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Article ; Online: Contribution of an alternative 16S rRNA helix to biogenesis of the 30S subunit of the ribosome.

Warner, Benjamin R / Fredrick, Kurt

2024

Abstract: 30S subunits become inactive upon exposure to low Mg2+ concentration, due to a reversible conformational change that entails nucleotides (nt) in the neck helix (h28) and 3' tail of 16S rRNA. This active-to-inactive transition involves partial unwinding ... ...

Abstract	30S subunits become inactive upon exposure to low Mg2+ concentration, due to a reversible conformational change that entails nucleotides (nt) in the neck helix (h28) and 3' tail of 16S rRNA. This active-to-inactive transition involves partial unwinding of h28 and re-pairing of nt 921-923 with nt 1532-1534, which requires flipping of the 3' tail by ~180 degrees. Growing evidence suggests that immature 30S particles adopt the inactive conformation in the cell, and transition to the active state occurs at a late stage of maturation. Here, we target nucleotides that form the alternative helix (hALT) of the inactive state. Using an orthogonal ribosome system, we find that disruption of hALT decreases translation activity in the cell modestly, by ~2-fold, without compromising ribosome fidelity. Ribosomes carrying substitutions at positions 1532-1533 support growth of E. coli strain Δ7 prrn (which carries a single rRNA operon), albeit at rates 10-20% slower than wild-type ribosomes. These mutant Δ7 prrn strains accumulate free 30S particles and precursor 17S rRNA, indicative of biogenesis defects. Analysis of purified control and mutant subunits suggests that hALT stabilizes the inactive state by 1.2 kcal/mol with little-to-no impact on the active state or the transition state of conversion.
Language	English
Publishing date	2024-04-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	1241540-6
ISSN	1469-9001 ; 1355-8382
ISSN (online)	1469-9001
ISSN	1355-8382
DOI	10.1261/rna.079960.124
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Article ; Online: Analysis of programmed frameshifting during translation of

Naeem, Fawwaz M / Gemler, Bryan T / McNutt, Zakkary A / Bundschuh, Ralf / Fredrick, Kurt

RNA (New York, N.Y.)

2024 Volume 30, Issue 2, Page(s) 136–148

Abstract: Ribosomes of Bacteroidia fail to recognize Shine-Dalgarno (SD) sequences due to sequestration of the 3' tail of the 16S rRNA on the 30S platform. Yet in these organisms, ... ...

Abstract	Ribosomes of Bacteroidia fail to recognize Shine-Dalgarno (SD) sequences due to sequestration of the 3' tail of the 16S rRNA on the 30S platform. Yet in these organisms, the
MeSH term(s)	Protein Biosynthesis/genetics ; RNA, Ribosomal, 16S/metabolism ; Frameshift Mutation ; Ribosomes/metabolism ; Escherichia coli/genetics ; Frameshifting, Ribosomal/genetics ; Flavobacterium
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2024-01-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	1241540-6
ISSN	1469-9001 ; 1355-8382
ISSN (online)	1469-9001
ISSN	1355-8382
DOI	10.1261/rna.079721.123
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Article ; Online: Roles of the leader-trailer helix and antitermination complex in biogenesis of the 30S ribosomal subunit.

Warner, Benjamin R / Bundschuh, Ralf / Fredrick, Kurt

Nucleic acids research

2023 Volume 51, Issue 10, Page(s) 5242–5254

Abstract: Ribosome biogenesis occurs co-transcriptionally and entails rRNA folding, ribosomal protein binding, rRNA processing, and rRNA modification. In most bacteria, the 16S, 23S and 5S rRNAs are co-transcribed, often with one or more tRNAs. Transcription ... ...

