Elsevier

Biochimie

Volume 84, Issue 8, August 2002, Pages 791-803
Biochimie

RNA editing by adenosine deaminases generates RNA and protein diversity

https://doi.org/10.1016/S0300-9084(02)01446-3Get rights and content

Abstract

RNA editing is defined as a post-transcriptional change of a gene-encoded sequence at the RNA level, excluding alterations due to processes such as pre-mRNA splicing and 3′-end formation. RNA editing is found in many organisms and can occur either by the insertion or deletion of nucleotides or by the substitution of bases by modification. The nucleoside inosine (I) was first detected in cytoplasmic tRNA and was later found in messenger RNA precursors (pre-mRNAs) and in viral transcripts. It is formed by hydrolytic deamination of a genomically encoded adenosine (A) at C6 of the base and this reaction is catalysed by a family of related enzymes. ADARs (for adenosine deaminases acting on RNA) catalyse A to I conversion either promiscuously or site-specifically in pre-mRNAs, viral RNAs and synthetic double-stranded RNAs (dsRNAs), whereas ADATs (for adenosine deaminases acting on tRNA) are involved in inosine formation in tRNAs. ADAT1 generates I at position 37 (3′ of the anticodon) in eukaryotic tRNAAla. ADAT2 and ADAT3 function as a heterodimer which catalyses inosine formation at the wobble position (position 34) in eukaryotic tRNAs. Here, we review the state of knowledge on ADARs and ADATs and their RNA substrates, with an emphasis on the developments over the past few years that have increased the understanding of the mechanism of action of these enzymes and of the functional consequences of the widespread modification they catalyse.

Introduction

RNA editing has been defined as a co- or post-transcriptional RNA processing reaction other than capping, splicing or 3′-end formation that changes the nucleotide sequence of the RNA substrate. RNA editing reactions occur in many organisms and operate by different molecular mechanisms, either by insertion or deletion of nucleotides or by base modification. The first case of RNA editing discovered was the insertion and deletion of uridine nucleotides in trypanosome mitochondrial mRNAs, which is required to generate functional proteins 〚1〛, 〚2〛. Base conversion appears to be the major type of RNA editing in the nucleus of higher eukaryotes 〚3〛 and the best-characterized reactions are hydrolytic deaminations 〚4〛, 〚5〛, 〚6〛 where a genomically encoded cytidine (C) or adenosine (A) is converted to uridine (U) and inosine (I), respectively 〚7〛, 〚8〛, 〚9〛 (see Fig. 1 for the A to I reaction mechanism).

The nucleoside inosine was first detected in cytoplasmic tRNA 〚10〛, 〚11〛 and later in messenger RNA precursors (pre-mRNAs) and in viral transcripts 〚8〛, 〚9〛, 〚12〛. Only a few pre-mRNA substrates have been identified. Nevertheless, it has been estimated that IMP is present at high amounts in rat poly(A)+ RNAs, particularly in brain, where one IMP is present for every 17,000 nucleotides, suggesting an important role for adenosine deamination 〚13〛. Indeed, it is clear that the impact of such a conversion in a tRNA or a pre-mRNA can be significant. Inosine in tRNA anticodons is believed to play a crucial role in translation by enlarging the codon recognition capacity, increasing the decoding efficiency and preventing frameshifts 〚14〛, 〚15〛, 〚16〛. A to I conversions in pre-mRNA coding or non-coding sequences (introns, UTRs) can alter the specificity of a codon or can affect splicing, generating protein isoforms with different functions not expected from the corresponding genomic sequence 〚8〛, 〚9〛, 〚12〛, 〚17〛. Thus, the consequences of RNA editing challenged the idea that the gene number is the major determinant to generate RNA and protein diversity in an organism.

In this review, we focus on the A to I conversion reactions and provide an overview of the superfamily of RNA-dependent adenosine deaminases which catalyse the reaction and their known substrates, the mechanism of action of these enzymes and also the effects of this widespread modification on the function of the target transcripts.

