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Single-particle cryo-electron microscopy of macromolecular assemblies
KTH, School of Technology and Health (STH), Structural Biotechnology. (Strukturell bioteknik)
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In this thesis, single-particle cryo-electron microscopy (cryo-EM) was used to study the structure of three macromolecular assemblies: the two hemocyanin isoforms from Rapana thomasiana, the Pyrococcus furiosus chaperonin, and the ribosome from Escherichia coli.

Hemocyanins are large respiratory proteins in arthropods and molluscs. Most molluscan hemocyanins exist as two distinct isoforms composed of related polypeptides. In most species the two isoforms differ in terms of their oligomeric stability, and thus we set out to investigate the two Rapana thomasiana hemocyanins (RtH) in order to explain this behaviour. Our findings showed that the two RtHio forms are identical at the experimental resolution. Furthermore, three previously unreported connections that most likely contribute to the oligomeric stability were identified.

Chaperonins are double-ring protein complexes that assist the folding process of nascent, non-native polypeptide chains. The chaperonin from the hyperthermophilic archaea Pyrococcus furiosus belongs to Group II chaperonins, and unlike most othergroup II chaperonins it appears to be homo-oligomeric. The 3D reconstruction of the Pyrococcus furiousus chaperonin revealed a di-octameric structure in a partially closed/open state, something in between the closed folding-active state and the open substrate-accepting state.

The ribosome is the molecular machine where protein synthesis takes place. In bacteria there is a unique RNA molecule called transfer-messenger RNA (tmRNA) that together with its helper protein SmpB rescues ribosomes trapped on defective messenger RNAs (mRNAs) through a process called trans-translation. tmRNA is about 4 times the size of a normal tRNA, and it is composed of a tRNA-like domain (TLD) that is connected to the mRNA-like domain (MLD) by several pseudoknots (PKs) and RNA helices. During trans-translation, tmRNA utilize its TLD to receive the incomplete polypeptide from the peptidyl-tRNA in the ribosomal P site of the stalledribosome. Subsequently, its MLD is used to tag the incomplete polypeptide with adegradation signal. When tmRNA enters a stalled ribosome the MLD and pseudoknots form a highly structured arc that encircles the beak of the small ribosomal subunit. Byutilizing maximum-likelihood based methods for heterogeneity analysis we could observe the Escherichia coli ribosome in a number of different tmRNA·SmpB-boundstates. The cryo-EM map of the post-accommodated state revealed that the TLD·SmpBpart of the tmRNA·SmpB complex mimics native tRNAs in the A site of stalled ribosomes. The density map also showed that the tmRNA arc remains well structuredand that it is still attached to the beak of the small ribosomal subunit. Thereconstructions of the double-translocation tmRNA-bound ribosome complex showed that the pseudoknots of tmRNA still form an arc, and that they are located at positions similar to the ones assigned for the pseudoknots in the post-accommodated state. In addition, the tmRNA arc exists in two states; one stable and highly structured and another more flexible and disorganized.

Place, publisher, year, edition, pages
Stockholm: KTH , 2009. , 41 p.
Series
Trita-STH : report, ISSN 1653-3836 ; 2009:5
National Category
Industrial Biotechnology
Identifiers
URN: urn:nbn:se:kth:diva-11769ISBN: 978-91-7415-509-9 (print)OAI: oai:DiVA.org:kth-11769DiVA: diva2:281304
Public defence
2010-01-29, Hörsalen, Novum plan 4, Hälsovägen 7, Huddinge, 10:00 (English)
Opponent
Supervisors
Note
QC 20100708Available from: 2009-12-15 Created: 2009-12-15 Last updated: 2010-07-21Bibliographically approved
List of papers
1. Rapana thomasiana hemocyanin (RtH): Comparison of the two isoforms, RtH1 and RtH2, at 19 Å and 16 Å resolution
Open this publication in new window or tab >>Rapana thomasiana hemocyanin (RtH): Comparison of the two isoforms, RtH1 and RtH2, at 19 Å and 16 Å resolution
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2006 (English)In: Micron, ISSN 0968-4328, E-ISSN 1878-4291, Vol. 37, no 6, 566-576 p.Article in journal (Refereed) Published
Abstract [en]

