Cloning and characterization of two subunits of Arabidopsis thaliana nuclear cap-binding complex

Kmieciak, Maciej; Simpson, Craig G.; Lewandowska, Dominika; Brown, John W.; Jarmołowski, Artur

doi:10.1016/s0378-1119(01)00859-9

Cited by 46 publications

(53 citation statements)

References 39 publications

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“…The presence of both U2 introns in the triple intron construct increased splicing efficiency of the U12 intron to 20% compared with the 5% efficiency in the single intron construct. This suggested that the splicing efficiency of the U12 intron was enhanced by exon bridging interactions between flanking U2 introns, as observed previously for the CBP20 U12 intron (Kmieciak et al, 2002).To examine the effect of overexpression of UBP1 and RBP45 on exon-bridging interactions, the three-intron construct, pGSH.9, was cotransfected with HA-tagged UBP1 or RBP45. Overexpression of UBP1 with pGSH.9 in tobacco protoplasts had little effect on splicing pattern or efficiency.…”

supporting

confidence: 55%

“…As with U2 introns, U12 intron splicing follows a two-step reaction that involves the formation of a characteristic intron lariat intermediate at an adenosine that can be at one of two possible positions within the stringent branchpoint consensus (Tarn and Steitz, 1996a;McConnell et al, 2002). In addition, exon bridging interactions between complexes forming on splice sites of U12 introns and flanking U2 introns can enhance U12-dependent intron splicing (Wu and Krainer, 1996;Dietrich et al, 2001b;Hastings and Krainer, 2001;Kmieciak et al, 2002), and some U12 introns are involved in alternative splicing (Dietrich et al, 2001b;Zhu and Brendel, 2003).The distinguishing feature of U2 introns in plants, compared with introns from vertebrates and yeast (Saccharomyces cerevisiae), is their UA richness, which is required for efficient U2 intron splicing and for 59 and 39 splice site selection (Goodall and Filipowicz, 1989;Simpson and Filipowicz, 1996;Brown and Simpson, 1998;Lorković et al, 2000;Reddy, 2001). The role of UA-rich elements in plant splicing is still poorly understood, but they may minimize secondary structure of plant introns or bind specific UA binding proteins to recruit splicing factors early in spliceosome formation (Simpson and Filipowicz, 1996;Brown and Simpson, 1998;Lorković et al, 2000;Reddy, 2001).…”

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confidence: 99%

“…Of these, only UBP1 so far has been shown to affect splicing, where overexpression of UBP1 enhanced splicing of otherwise poorly spliced U2-type introns . Putative plant U12 introns are also UA rich in comparison with exonic sequences (Zhu and Brendel, 2003; our unpublished results), but it remains to be seen whether UA richness determines splice site selection or influences splicing efficiency.To date, the splicing of only one plant U12-dependent intron has been experimentally analyzed in vivo (Kmieciak et al, 2002). Here, we present an analysis of sequence elements that are involved in plant U12 intron splicing efficiency using three different Arabidopsis U12-dependent introns.…”

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confidence: 99%

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Determinants of Plant U12-Dependent Intron Splicing Efficiency