Section snippets

The enzymes

The enzymes catalysing A to I conversion in pre-mRNAs are known as adenosine deaminases that act on RNA (ADARs) 〚18〛. These enzymes form a protein family with members throughout the metazoan kingdom. In humans, three ADARs and their corresponding genes were identified, ADAR1, ADAR2 and ADAR3 〚8〛, 〚9〛, 〚17〛, whereas in lower metazoan organisms, such as Drosophila melanogaster 〚19〛 or Caenorhabditis elegans 〚20〛, only one ADAR gene has been found. ADAR1 and ADAR2 are expressed in almost all cell

The substrates

Studies to identify modified nucleosides in tRNAs led to the detection for the first time in yeast tRNAAla of inosine at position 34 (the first anticodon position or wobble position) and N1-methylinosine (m1I) at position 37 (3′ adjacent to the anticodon) 〚10〛, 〚11〛 (Table 1, Fig. 4b). m1I formation at position 37 occurs in two steps, adenosine deamination followed by methylation 〚11〛, 〚100〛. Further investigations revealed that inosine was present either in all eukaryotic tRNAAla at these two

Evolution

The catalytic domain of ADARs and ADATs, even though these enzymes are specific for adenosine, shows the sequence signatures of cytidine deaminases acting on mononucleotides (CDAs) or on RNA (CDARs) and not those of adenosine deaminases acting on mononucleotides (ADAs) 〚8〛, 〚110〛 (Fig. 3). However, ADAR and ADAT1 deaminase domain sequences appeared to be more related to each other than to those of CDAs, CDARs and other ADATs (Fig. 3). In contrast, the deaminase domains of ADAT2 and ADAT3 show a

Conclusions

RNA editing is now recognized as an important mechanism to generate RNA and protein diversity. Different means are used by ADARs to modify the genomically encoded information. ADAR-mediated A to I editing can selectively alter codon specificity when taking place within mRNA coding regions and seemingly subtle changes in amino acid sequences can affect the functional properties of the corresponding proteins. Considering the fact that in vivo editing ranges from a few percent to almost 100% and

Acknowledgments

We thank Mary O'Connell for critically reading the manuscript. Work in the authors' laboratory is supported by the University of Basel, the Swiss National Science Foundation and the Louis-Jeantet-Foundation for Medicine. Myriam Schaub is the recipient of a fellowship from the Association pour la Recherche sur le Cancer (ARC) and the Human Frontier Science Program (HFSP) Organization.

References (118)

  • C.X. George et al.

    Characterization of the 5′-flanking region of the human RNA-specific adenosine deaminase ADAR1 gene and identification of an interferon-inducible ADAR1 promoter

    Gene

    (1999)
  • K. Kawakubo et al.

    Human RNA-specific adenosine deaminase (ADAR1) gene specifies transcripts that initiate from a constitutively active alternative promoter

    Gene

    (2000)
  • A. Herbert

    RNA editing, introns and evolution

    Trends Genet

    (1996)
  • R.A. Reenan

    The RNA world meets behavior: A → I pre-mRNA editing in animals

    Trends Genet

    (2001)
  • B. Sommer et al.

    RNA editing in brain controls a determinant of ion flow in glutamate-gated channels

    Cell

    (1991)
  • M. Köhler et al.

    Determinants of Ca2+ permeability in both TM1 and TM2 of high affinity kainate receptor channels: diversity by RNA editing

    Neuron

    (1993)
  • M. Higuchi et al.

    NA editing of AMPA receptor subunit GluR-B: a base-paired intron-exon structure determines position and efficiency

    Cell

    (1993)
  • B.L. Bass

    RNA editing and hypermutation by adenosine deamination

    Trends Biochem. Sci

    (1997)
  • J.P. Petschek et al.

    RNA editing in Drosophila 4f-rnp gene nuclear transcripts by multiple A-to-G conversions

    J. Mol. Biol

    (1996)
  • J.P. Petschek et al.

    RNA editing and alternative splicing generate mRNA transcript diversity from the Drosophila 4f-rnp locus

    Gene

    (1997)
  • D.E. Patton et al.

    RNA editing generates a diverse array of transcripts encoding squid Kv2 K+ channels with altered functional properties

    Neuron

    (1997)
  • D.G. Murphy et al.

    Numerous transitions in human parainfluenza virus 3 RNA recovered from persistently infected cells

    Virology

    (1991)
  • P.J. O'Hara et al.

