Mitochondrial splicing requires a protein from a novel helicase family

Séraphin, Bertrand; Simon, Michel; Boulet, Annick; Faye, Gérard

doi:10.1038/337084a0

Cited by 206 publications

(162 citation statements)

References 24 publications

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“…Yeast mitochondria also contain a DEAD-box protein, Mss116p, whose core helicase region has 52% similarity to that of CYT-19 but more divergent N-and C-terminal domains. 10,19 The disruption of the MSS116 gene inhibits splicing of all S. cerevisiae mt group I and group II introns, some RNA processing reactions, and translation of a subset of mt mRNAs, and all of these defects can be suppressed by the expression of CYT-19. 10 Experiments using the yeast group II intron aI2, which requires an intron-encoded maturase for structural stabilization, indicated that DEAD-box protein activity accelerates a step after maturase binding, likely the resolution of stable folding intermediates or non-native structures that constitute kinetic traps.…”

Section: Introductionmentioning

confidence: 99%

Involvement of DEAD-box Proteins in Group I and Group II Intron Splicing. Biochemical Characterization of Mss116p, ATP Hydrolysis-dependent and -independent Mechanisms, and General RNA Chaperone Activity

Halls

Mohr

Campo

et al. 2007

Journal of Molecular Biology

154

242

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The RNA-catalyzed splicing of group I and group II introns is facilitated by proteins that stabilize the active RNA structure or act as RNA chaperones to disrupt stable inactive structures that are kinetic traps in RNA folding. In Neurospora crassa and Saccharomyces cerevisiae, the latter function is fulfilled by specific DEAD-box proteins, denoted CYT-19 and Mss116p, respectively. Previous studies showed that purified CYT-19 stimulates the in vitro splicing of structurally diverse group I and group II introns and uses the energy of ATP binding or hydrolysis to resolve kinetic traps. Here, we purified Mss116p and show that it has RNA-dependent ATPase activity, unwinds RNA duplexes in a non-polar fashion, and promotes ATP-independent strand-annealing. Further, we show that Mss116p binds RNA non-specifically and promotes in vitro splicing of both group I and group II intron RNAs, as well as RNA cleavage by the aI5γ-derived D135 ribozyme. However, Mss116p also has ATP-hydrolysis-independent effects on some of these reactions, which are not shared by CYT-19 and may reflect differences in its RNA-binding properties. We also show that a non-mitochondrial DEAD-box protein, yeast Ded1p, can function almost as efficiently as CYT-19 and Mss116p in splicing the yeast aI5γ group II intron and less efficiently in splicing the bI1 group II intron. Together, our results show that Mss116p, like CYT-19, can act broadly as an RNA chaperone to stimulate the splicing of diverse group I and group II introns and that Ded1p also has an RNA chaperone activity that can be assayed by its effect on splicing mitochondrial introns. Nevertheless, these DEAD-box protein RNA chaperones are not completely interchangeable and appear to function in somewhat different ways using biochemical activities that have likely been tuned by coevolution to function optimally on specific RNA substrates.

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Section: Introductionmentioning

confidence: 99%

Involvement of DEAD-box Proteins in Group I and Group II Intron Splicing. Biochemical Characterization of Mss116p, ATP Hydrolysis-dependent and -independent Mechanisms, and General RNA Chaperone Activity

Halls

Mohr

Campo

et al. 2007

Journal of Molecular Biology

154

242

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“…Recent studies have extended these findings by showing that CYT-19 plus ATP can also resolve a variety of other nonnative secondary and tertiary structures of the same intron (S.M. and A.M.L., unpublished data) and misfolded forms of the Tetrahymena L-21 ScaI ribozyme (H. Bhaskaran and R. Russell, personal communication).Saccharomyces cerevisiae mitochondria contain a DEAD-box protein Mss116p, which is related to CYT-19 and functions in splicing both group I and II introns (12,15,16). CYT-19 and Mss116p have 52% similarity in their core regions containing eight conserved motifs, but are more divergent in their C-terminal domains (12).…”

mentioning

confidence: 99%

“…Saccharomyces cerevisiae mitochondria contain a DEAD-box protein Mss116p, which is related to CYT-19 and functions in splicing both group I and II introns (12,15,16). CYT-19 and Mss116p have 52% similarity in their core regions containing eight conserved motifs, but are more divergent in their C-terminal domains (12).…”

mentioning

confidence: 99%

A DEAD-box protein alone promotes group II intron splicing and reverse splicing by acting as an RNA chaperone