Lewandowska

Simpson²,

Clark³

et al. 2004

Plant Cell

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Factors affecting splicing of plant U12-dependent introns have been examined by extensive mutational analyses in an in vivo tobacco (Nicotiana tabacum) protoplast system using introns from three different Arabidopsis thaliana genes: CBP20, GSH2, and LD. The results provide evidence that splicing efficiency of plant U12 introns depends on a combination of factors, including UA content, exon bridging interactions between the U12 intron and flanking U2-dependent introns, and exon splicing enhancer sequences (ESEs). Unexpectedly, all three plant U12 introns required an adenosine at the upstream purine position in the branchpoint consensus UCCUURAUY. The exon upstream of the LD U12 intron is a major determinant of its higher level of splicing efficiency and potentially contains two ESE regions. These results suggest that in plants, U12 introns represent a level at which expression of their host genes can be regulated. INTRODUCTIONPre-mRNA splicing in eukaryotes is a fundamental step in gene expression and represents an important level at which the expression of protein-coding genes can be regulated (Reed, 2000;Smith and Valcá rcel, 2000;Graveley, 2001;Hastings and Krainer, 2001;Cartegni et al., 2002;Black, 2003). In higher eukaryotes, there are two classes of nuclear pre-mRNA introns. The most abundant class consists of U2-dependent introns (U2 introns), whereas the second rarer class (<0.4% of introns) consists of U12-dependent introns (U12 introns). U12 introns have been found in the nuclear genomes of vertebrates, plants, and insects (Hall and Padgett, 1994;Sharp and Burge, 1997;Tarn and Steitz, 1997; Krainer, 1998, 1999;Burge et al., 1998;Levine and Durbin, 2001;Patel and Steitz, 2003). Introns belonging to these two distinct classes are spliced by two different spliceosomes: the major U2-type spliceosome and the less abundant U12-type spliceosome (Hall and Padgett, 1996;Tarn and Steitz 1996a. Although the first U12 introns to be described had AT-AC-terminal dinucleotides, the majority of U12-type introns contain GT-AG, and a small number contain other noncanonical terminal dinucleotides, such as AT-AA, AT-AG, AT-AT, GT-AT, or GT-GG (Jackson, 1991;Hall and Padgett, 1994;Dietrich et al., 1997Dietrich et al., , 2001aSharp and Burge, 1997;Burge et al., 1998;Wu and Krainer, 1999;Levine and Durbin, 2001;Zhu and Brendel, 2003). Moreover, functional analyses have shown that AT-AC-terminal dinucleotides are not a defining feature of U12 introns (Dietrich et al., 1997(Dietrich et al., , 2001a. Instead, U12 introns contain highly conserved sequences in the 59 splice site (exon:G/ATATCCTY) and branchpoint region (TCCTTRAY) (Hall and Padgett, 1994;Sharp and Burge, 1997;Burge et al., 1998), which are both required for prespliceosome complex formation (Frilander and Steitz, 1999). The 39 splice site consensus sequence of U12 introns (YAC/G:exon) is less informative than their 59 splice site and branchpoint sequences. U12 introns also lack a polypyrimidine tract and have a short distance between the branchpoint and 39 splice si...

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supporting

confidence: 55%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Determinants of Plant U12-Dependent Intron Splicing Efficiency

Lewandowska

Simpson²,

Clark³

et al. 2004

Plant Cell

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“…We selected CBP80 ( CAP-BINDING PROTEIN 80 ; At2g13540) intron number 3 (similar in size to the GUT15 tRNA-like hosting intron) [20], which does not naturally possess any tRNA-resembling elements. The original intron construct was modified to contain either the GUT15 tRNA-like sequence or tRNA-Ala AGC (called pCBP80(tRNA-like) and pCBP80(Ala), respectively) (Fig.…”

Section: Resultsmentioning

confidence: 99%

A stable tRNA-like molecule is generated from the long noncoding RNA GUT15 in Arabidopsis

et al. 2018

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The Arabidopsis GUT15 RNA belongs to a class of noncoding RNAs that are expressed from the intergenic regions of protein-coding genes. We show that the RNA polymerase II transcribed GUT15 transcript serves as a precursor for two stable RNA species, a tRNA-like molecule and GUT15-tRF-F5, which are both encoded by the final intron in the GUT15 gene. The GUT15-encoded tRNA-like molecule cannot be autonomously transcribed by RNA polymerase III. However, this molecule contains a CCA motif, suggesting that it may enter the tRNA maturation pathway. The GUT15-encoded tRNA-like sequence has an inhibiting effect on the splicing of its host intron. Moreover, we demonstrate that the canonical tRNA genes nested within introns do not affect the splicing patterns of their host protein-coding transcripts.

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“…80 (CBP80), also known as the Abscisic Acid Hypersensitive 1 protein (ABH1). 19,20 The CBC is known to influence the splicing efficiency of the first intron of pre-mRNAs, as well as the pattern of pre-mRNA alternative splicing. 21 It has also been shown that the lack of either of these proteins impairs the biogenesis of certain miRNAs.…”

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confidence: 99%