Abstract	Ribosome biogenesis occurs co-transcriptionally and entails rRNA folding, ribosomal protein binding, rRNA processing, and rRNA modification. In most bacteria, the 16S, 23S and 5S rRNAs are co-transcribed, often with one or more tRNAs. Transcription involves a modified RNA polymerase, called the antitermination complex, which forms in response to cis-acting elements (boxB, boxA and boxC) in the nascent pre-rRNA. Sequences flanking the rRNAs are complementary and form long helices known as leader-trailer helices. Here, we employed an orthogonal translation system to interrogate the functional roles of these RNA elements in 30S subunit biogenesis in Escherichia coli. Mutations that disrupt the leader-trailer helix caused complete loss of translation activity, indicating that this helix is absolutely essential for active subunit formation in the cell. Mutations of boxA also reduced translation activity, but by only 2- to 3-fold, suggesting a smaller role for the antitermination complex. Similarly modest drops in activity were seen upon deletion of either or both of two leader helices, termed here hA and hB. Interestingly, subunits formed in the absence of these leader features exhibited defects in translational fidelity. These data suggest that the antitermination complex and precursor RNA elements help to ensure quality control during ribosome biogenesis.
MeSH term(s)	RNA, Ribosomal/metabolism ; Ribosomes/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/metabolism ; Ribosomal Proteins/metabolism ; Ribosome Subunits, Small/metabolism ; RNA, Ribosomal, 5S/metabolism ; RNA, Ribosomal, 16S/metabolism ; RNA, Ribosomal, 23S/metabolism
Chemical Substances	RNA, Ribosomal ; Escherichia coli Proteins ; Ribosomal Proteins ; RNA, Ribosomal, 5S ; RNA, Ribosomal, 16S ; RNA, Ribosomal, 23S
Language	English
Publishing date	2023-04-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkad316
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Article ; Online: Another look at mutations in ribosomal protein S4 lends strong support to the domain closure model.

Fredrick, Kurt

Journal of bacteriology

2015 Volume 197, Issue 6, Page(s) 1014–1016

Abstract: Ribosomes employ a "kinetic discrimination" mechanism, in which correct substrates are incorporated more rapidly than incorrect ones. The structural basis of this mechanism may involve 30S domain closure, a global conformational change that coincides ... ...

Abstract	Ribosomes employ a "kinetic discrimination" mechanism, in which correct substrates are incorporated more rapidly than incorrect ones. The structural basis of this mechanism may involve 30S domain closure, a global conformational change that coincides with codon recognition. In a direct screen for fidelity-altering mutations, Agarwal and coworkers (D. Agarwal, D. Kamath, S. T. Gregory, and M. O'Connor, J Bacteriol 197:1017-1025, 2015, doi:10.1128/JB.02485-14) isolated mutations that progressively truncate the C terminus of S4. All of these promote miscoding and undoubtedly destabilize the S4-S5 interface, consistent with the domain closure model.
MeSH term(s)	Escherichia coli/metabolism ; Escherichia coli Proteins/metabolism ; Ribosomal Proteins/metabolism
Chemical Substances	Escherichia coli Proteins ; Ribosomal Proteins ; ribosomal protein S4 ; ribosomal protein S5
Language	English
Publishing date	2015-03
Publishing country	United States
Document type	Comment ; Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2968-3
ISSN	1098-5530 ; 0021-9193
ISSN (online)	1098-5530
ISSN	0021-9193
DOI	10.1128/JB.02579-14
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Article ; Online: RNA Polymerase's Relationship with the Ribosome: Not So Physical, Most of the Time.

Chen, Menglin / Fredrick, Kurt

Journal of molecular biology

2020 Volume 432, Issue 14, Page(s) 3981–3986

Abstract: In bacteria, the rates of transcription elongation and translation elongation are coordinated, changing together in response to growth conditions. It has been proposed that this is due to physical coupling of RNA polymerase and the lead ribosome on ... ...

Abstract	In bacteria, the rates of transcription elongation and translation elongation are coordinated, changing together in response to growth conditions. It has been proposed that this is due to physical coupling of RNA polymerase and the lead ribosome on nascent mRNA, an interaction important for preventing premature transcription termination by Rho factor. Recent studies challenge this view and provide evidence that coordination is indirect, mediated in Escherichia coli by the alarmone (p)ppGpp. Here, we discuss these new findings and how they shape our understanding of the functional relationship between RNA polymerase and the ribosome as well as the basis of transcriptional polarity.
MeSH term(s)	DNA-Directed RNA Polymerases/genetics ; Escherichia coli/genetics ; RNA/genetics ; RNA, Messenger/genetics ; Rho Factor/genetics ; Ribosomes/genetics ; Transcription Termination, Genetic
Chemical Substances	RNA, Messenger ; Rho Factor ; RNA (63231-63-0) ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
Language	English
Publishing date	2020-03-19
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2020.03.018
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Article ; Online: Maturation of 23S rRNA includes removal of helix H1 in many bacteria.

