Size heterogeneity of ribosomal RNA in eukaryote evolution—1. rRNA molecular weights in species containing intact large ribosomal subunit RNA

AbstractSynthesis of eukaryotic ribosomes involves the assembly and maturation of precursor particles (pre-ribosomal particles) containing ribosomal RNA (rRNA) precursors, ribosomal proteins (RPs) and a plethora of assembly factors (AFs). Formation of the earliest precursors of the 60S ribosomal subunit (pre-60S r-particle) is among the least understood stages of ribosome biogenesis. It involves the Npa1 complex, a protein module suggested to play a key role in the early structuring of the pre-rRNA. Npa1 displays genetic interactions with the DExD-box protein Dbp7 and interacts physically with the snR190 box C/D snoRNA. We show here that snR190 functions as a snoRNA chaperone, which likely cooperates with the Npa1 complex to initiate compaction of the pre-rRNA in early pre-60S r-particles. We further show that Dbp7 regulates the dynamic base-pairing between snR190 and the pre-rRNA within the earliest pre-60S r-particles, thereby participating in structuring the peptidyl transferase center (PTC) of the large ribosomal subunit.

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Principles of 60S ribosomal subunit assembly emerging from recent studies in yeast

Biochemical Journal ◽

10.1042/bcj20160516 ◽

2017 ◽

Vol 474 (2) ◽

pp. 195-214 ◽

Cited By ~ 44

Author(s):

Salini Konikkat ◽

John L. Woolford,

Keyword(s):

Ribosomal Rna ◽

Ribosomal Proteins ◽

Ribosome Biogenesis ◽

Ribosomal Subunit ◽

Ribosome Assembly ◽

Small Nucleolar Rnas ◽

Large Ribosomal Subunit ◽

Yeast Saccharomyces Cerevisiae ◽

Subunit Assembly ◽

Nucleolar Rnas

Ribosome biogenesis requires the intertwined processes of folding, modification, and processing of ribosomal RNA, together with binding of ribosomal proteins. In eukaryotic cells, ribosome assembly begins in the nucleolus, continues in the nucleoplasm, and is not completed until after nascent particles are exported to the cytoplasm. The efficiency and fidelity of ribosome biogenesis are facilitated by >200 assembly factors and ∼76 different small nucleolar RNAs. The pathway is driven forward by numerous remodeling events to rearrange the ribonucleoprotein architecture of pre-ribosomes. Here, we describe principles of ribosome assembly that have emerged from recent studies of biogenesis of the large ribosomal subunit in the yeast Saccharomyces cerevisiae. We describe tools that have empowered investigations of ribosome biogenesis, and then summarize recent discoveries about each of the consecutive steps of subunit assembly.

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Fanconi anemia protein FANCI functions in ribosome biogenesis

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1811557116 ◽

2019 ◽

Vol 116 (7) ◽

pp. 2561-2570 ◽

Cited By ~ 9

Author(s):

Samuel B. Sondalle ◽

Simonne Longerich ◽

Lisa M. Ogawa ◽

Patrick Sung ◽

Susan J. Baserga

Keyword(s):

Dna Repair ◽

Fanconi Anemia ◽

Ribosomal Rna ◽

Ribosome Biogenesis ◽

Bone Marrow Failure ◽

Ribosomal Subunit ◽

Rrna Processing ◽

Large Ribosomal Subunit ◽

Interstrand Cross Links ◽

Cross Links

Fanconi anemia (FA) is a disease of DNA repair characterized by bone marrow failure and a reduced ability to remove DNA interstrand cross-links. Here, we provide evidence that the FA protein FANCI also functions in ribosome biogenesis, the process of making ribosomes that initiates in the nucleolus. We show that FANCI localizes to the nucleolus and is functionally and physically tied to the transcription of pre-ribosomal RNA (pre-rRNA) and to large ribosomal subunit (LSU) pre-rRNA processing independent of FANCD2. While FANCI is known to be monoubiquitinated when activated for DNA repair, we find that it is predominantly in the deubiquitinated state in the nucleolus, requiring the nucleoplasmic deubiquitinase (DUB) USP1 and the nucleolar DUB USP36. Our model suggests a possible dual pathophysiology for FA that includes defects in DNA repair and in ribosome biogenesis.

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Cryo-EM structure of the highly atypical cytoplasmic ribosome of Euglena gracilis

Nucleic Acids Research ◽

10.1093/nar/gkaa893 ◽

2020 ◽

Vol 48 (20) ◽

pp. 11750-11761

Author(s):

Donna Matzov ◽

Masato Taoka ◽

Yuko Nobe ◽

Yoshio Yamauchi ◽

Yehuda Halfon ◽

...