    Vesicular stomatitis virus defective interfering particles can contain extensive genomic sequence rearrangements and base substitutions

    Cell

    (1984)
  • P. Rueda et al.

    Loss of conserved cysteine residues in the attachment (G) glycoprotein of two human respiratory syncytial virus escape mutants that contain multiple A-G substitutions (hypermutations)

    Virology

    (1994)
  • R. Cattaneo et al.

    Biased hypermutation and other genetic changes in defective measles viruses in human brain infections

    Cell

    (1988)
  • B.L. Bass et al.

    Biased hypermutation of viral RNA genomes could be due to unwinding/modification of double-stranded RNA

    Cell

    (1989)
  • F. Lai et al.

    Mutagenic analysis of double-stranded RNA adenosine deaminase, a candidate enzyme for RNA editing of glutamate-gated ion channel transcripts

    J. Biol. Chem

    (1995)
  • M.A. O'Connell et al.

    Purification of human double-stranded RNA-specific editase1 (hRed1), involved in editing of brain glutamate receptor B pre-mRNA

    J. Biol. Chem

    (1997)
  • K.A. Lehmann et al.

    The importance of internal loops within RNA substrates of ADAR1

    J. Mol. Biol

    (1999)
  • H.Y. Yi-Brunozzi et al.

    Conformational changes that occur during an RNA editing adenosine deamination reaction

    J. Biol. Chem

    (2001)
  • M.J. Palladino et al.

    A-to-I pre-mRNA editing in Drosophila is primarily involved in adult nervous system function and integrity

    Cell

    (2000)
  • R.A. Reenan et al.

    The mle(napts) RNA helicase mutation in Drosophila results in a splicing catastrophe of the para Na+ channel transcript in a region of RNA editing

    Neuron

    (2000)
  • J.M. Gott et al.

    Functions and mechanisms of RNA editing

    Annu. Rev. Genet.

    (2000)
  • H.C. Smith et al.

    A guide to RNA editing

    RNA

    (1997)
  • A.G. Polson et al.

    The mechanism of adenosine to inosine conversion by the double-stranded RNA unwinding/modifying activity: a high-performance liquid chromatography-mass spectrometry analysis

    Biochemistry

    (1991)
  • S. Maas et al.

    Changing genetic information through RNA editing

    Bioessays

    (2000)
  • L.P. Keegan et al.

    The many roles of an RNA editor

    Nat. Rev. Genet.

    (2001)
  • R.W. Holley et al.

    Nucleotide sequences in the yeast alanine transfer RNA

    J. Biol. Chem.

    (1965)
  • R.B. Emeson et al.

    Adenosine-to-inosine RNA editing: substrates and consequences

  • M. Paul et al.

    Inosine exists in mRNA at tissue-specific levels and is most abundant in brain mRNA

    EMBO J.

    (1998)
  • G.R. Björk

    Biosynthesis and function of modified nucleosides in tRNA

  • J.F. Curran

    Modified nucleosides in translation

  • R.F. Hough et al.

    Adenosine deaminases that act on RNA

  • B.L. Bass et al.

    A standardized nomenclature for adenosine deaminases that act on RNA

    RNA

    (1997)
  • M.J. Palladino et al.

    dADAR, a Drosophila double-stranded RNA-specific adenosine deaminase is highly developmentally regulated and is itself a target for RNA editing

    RNA

    (2000)
  • R.F. Hough et al.

    Caenorhabditis elegans mRNAs that encode a protein similar to ADARs derive from an operon containing six genes

    Nucleic Acids Res

    (1999)
  • R.W. Wagner et al.

    Double-stranded RNA unwinding and modifying activity is detected ubiquitously in primary tissues and cell lines

    Mol. Cell Biol

    (1990)
  • C.X. Chen et al.

    A third member of the RNA-specific adenosine deaminase gene family, ADAR3, contains both single- and double-stranded RNA binding domains

    RNA

    (2000)
  • A. Gerber et al.

    Two forms of human double-stranded RNA-specific editase 1 (hRED1) generated by the insertion of an Alu cassette

    RNA

    (1997)
  • F. Lai et al.

    iting of glutamate receptor B subunit ion channel RNAs by four alternatively spliced DRADA2 double-stranded RNA adenosine deaminases

    Mol. Cell. Biol

    (1997)
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