortega J. Binding properties of YjeQ (RsgA), RbfA, RimM and Era to assembly intermediates of the 30S subunit. Nucleic Acids Res. 2016 Nov 16;44(20):9918-9932. Epub 2016 Jul 5. PMID:27382067 doi:http://dx.doi.org/10.1093/nar/gkw613
- ↑ Nowotny V, Nierhaus KH. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry. 1988 Sep 6;27(18):7051-5. PMID:2461734
- ↑ Nowotny V, Nierhaus KH. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry. 1988 Sep 6;27(18):7051-5. PMID:2461734
- ↑ Lopez-Alonso JP, Kaminishi T, Kikuchi T, Hirata Y, Iturrioz I, Dhimole N, Schedlbauer A, Hase Y, Goto S, Kurita D, Muto A, Zhou S, Naoe C, Mills DJ, Gil-Carton D, Takemoto C, Himeno H, Fucini P, Connell SR. RsgA couples the maturation state of the 30S ribosomal decoding center to activation of its GTPase pocket. Nucleic Acids Res. 2017 May 8. doi: 10.1093/nar/gkx324. PMID:28482099 doi:http://dx.doi.org/10.1093/nar/gkx324
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