1
|
Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Diercks T, López-Alonso JP, Lavin JL, Kaminishi T, Çapuni R, Dhimole N, de Astigarraga E, Gil-Carton D, Fucini P, Connell SR. A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit. Sci Adv 2021; 7:7/23/eabf7547. [PMID: 34088665 PMCID: PMC8177701 DOI: 10.1126/sciadv.abf7547] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 04/20/2021] [Indexed: 05/03/2023]
Abstract
While a structural description of the molecular mechanisms guiding ribosome assembly in eukaryotic systems is emerging, bacteria use an unrelated core set of assembly factors for which high-resolution structural information is still missing. To address this, we used single-particle cryo-electron microscopy to visualize the effects of bacterial ribosome assembly factors RimP, RbfA, RsmA, and RsgA on the conformational landscape of the 30S ribosomal subunit and obtained eight snapshots representing late steps in the folding of the decoding center. Analysis of these structures identifies a conserved secondary structure switch in the 16S ribosomal RNA central to decoding site maturation and suggests both a sequential order of action and molecular mechanisms for the assembly factors in coordinating and controlling this switch. Structural and mechanistic parallels between bacterial and eukaryotic systems indicate common folding features inherent to all ribosomes.
Collapse
Affiliation(s)
- Andreas Schedlbauer
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Idoia Iturrioz
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Borja Ochoa-Lizarralde
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Tammo Diercks
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Jorge Pedro López-Alonso
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | | | - Tatsuya Kaminishi
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
- Department of Genetics, Graduate School of Medicine, Osaka University, Japan
| | - Retina Çapuni
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Neha Dhimole
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Elisa de Astigarraga
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - David Gil-Carton
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Paola Fucini
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain.
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Sean R Connell
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain.
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| |
Collapse
|
2
|
Roberts A, Austin W, Evans K, Bird C, Schweizer M, Darling K. A New Integrated Approach to Taxonomy: The Fusion of Molecular and Morphological Systematics with Type Material in Benthic Foraminifera. PLoS One 2016; 11:e0158754. [PMID: 27388271 PMCID: PMC4936703 DOI: 10.1371/journal.pone.0158754] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 06/21/2016] [Indexed: 11/19/2022] Open
Abstract
A robust and consistent taxonomy underpins the use of fossil material in palaeoenvironmental research and long-term assessment of biodiversity. This study presents a new integrated taxonomic protocol for benthic foraminifera by unequivocally reconciling the traditional taxonomic name to a specific genetic type. To implement this protocol, a fragment of the small subunit ribosomal RNA (SSU rRNA) gene is used in combination with 16 quantitative morphometric variables to fully characterise the benthic foraminiferal species concept of Elphidium williamsoni Haynes, 1973. A combination of live contemporary topotypic specimens, original type specimens and specimens of genetic outliers were utilised in this study. Through a series of multivariate statistical tests we illustrate that genetically characterised topotype specimens are morphologically congruent with both the holotype and paratype specimens of E. williamsoni Haynes, 1973. We present the first clear link between morphologically characterised type material and the unique SSU rRNA genetic type of E. williamsoni. This example provides a standard framework for the benthic foraminifera which bridges the current discontinuity between molecular and morphological lines of evidence, allowing integration with the traditional Linnaean roots of nomenclature to offer a new prospect for taxonomic stability.