Keyword(s):

Ribosomal Rna ◽

Euglena Gracilis ◽

Ribosomal Proteins ◽

Ribosomal Subunit ◽

Catalytic Rna ◽

Central Component ◽

Large Ribosomal Subunit ◽

Eukaryotic Alga ◽

Cytoplasmic Ribosome ◽

Exit Tunnel

Abstract Ribosomal RNA is the central component of the ribosome, mediating its functional and architectural properties. Here, we report the cryo-EM structure of a highly divergent cytoplasmic ribosome from the single-celled eukaryotic alga Euglena gracilis. The Euglena large ribosomal subunit is distinct in that it contains 14 discrete rRNA fragments that are assembled non-covalently into the canonical ribosome structure. The rRNA is substantially enriched in post-transcriptional modifications that are spread far beyond the catalytic RNA core, contributing to the stabilization of this highly fragmented ribosome species. A unique cluster of five adenosine base methylations is found in an expansion segment adjacent to the protein exit tunnel, such that it is positioned for interaction with the nascent peptide. As well as featuring distinctive rRNA expansion segments, the Euglena ribosome contains four novel ribosomal proteins, localized to the ribosome surface, three of which do not have orthologs in other eukaryotes.

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Supersized Ribosomal RNA Expansion Segments in Asgard Archaea

Genome Biology and Evolution ◽

10.1093/gbe/evaa170 ◽

2020 ◽

Vol 12 (10) ◽

pp. 1694-1710

Author(s):

Petar I Penev ◽

Sara Fakhretaha-Aval ◽

Vaishnavi J Patel ◽

Jamie J Cannone ◽

Robin R Gutell ◽

...

Keyword(s):

Sequence Analysis ◽

Ribosomal Rna ◽

Common Core ◽

Ribosomal Proteins ◽

Common Ancestor ◽

Ribosomal Subunit ◽

Large Ribosomal Subunit ◽

Cell Lineages ◽

Accretion Model ◽

The Common

Abstract The ribosome’s common core, comprised of ribosomal RNA (rRNA) and universal ribosomal proteins, connects all life back to a common ancestor and serves as a window to relationships among organisms. The rRNA of the common core is similar to rRNA of extant bacteria. In eukaryotes, the rRNA of the common core is decorated by expansion segments (ESs) that vastly increase its size. Supersized ESs have not been observed previously in Archaea, and the origin of eukaryotic ESs remains enigmatic. We discovered that the large ribosomal subunit (LSU) rRNA of two Asgard phyla, Lokiarchaeota and Heimdallarchaeota, considered to be the closest modern archaeal cell lineages to Eukarya, bridge the gap in size between prokaryotic and eukaryotic LSU rRNAs. The elongated LSU rRNAs in Lokiarchaeota and Heimdallarchaeota stem from two supersized ESs, called ES9 and ES39. We applied chemical footprinting experiments to study the structure of Lokiarchaeota ES39. Furthermore, we used covariation and sequence analysis to study the evolution of Asgard ES39s and ES9s. By defining the common eukaryotic ES39 signature fold, we found that Asgard ES39s have more and longer helices than eukaryotic ES39s. Although Asgard ES39s have sequences and structures distinct from eukaryotic ES39s, we found overall conservation of a three-way junction across the Asgard species that matches eukaryotic ES39 topology, a result consistent with the accretion model of ribosomal evolution.

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Studies on the attachment and release of 5 s ribosomal RNA from the large ribosomal subunit

Journal of Molecular Biology ◽

10.1016/0022-2836(69)90331-3 ◽

1969 ◽

Vol 39 (1) ◽

pp. 31-44 ◽

Cited By ~ 22

Author(s):

Nilima Sarkar ◽

Donald G. Comb

Keyword(s):

Ribosomal Rna ◽

Ribosomal Subunit ◽

Large Ribosomal Subunit

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Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens

Nature Communications ◽

10.1038/s41467-021-23753-1 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Caillan Crowe-McAuliffe ◽

Victoriia Murina ◽

Kathryn Jane Turnbull ◽

Marje Kasari ◽

Merianne Mohamad ◽

...

Keyword(s):

Antibiotic Resistance ◽

Ribosomal Rna ◽

Ribosomal Subunit ◽

Resistance Mechanisms ◽

Structural Basis ◽

Large Ribosomal Subunit ◽

Gram Positive ◽

Gram Positive Bacteria ◽

Antibiotic Release ◽

Peptidyltransferase Center

AbstractTarget protection proteins confer resistance to the host organism by directly binding to the antibiotic target. One class of such proteins are the antibiotic resistance (ARE) ATP-binding cassette (ABC) proteins of the F-subtype (ARE-ABCFs), which are widely distributed throughout Gram-positive bacteria and bind the ribosome to alleviate translational inhibition from antibiotics that target the large ribosomal subunit. Here, we present single-particle cryo-EM structures of ARE-ABCF-ribosome complexes from three Gram-positive pathogens: Enterococcus faecalis LsaA, Staphylococcus haemolyticus VgaALC and Listeria monocytogenes VgaL. Supported by extensive mutagenesis analysis, these structures enable a general model for antibiotic resistance mediated by these ARE-ABCFs to be proposed. In this model, ABCF binding to the antibiotic-stalled ribosome mediates antibiotic release via mechanistically diverse long-range conformational relays that converge on a few conserved ribosomal RNA nucleotides located at the peptidyltransferase center. These insights are important for the future development of antibiotics that overcome such target protection resistance mechanisms.

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