Shatoff, Elan A / Gemler, Bryan T / Bundschuh, Ralf / Fredrick, Kurt

RNA biology

2021 Volume 18, Issue sup2, Page(s) 856–865

Abstract: In most bacteria, the three ribosomal RNAs (rRNAs) are encoded together in each of several near-identical operons. As soon as the nascent precursor rRNA emerges from RNA polymerase, ribosome assembly begins. This process entails ribosomal protein binding, ...

Abstract	In most bacteria, the three ribosomal RNAs (rRNAs) are encoded together in each of several near-identical operons. As soon as the nascent precursor rRNA emerges from RNA polymerase, ribosome assembly begins. This process entails ribosomal protein binding, rRNA folding, rRNA modification, and rRNA processing. In the model organisms
MeSH term(s)	Bacterial Physiological Phenomena ; Base Sequence ; Chromosome Mapping ; Escherichia coli/genetics ; Gene Expression Regulation, Bacterial ; High-Throughput Nucleotide Sequencing ; Models, Molecular ; Nucleic Acid Conformation ; RNA Processing, Post-Transcriptional ; RNA, Bacterial ; RNA, Ribosomal, 23S/chemistry ; RNA, Ribosomal, 23S/genetics ; RNA, Ribosomal, 23S/metabolism ; Structure-Activity Relationship
Chemical Substances	RNA, Bacterial ; RNA, Ribosomal, 23S
Language	English
Publishing date	2021-11-23
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1555-8584
ISSN (online)	1555-8584
DOI	10.1080/15476286.2021.2000793
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Article ; Online: Measures of single- versus multiple-round translation argue against a mechanism to ensure coupling of transcription and translation.

Chen, Menglin / Fredrick, Kurt

Proceedings of the National Academy of Sciences of the United States of America

2018 Volume 115, Issue 42, Page(s) 10774–10779

Abstract: In prokaryotes, the synthesis of RNA and protein occurs simultaneously in the cytoplasm. A number of studies indicate that translation can strongly impact transcription, a phenomenon often attributed to physical coupling between RNA polymerase (RNAP) and ...

Abstract	In prokaryotes, the synthesis of RNA and protein occurs simultaneously in the cytoplasm. A number of studies indicate that translation can strongly impact transcription, a phenomenon often attributed to physical coupling between RNA polymerase (RNAP) and the lead ribosome on the nascent mRNA. Whether there generally exists a mechanism to ensure or promote RNAP-ribosome coupling remains unclear. Here, we used an efficient hammerhead ribozyme and developed a reporter system to measure single- versus multiple-round translation in
MeSH term(s)	DNA-Directed RNA Polymerases/chemistry ; DNA-Directed RNA Polymerases/genetics ; DNA-Directed RNA Polymerases/metabolism ; Escherichia coli/growth & development ; Escherichia coli/metabolism ; Models, Molecular ; Mutation ; Protein Biosynthesis ; Protein Conformation ; Ribosomes/metabolism ; Transcription, Genetic
Chemical Substances	DNA-Directed RNA Polymerases (EC 2.7.7.6)
Language	English
Publishing date	2018-10-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1812940115
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Article: Another Look at Mutations in Ribosomal Protein S4 Lends Strong Support to the Domain Closure Model

Fredrick, Kurt

Journal of bacteriology. 2015 Mar. 15, v. 197, no. 6

2015

Abstract: Ribosomes employ a “kinetic discrimination” mechanism, in which correct substrates are incorporated more rapidly than incorrect ones. The structural basis of this mechanism may involve 30S domain closure, a global conformational change that coincides ... ...

Abstract	Ribosomes employ a “kinetic discrimination” mechanism, in which correct substrates are incorporated more rapidly than incorrect ones. The structural basis of this mechanism may involve 30S domain closure, a global conformational change that coincides with codon recognition. In a direct screen for fidelity-altering mutations, Agarwal and coworkers (D. Agarwal, D. Kamath, S. T. Gregory, and M. O'Connor, J Bacteriol 197:1017–1025, 2015, doi: 10.1128/JB.02485-14) isolated mutations that progressively truncate the C terminus of S4. All of these promote miscoding and undoubtedly destabilize the S4-S5 interface, consistent with the domain closure model.
Keywords	models ; mutation ; ribosomes
Language	English
Dates of publication	2015-0315
Size	p. 1014-1016.
Publishing place	American Society for Microbiology
Document type	Article
ZDB-ID	2968-3
ISSN	1098-5530 ; 0021-9193
ISSN (online)	1098-5530
ISSN	0021-9193
DOI	10.1128/JB.02579-14
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Article ; Online: Ribosomes lacking bS21 gain function to regulate protein synthesis in Flavobacterium johnsoniae.

