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  • Review Article
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Strategies for RNA folding and assembly

Nature Reviews Molecular Cell Biology volume 5, pages 908–919 (2004)Cite this article

Key Points

  • RNA structure comprises secondary and tertiary motifs, which fold in a hierarchical sequence of events. The difficulty that RNA molecules have in defining a single native structure is known as 'the RNA-folding problem'.

  • In vitro, some RNAs are able to self-fold under precise conditions of salt and temperature. In vivo, proteins with a wide variety of activities help RNAs to fold and to assemble into ribonucleoprotein (RNP) particles.

  • Some proteins recognize specific sequences or structures, and by binding they stabilize these structures. RNA helicases, which are specifically recruited to their target RNA, unfold RNA structures by ATP hydrolysis.

  • A growing number of proteins have been assigned RNA-chaperone activity, which is defined as a structural destabilizing activity that non-specifically resolves misfolded conformations without ATP consumption. The influence that proteins with RNA-chaperone activity have on the global folding state of RNA molecules within cells remains a mystery.

  • The ribosome is a highly dynamic RNP complex. The assembly of three large RNAs and more than 50 proteins requires a precise coordinated sequence of events. The interplay between ribosomal proteins and RNA is still unclear; however, a large number of ribosomal proteins have RNA-chaperone activity — an unfolding activity, which could be of advantage not only during assembly but also during translation to prevent the RNA from misfolding.

  • The spliceosome consists of five small nuclear RNP particles (snRNPs) and many other proteins, which assemble anew on each intron. In the course of intron excision and exon ligation, many interactions between the snRNAs and pre-mRNA are formed and then rearranged to allow the reactions to proceed. These dynamic RNA interactions need protein assistance. This review discusses spliceosomal proteins that have the potential to assist RNA folding and refolding within this large RNP complex.

Abstract

RNA is structurally very flexible, which provides the basis for its functional diversity. An RNA molecule can often adopt different conformations, which enables the regulation of its function through folding. Proteins help RNAs reach their functionally active conformation by increasing their structural stability or by chaperoning the folding process. Large, dynamic RNA–protein complexes, such as the ribosome or the spliceosome, require numerous proteins that coordinate conformational switches of the RNA components during assembly and during their respective activities.

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Figure 1: One sequence, two ribozymes.
Figure 2: Folding of a small RNA with a three-way junction.
Figure 3: Group-I intron RNA folding might involve several pathways.
Figure 4: Protein-facilitated RNA folding.
Figure 5: Proteins with a predicted influence on the spliceosomal RNA structure.

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Acknowledgements

The preparation of this review was supported by the Austrian Science Fund FWF grants to A.B. as part of the Special Research Program on RNA.

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Authors and Affiliations

  1. Department of Microbiology and Genetics, Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohrgasse 9, Vienna, A-1030, Austria

    Renée Schroeder & Katharina Semrad

  2. Department of Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, Dr. Bohrgasse 9, Vienna, A-1030, Austria

    Andrea Barta

Authors
  1. Renée Schroeder
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  2. Andrea Barta
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Correspondence to Renée Schroeder.

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DATABASES

Entrez

CspA

CspE

DbpA

DnaK

FinO

Hfq

H-NS

ryhB

S12

SrmB

StpA

Interpro

CSD

KH

RRM

Saccharomyces genome database

CBP2

Prp28

Swiss-Prot

FMRP

hnRNP A1

I-AniI

SF2/ASF

U1 snRNP

U1C snRNP

U2AF65

FURTHER INFORMATION

Ribosomal modifications database

RNA structure database

Tetrahymena genome project

Glossary

RNA-FOLDING PROBLEM

The RNA-folding problem was first described by D. Herschlag and corresponds to the multitude of possible structures that RNA can adopt. Only a single or a few possible structures usually lead to function, therefore the RNA must avoid the problem of folding into alternative, non-functional structures.

GROUP-I INTRONS

A group of autocatalytic intervening sequences with a common core structure and a common splicing mechanism, which is initiated by the nucleophilic attack of the 3′ hydroxyl group of the cofactor guanosine.

RIBOSWITCH

A conformational switch in an RNA molecule that is induced by a small metabolite, and which leads to a switch in gene-regulatory function.

RIBOZYME

An enzyme whose catalytic component is an RNA.

A-FORM DOUBLE HELIX

A right-handed double helix that is formed by the base pairing of complementary RNA strands. Every 2.3 nm, the helix turns, which results in 11 base pairs per turn. The B-form helix, which is also right-handed and is usually present in double-stranded DNA, turns every 3.4 nm, which results in 10 base pairs per turn.