Three-dimensional (3D) reconstructions of the two 8.4 MDa Rapana thomasiana hemocyanin isoforms, RtH1 and RtH2, have been obtained by cryoelectron microscopy of molecules embedded in vitreous ice and single particle image processing. The final 3D structures of the RtH1 and RtH2 didecamers at 19 angstrom and 16 angstrom resolution, respectively, are very similar to earlier reconstructions of gastropodan hemocyanins, revealing structural features such as the obliquely oriented subunits, the five- and two-fold symmetrical axes. Three new interactions are defined; two of them connecting the arch and the wall while the third is formed between the collar and the wall. The collar-wall connection and one of the arch-wall connections are positioned between two individual subunit dimers, while the second arch-wall connection is located between two subunits within the subunit dimer. All three interactions establish connections to the first tier of the wall. Furthermore, for each interaction we have allocated two first tier functional units most likely involved in forming the connections.

Keyword
cryoelectron microscopy; Rapana thomasiana; hemocyanin; mollusc
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-11767 (URN)10.1016/j.micron.2005.11.014 (DOI)000239696200009 ()2-s2.0-33745958772 (Scopus ID)
Note
QC 20100708Available from: 2009-12-15 Created: 2009-12-15 Last updated: 2017-12-12Bibliographically approved
2. Low resolution structure and apparent melting temperature of the chaperonin from Pyrococcus furiosus
Open this publication in new window or tab >>Low resolution structure and apparent melting temperature of the chaperonin from Pyrococcus furiosus
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(English)Manuscript (preprint) (Other academic)
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-14017 (URN)
Note

QC 20100708

Available from: 2010-07-08 Created: 2010-07-08 Last updated: 2016-06-22Bibliographically approved
3. tmRNA-SmpB complex mimics native aminoacyl-tRNAs in the A site of stalled ribosomes
Open this publication in new window or tab >>tmRNA-SmpB complex mimics native aminoacyl-tRNAs in the A site of stalled ribosomes
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2010 (English)In: Journal of Structural Biology, ISSN 1047-8477, E-ISSN 1095-8657, Vol. 169, no 3, 342-348 p.Article in journal (Refereed) Published
Abstract [en]

Bacterial ribosomes stalled on faulty, often truncated, mRNAs lacking stop codons are rescued by trans-translation. It relies on an RNA molecule (tmRNA) capable of replacing the faulty mRNA with its own open reading frame (ORF). Translation of tmRNA ORF results in the tagging of faulty protein for degradation and its release from the ribosome. We used single-particle cryo-electron microscopy to visualize tmRNA together with its helper protein SmpB on the 70S Escherichia coli ribosome in states subsequent to GTP hydrolysis on elongation factor Tu (EF-Tu). Three-dimensional reconstruction and heterogeneity analysis resulted in a 15 A resolution structure of the tmRNA-SmpB complex accommodated in the A site of the ribosome, which shows that SmpB mimics the anticodon- and D-stem of native tRNAs missing in the tRNA-like domain of tmRNA. We conclude that the tmRNA-SmpB complex accommodates in the ribosomal A site very much like an aminoacyl-tRNA during protein elongation. (C) 2009 Elsevier Inc. All rights reserved.

Keyword
Trans-translation, tmRNA, SmpB, Cryo-electron microscopy, Single-particle, Heterogeneity analysis, TRANSFER-MESSENGER-RNA, SMALL PROTEIN-B, ESCHERICHIA-COLI, ELECTRON-MICROSCOPY, GTPASE ACTIVATION, PEPTIDYL-TRANSFER, STRUCTURAL BASIS, TRANSLATION, BINDING, RESCUE
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-14018 (URN)10.1016/j.jsb.2009.10.015 (DOI)000275296100010 ()
Note
QC 20100708Available from: 2010-07-08 Created: 2010-07-08 Last updated: 2017-12-12Bibliographically approved
4. Structural analysis of double translocated tmRNA on the 70S ribosome indicates flexibility of the tmRNA structure.
Open this publication in new window or tab >>Structural analysis of double translocated tmRNA on the 70S ribosome indicates flexibility of the tmRNA structure.
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(English)Manuscript (preprint) (Other academic)
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-14019 (URN)
Note
QC 20100708Available from: 2010-07-08 Created: 2010-07-08 Last updated: 2010-07-21Bibliographically approved

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