Mohr

Matsuura

Perlman

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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Group II intron RNAs self-splice in vitro but only at high salt and͞or Mg 2؉ concentrations and have been thought to require proteins to stabilize their active structure for efficient splicing in vivo. Here, we show that a DEAD-box protein, CYT-19, can by itself promote the splicing and reverse splicing of the yeast aI5␥ and bI1 group II introns under near-physiological conditions by acting as an ATPdependent RNA chaperone, whose continued presence is not required after RNA folding. Our results suggest that the folding of some group II introns may be limited by kinetic traps and that their active structures, once formed, do not require proteins or high Mg 2؉ concentrations for structural stabilization. Thus, during evolution, group II introns could have spliced and transposed by reverse splicing by using ubiquitous RNA chaperones before acquiring more specific protein partners to promote their splicing and mobility. More generally, our results provide additional evidence for the widespread role of RNA chaperones in folding cellular RNAs.catalytic RNA ͉ ribozyme ͉ RNA helicase ͉ RNA structure G roup II introns are mobile catalytic RNAs that splice via a lariat intermediate and may be ancestors of eukaryotic spliceosomal introns (1-3). To catalyze splicing, the intron RNAs fold into a conserved three-dimensional structure, which aligns the splice sites and branch-point nucleotide residue and uses bound Mg 2ϩ ions to activate the appropriate bonds for catalysis. The conserved three-dimensional structure of group II introns consists of six double-helical domains (D1 to D6), which interact with each other via tertiary contacts (3). Some group II introns self-splice in vitro, but only under nonphysiological conditions, including high monovalent salt and Mg 2ϩ concentrations, which were thought essential for RNA folding and structural stabilization. Thus far, most of what is known about group II intron RNA structure, folding, and reactivity has come from studies under such conditions (1-3).The efficient splicing of group II introns in vivo requires proteins to help the intron RNA fold into the catalytically active structure (reviewed in refs. 2-4). Mobile group II introns encode proteins, which have reverse transcriptase (RT) activity and also promote the splicing of the intron in which they are encoded (''maturase'' activity). Other group II introns do not encode maturases and instead rely on host proteins, which appear to differ in different organisms (2-4). Until now, a protein-dependent in vitro splicing system has been developed only for the RT͞maturase protein encoded by the mobile Lactococcus lactis Ll.LtrB intron (5, 6). Studies using this system showed that the maturase binds specifically to the intron RNA and promotes its splicing by stabilizing the catalytically active RNA structure (7,8).In addition to proteins that stabilize specific RNA structures, cellular RNAs may require RNA chaperones to disrupt stable inactive structure (''kinetic traps'') during RNA folding (9, 10). In the case of group I and II int...

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“…This activity could be provided by the RNase subunit of the mitochondrial degradosome encoded by the DSS1/MSU1 gene, probably in association with another RNA helicase. An obvious candidate would be the Mss1p mitochondrial RNA helicase (Seraphin et al, 1989), which can partially rescue mitochondrial gene expression in suv3⌬ strains when overexpressed from a multicopy plasmid (Minczuk et al, 2002).…”

Section: Discussionmentioning

confidence: 99%

Balance between Transcription and RNA Degradation Is Vital forSaccharomyces cerevisiaeMitochondria: Reduced Transcription Rescues the Phenotype of Deficient RNA Degradation

Rogowska

Puchta

Czarnecka

et al. 2006

MBoC

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The Saccharomyces cerevisiae SUV3 gene encodes the helicase component of the mitochondrial degradosome (mtEXO), the principal 3 -to-5 exoribonuclease of yeast mitochondria responsible for RNA turnover and surveillance. Inactivation of SUV3 (suv3⌬) causes multiple defects related to overaccumulation of aberrant transcripts and precursors, leading to a disruption of mitochondrial gene expression and loss of respiratory function. We isolated spontaneous suppressors that partially restore mitochondrial function in suv3⌬ strains devoid of mitochondrial introns and found that they correspond to partial loss-of-function mutations in genes encoding the two subunits of the mitochondrial RNA polymerase (Rpo41p and Mtf1p) that severely reduce the transcription rate in mitochondria. These results show that reducing the transcription rate rescues defects in RNA turnover and demonstrates directly the vital importance of maintaining the balance between RNA synthesis and degradation. INTRODUCTIONThe degradation of RNA is an essential element in the expression of genetic information. It is required to control RNA abundance and thus gene expression and to eliminate aberrant or defective molecules that inevitably form during RNA synthesis and maturation (RNA surveillance) (Vasudevan and Peltz, 2003). The posttranscriptional mechanisms affecting mitochondrial gene expression, including RNA turnover, are of particular importance because transcriptional control is relatively simple and rudimentary. The single RNA polymerase (RNAP) of Saccharomyces cerevisiae mitochondria is composed of only two nuclear-encoded protein subunits-the core enzyme encoded by the RPO41 gene and a transcription initiation factor encoded by the MTF1 gene (Masters et al., 1987;Jang and Jaehning, 1991). The RNAP holoenzyme recognizes a simple nonanucleotide promoter sequence (Osinga et al., 1982;Mangus et al., 1994) and initiates synthesis of at least 13 primary multicistronic transcripts that undergo extensive processing to form mature RNAs (Christianson and Rabinowitz, 1983;Tzagoloff and Myers, 1986;Foury et al., 1998;Gagliardi et al., 2004;Schafer, 2005). Such organization leaves little room for regulation at the transcription initiation level and makes posttranscriptional processes, including RNA degradation, key control points for mitochondrial gene expression.The enzymes controlling RNA turnover in cells and organelles show great evolutionary divergence and are only partially conserved between mitochondria of different organisms (Gagliardi et al., 2004). The enzymatic activity responsible for turnover is, however, on the basic level, similar in all the systems discovered so far-it is that of a 3Ј-to-5Ј processive exoribonuclease, either hydrolytic or phosphorolytic. In most cases, the exoribonuclease activity is contained in a larger multiprotein complex that, in addition to exoribonucleases, also contains RNA helicases, and in certain cases, endonucleases. A model example of such a complex is the eubacterial degradosome (Carpousis, 2002).The first mitoc...

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Mitochondrial splicing requires a protein from a novel helicase family

Cited by 206 publications

References 24 publications

Involvement of DEAD-box Proteins in Group I and Group II Intron Splicing. Biochemical Characterization of Mss116p, ATP Hydrolysis-dependent and -independent Mechanisms, and General RNA Chaperone Activity

Involvement of DEAD-box Proteins in Group I and Group II Intron Splicing. Biochemical Characterization of Mss116p, ATP Hydrolysis-dependent and -independent Mechanisms, and General RNA Chaperone Activity

A DEAD-box protein alone promotes group II intron splicing and reverse splicing by acting as an RNA chaperone

Balance between Transcription and RNA Degradation Is Vital forSaccharomyces cerevisiaeMitochondria: Reduced Transcription Rescues the Phenotype of Deficient RNA Degradation

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