SMALL NUCLEOLYTIC RIBOZYMES

A group of self-cleaving ribozymes, which includes the hammerhead, hairpin and hepatitis delta virus ribozymes. Their core structures range in size from 40 to 155 nucleotides and they produce 2′–3′ cyclic phosphate and 5′ hydroxyl ends after cleavage.

LARGE RIBOZYMES

A class of ribozymes that includes RNase P, self-splicing group-I and group-II introns. They are several hundred nucleotides in size and they produce 3′ hydroxyl ends and 5′ phosphates (RNase P) or new phosphodiester linkages (introns).

GROUP-II INTRONS

A rare class of autocatalytic introns, the excision of which is assisted by, but does not require, trans-acting proteins. The splicing mechanism is identical to that of the spliceosome. Splicing is initiated by a nucleophilic attack of the 2′ hydroxyl group of an endogenous adenosine at the 5′ splice site, forming a lariat structure.

RNA HELICASE

An enzyme that resolves RNA base pairing through ATP hydrolysis, which leads to unfolding.

DEAD-BOX PROTEINS AND DEXD/H ATPases

RNA helicases that contain the DEAD (Asp-Glu-Ala-Asp) or DEXD/H (Asp-Glu-X-Asp/His, where X represents any amino acid) motif. These proteins unwind RNA through ATP hydrolysis.

RNA-BINDING DOMAINS IN PROTEINS

The RRM (RNA-recognition motif) contains two short consensus sequences embedded in a structurally conserved region of approximately 80 amino acids. The KH (K-homology) domain is ∼ 60 amino acids long with a characteristic pattern of hydrophobic amino acids and is structurally similar to the RRM domain. RGG (Arg-Gly-Gly) is a hallmark amino-acid motif present in many RNA-binding proteins. Zn-knuckle is a conserved CX2CX4HX4C (where X represents any amino acid) motif that coordinates zinc binding.

CHAPERONE

A protein or RNA molecule that facilitates the folding of a protein or RNA by preventing misfolding and aggregation, or by resolving misfolded structures.

NUCLEOID

The bacterial genome that contains compacted DNA, but which is not separated by a membrane (as it is in eukaryotes).

SMALL NUCLEAR RIBONUCLEOPROTEIN PARTICLE

(snRNP). A nuclear particle that consists of a short RNA (<300 nucleotides) and one or more tightly bound proteins. They are involved in pre-mRNA processing and tRNA biogenesis.

SM AND SM-LIKE PROTEINS

A group of seven core proteins that form heteroheptameric complexes, which bind to U-rich sequences in snRNPs that are involved in splicing. The exception is U6 snRNP, which contains Sm-like (Lsm) proteins.

HETEROGENOUS NUCLEAR RIBONUCLEOPROTEIN

(hnRNP). A group of more than 20 different nuclear proteins that were found associated as a complex with heterogenous nuclear RNA. This diverse group of RNA-binding proteins have various nuclear and cytoplasmic functions.

F-PLASMID CONJUGATIVE TRANSFER

DNA transfer from a donor cell to a recipient cell by direct physical contact that is mediated by genes that are encoded on the fertility (F) plasmid.

KINETIC FOLDING TRAP

An aberrant and metastable RNA structure that slows down folding.

OSMOLYTE

A small organic compound that accumulates in water-stressed organisms.

THERMOPHILIC, MESOPHILIC, PSYCHROPHILIC

Tolerating high, intermediate and low temperatures, respectively.

C2′-ENDO SUGAR CONFORMATION

A ribose conformation in which the C2′ carbon is orientated towards the C5′ carbon, which is typical of B-form helices. A-form RNA helices adopt the C3′-endo sugar conformation.

INTRON BRANCH SITE

An adenosine within the branch-site sequence, the 2′-OH of which is ligated to the 5′ end of the intron in the first step of splicing, which results in a branched RNA molecule (lariat)

SPLICEOSOME

A large dynamic nuclear complex, which consists of five snRNPs as well as numerous proteins. It mediates the excision of pre-mRNA introns and the ligation of exons, thereby generating the mature mRNA.

SR PROTEINS

A protein family of highly conserved RNA-splicing factors, with at least one RRM motif and patches of serine (S) and arginine (R) di-peptides.

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Schroeder, R., Barta, A. & Semrad, K. Strategies for RNA folding and assembly. Nat Rev Mol Cell Biol 5, 908–919 (2004). https://doi.org/10.1038/nrm1497

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