Collapse
Affiliation(s)
- Angela Roberts
- School of Geography and Geosciences, University of St Andrews, St Andrews, Fife, Scotland, KY16 9AL, United Kingdom
| | - William Austin
- School of Geography and Geosciences, University of St Andrews, St Andrews, Fife, Scotland, KY16 9AL, United Kingdom
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll, Scotland, PA37 1QA, United Kingdom
| | - Katharine Evans
- School of Geosciences, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JW, United Kingdom
| | - Clare Bird
- School of Geosciences, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JW, United Kingdom
| | - Magali Schweizer
- School of Geosciences, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JW, United Kingdom
- UMR CNRS 6112, LPG-BIAF Recent and Fossil Bio-Indicators, University of Angers, 2 bd Lavoisier, 49045, Angers Cedex, France
| | - Kate Darling
- School of Geography and Geosciences, University of St Andrews, St Andrews, Fife, Scotland, KY16 9AL, United Kingdom
- School of Geosciences, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JW, United Kingdom
| |
Collapse
|
3
|
Yang A, Narechania A, Kim E. Rickettsial endosymbiont in the "early-diverging" streptophyte green alga Mesostigma viride. J Phycol 2016; 52:219-229. [PMID: 27037587 DOI: 10.1111/jpy.12385] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 11/20/2015] [Indexed: 06/05/2023]
Abstract
A bacterial endosymbiont was unexpectedly found in the "axenic" culture strain of the streptophyte green alga Mesostigma viride (NIES-995). Phylogenetic analyses based on 16S rRNA gene sequences showed that the symbiont belongs to the order Rickettsiales, specifically to the recently designated clade "Candidatus Megaira," which is closely related to the well-known Rickettsia clade. Rickettsiales bacteria of the "Ca. Megaira" clade are found in a taxonomically diverse array of eukaryotic hosts, including chlorophycean green algae, several ciliate species, and invertebrates such as Hydra. Transmission electron microscopy, fluorescence in situ hybridi-zation, and SYBR Green I staining experiments revealed that the endosymbiont of M. viride NIES-995 is rod shaped, typically occurs in clusters, and is surrounded by a halo-like structure, presumably formed by secretory substances from the bacterium. Two additional M. viride strains (NIES-296 and NIES-475), but not SAG50-1, were found to house the rickettsial endosymbiont. Analyses of strain NIES-995 transcriptome data indicated the presence of at least 91 transcriptionally active genes of symbiont origins. These include genes for surface proteins (e.g., rOmpB) that are known to play key roles in bacterial attachment onto host eukaryotes in related Rickettsia species. The assembled M. viride transcriptome includes transcripts that code for a suite of predicted algal-derived proteins, such as Ku70, WASH, SCAR, and CDC42, which may be important in the formation of the algal-rickettsial association.
Collapse
Affiliation(s)
- Ashley Yang
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, New York, 10024, USA
| | - Apurva Narechania
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, New York, 10024, USA
| | - Eunsoo Kim
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, New York, 10024, USA
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, New York, 10024, USA
| |
Collapse
|
4
|
Jakob S, Ohmayer U, Neueder A, Hierlmeier T, Perez-Fernandez J, Hochmuth E, Deutzmann R, Griesenbeck J, Tschochner H, Milkereit P. Interrelationships between yeast ribosomal protein assembly events and transient ribosome biogenesis factors interactions in early pre-ribosomes. PLoS One 2012; 7:e32552. [PMID: 22431976 PMCID: PMC3303783 DOI: 10.1371/journal.pone.0032552] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 01/31/2012] [Indexed: 12/12/2022] Open
Abstract
Early steps of eukaryotic ribosome biogenesis require a large set of ribosome biogenesis factors which transiently interact with nascent rRNA precursors (pre-rRNA). Most likely, concomitant with that initial contacts between ribosomal proteins (r-proteins) and ribosome precursors (pre-ribosomes) are established which are converted into robust interactions between pre-rRNA and r-proteins during the course of ribosome maturation. Here we analysed the interrelationship between r-protein assembly events and the transient interactions of ribosome biogenesis factors with early pre-ribosomal intermediates termed 90S pre-ribosomes or small ribosomal subunit (SSU) processome in yeast cells. We observed that components of the SSU processome UTP-A and UTP-B sub-modules were recruited to early pre-ribosomes independently of all tested r-proteins. On the other hand, groups of SSU processome components were identified whose association with early pre-ribosomes was affected by specific r-protein assembly events in the head-platform interface of the SSU. One of these components, Noc4p, appeared to be itself required for robust incorporation of r-proteins into the SSU head domain. Altogether, the data reveal an emerging network of specific interrelationships between local r-protein assembly events and the functional interactions of SSU processome components with early pre-ribosomes. They point towards some of these components being transient primary pre-rRNA in vivo binders and towards a role for others in coordinating the assembly of major SSU domains.
Collapse
Affiliation(s)
- Steffen Jakob
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Uli Ohmayer
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Andreas Neueder
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Thomas Hierlmeier
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | | | - Eduard Hochmuth
- Lehrstuhl für Biochemie I, Universität Regensburg, Regensburg, Germany
| | - Rainer Deutzmann
- Lehrstuhl für Biochemie I, Universität Regensburg, Regensburg, Germany
| | | | - Herbert Tschochner
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Philipp Milkereit
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| |
Collapse
|