McNutt, Zakkary A / Roy, Bappaditya / Gemler, Bryan T / Shatoff, Elan A / Moon, Kyung-Mee / Foster, Leonard J / Bundschuh, Ralf / Fredrick, Kurt

Nucleic acids research

2023 Volume 51, Issue 4, Page(s) 1927–1942

Abstract: Ribosomes of Bacteroidia (formerly Bacteroidetes) fail to recognize Shine-Dalgarno (SD) sequences even though they harbor the anti-SD (ASD) of 16S rRNA. Inhibition of SD-ASD pairing is due to sequestration of the 3' tail of 16S rRNA in a pocket formed by ...

Abstract	Ribosomes of Bacteroidia (formerly Bacteroidetes) fail to recognize Shine-Dalgarno (SD) sequences even though they harbor the anti-SD (ASD) of 16S rRNA. Inhibition of SD-ASD pairing is due to sequestration of the 3' tail of 16S rRNA in a pocket formed by bS21, bS18, and bS6 on the 30S platform. Interestingly, in many Flavobacteriales, the gene encoding bS21, rpsU, contains an extended SD sequence. In this work, we present genetic and biochemical evidence that bS21 synthesis in Flavobacterium johnsoniae is autoregulated via a subpopulation of ribosomes that specifically lack bS21. Mutation or depletion of bS21 in the cell increases translation of reporters with strong SD sequences, such as rpsU'-gfp, but has no effect on other reporters. Purified ribosomes lacking bS21 (or its C-terminal region) exhibit higher rates of initiation on rpsU mRNA and lower rates of initiation on other (SD-less) mRNAs than control ribosomes. The mechanism of autoregulation depends on extensive pairing between mRNA and 16S rRNA, and exceptionally strong SD sequences, with predicted pairing free energies of < -13 kcal/mol, are characteristic of rpsU across the Bacteroidota. This work uncovers a clear example of specialized ribosomes in bacteria.
MeSH term(s)	Flavobacterium/cytology ; Flavobacterium/metabolism ; Protein Biosynthesis ; Ribosomes/metabolism ; RNA, Messenger/metabolism ; RNA, Ribosomal, 16S/genetics ; Bacterial Proteins/metabolism ; Ribosomal Proteins/metabolism
Chemical Substances	RNA, Messenger ; RNA, Ribosomal, 16S ; Bacterial Proteins ; Ribosomal Proteins
Language	English
Publishing date	2023-01-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkad047
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Article: CD47 is Required for Mesenchymal Progenitor Proliferation and Fracture Repair.

Zondervan, Robert L / Capobianco, Christina A / Jenkins, Daniel C / Reicha, John D / Fredrick, Livia M / Lam, Charles / Isenberg, Jeffery S / Ahn, Jaimo / Marcucio, Ralph S / Hankenson, Kurt D

bioRxiv : the preprint server for biology

2024

Abstract: CD47 is a ubiquitous and pleiotropic cell-surface receptor. Disrupting CD47 enhances injury repair in various tissues but the role of CD47 has not been studied in bone injuries. In a murine closed-fracture model, CD47-null mice showed decreased callus ... ...

Abstract	CD47 is a ubiquitous and pleiotropic cell-surface receptor. Disrupting CD47 enhances injury repair in various tissues but the role of CD47 has not been studied in bone injuries. In a murine closed-fracture model, CD47-null mice showed decreased callus bone volume, bone mineral content, and tissue mineral content as assessed by microcomputed tomography 10 days post-fracture, and increased fibrous volume as determined by histology. To understand the cellular basis for this phenotype, mesenchymal progenitors (MSC) were harvested from bone marrow. CD47-null MSC showed decreased large fibroblast colony formation (CFU-F), significantly less proliferation, and fewer cells in S-phase, although osteoblast differentiation was unaffected. However, consistent with prior research, CD47-null endothelial cells showed increased proliferation relative to WT cells. Similarly, in a murine ischemic fracture model, CD47-null mice showed reduced fracture callus bone volume and bone mineral content relative to WT. Consistent with our
Language	English
Publishing date	2024-03-06
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.03.06.583756
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