AtCyp59 is a multidomain cyclophilin from <i>Arabidopsis thaliana</i> that interacts with SR proteins and the C-terminal domain of the RNA polymerase II

Gullerová, Monika; Barta, Andrea; Lorković, Zdravko J.

doi:10.1261/rna.2226106

Cited by 72 publications

(98 citation statements)

References 58 publications

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“…Interestingly, CsCyp is not related to Arabidopsis Cyp59 (Fig. 1B), the only plant Cyp, besides CsCyp, known to interact with the CTD (Gullerova et al, 2006).…”

Section: Cscyp Belongs To the Subfamily Of Divergent Cypsmentioning

confidence: 99%

A Redox 2-Cys Mechanism Regulates the Catalytic Activity of Divergent Cyclophilins

et al. 2013

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The citrus (Citrus sinensis) cyclophilin CsCyp is a target of the Xanthomonas citri transcription activator-like effector PthA, required to elicit cankers on citrus. CsCyp binds the citrus thioredoxin CsTdx and the carboxyl-terminal domain of RNA polymerase II and is a divergent cyclophilin that carries the additional loop KSGKPLH, invariable cysteine (Cys) residues Cys-40 and Cys-168, and the conserved glutamate (Glu) Glu-83. Despite the suggested roles in ATP and metal binding, the functions of these unique structural elements remain unknown. Here, we show that the conserved Cys residues form a disulfide bond that inactivates the enzyme, whereas Glu-83, which belongs to the catalytic loop and is also critical for enzyme activity, is anchored to the divergent loop to maintain the active site open. In addition, we demonstrate that Cys-40 and Cys-168 are required for the interaction with CsTdx and that CsCyp binds the citrus carboxyl-terminal domain of RNA polymerase II YSPSAP repeat. Our data support a model where formation of the Cys-40-Cys-168 disulfide bond induces a conformational change that disrupts the interaction of the divergent and catalytic loops, via Glu-83, causing the active site to close. This suggests a new type of allosteric regulation in divergent cyclophilins, involving disulfide bond formation and a loop-displacement mechanism.

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“…Interestingly, CsCyp is not related to Arabidopsis Cyp59 (Fig. 1B), the only plant Cyp, besides CsCyp, known to interact with the CTD (Gullerova et al, 2006).…”

Section: Cscyp Belongs To the Subfamily Of Divergent Cypsmentioning

confidence: 99%

A Redox 2-Cys Mechanism Regulates the Catalytic Activity of Divergent Cyclophilins

et al. 2013

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“…Some plant SR and SR-like proteins have been shown to bind alternatively spliced introns (Day et al, 2012;Thomas et al, 2012). Complex interaction networks among SR proteins and interaction with many other snRNP and non-snRNP proteins (Golovkin and Reddy, 1998;Golovkin and Reddy, 1999;Lopato et al, 2002;Gullerova et al, 2006;Reddy, 2007;Barta et al, 2008) suggest an important role for this family of proteins in regulated splicing. Expression levels and AS patterns of SR proteins in plants vary in different tissues, implying their target specificity (Lopato et al, 1996(Lopato et al, , 1999a(Lopato et al, , 1999b(Lopato et al, , 2002Reddy, 1998, 1999;Lazar and Goodman, 2000;Kalyna et al, 2003;Kalyna and Barta, 2004).…”

Section: Trans-acting Factorsmentioning

confidence: 99%

Complexity of the Alternative Splicing Landscape in Plants

et al. 2013

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Alternative splicing (AS) of precursor mRNAs (pre-mRNAs) from multiexon genes allows organisms to increase their coding potential and regulate gene expression through multiple mechanisms. Recent transcriptome-wide analysis of AS using RNA sequencing has revealed that AS is highly pervasive in plants. Pre-mRNAs from over 60% of intron-containing genes undergo AS to produce a vast repertoire of mRNA isoforms. The functions of most splice variants are unknown. However, emerging evidence indicates that splice variants increase the functional diversity of proteins. Furthermore, AS is coupled to transcript stability and translation through nonsense-mediated decay and microRNA-mediated gene regulation. Widespread changes in AS in response to developmental cues and stresses suggest a role for regulated splicing in plant development and stress responses. Here, we review recent progress in uncovering the extent and complexity of the AS landscape in plants, its regulation, and the roles of AS in gene regulation. The prevalence of AS in plants has raised many new questions that require additional studies. New tools based on recent technological advances are allowing genome-wide analysis of RNA elements in transcripts and of chromatin modifications that regulate AS. Application of these tools in plants will provide significant new insights into AS regulation and crosstalk between AS and other layers of gene regulation.

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“…These proteins contain a prolyl-peptidyl isomerase domain important for protein structure and modification and have been shown to interact with SR proteins in vitro and in vivo, suggesting that they might regulate spliceosome assembly . Another multidomain cyclophilin, atCyp59 (prolyl-peptidyl isomerase, RRM zinc knuckle, and RS/RD domain), has been found to interact with SR proteins as well as with the C-terminal domain of RNA polymerase II and was suggested to connect splicing and transcription (Gullerova et al, 2006).…”

Section: Non-snrnp Proteinsmentioning

confidence: 99%

Localization and Dynamics of Nuclear Speckles in Plants

et al. 2011

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The generation of mature mRNAs from most genes (about 80%-90%) in autotrophic eukaryotes requires the removal of noncoding sequences (introns) and splicing of the coding regions (exons; Labadorf et al., 2010). During splicing in some precursor messenger RNAs (pre-mRNAs), the same splice sites are always used, referred to as constitutive splicing (CS), resulting in a single transcript from a gene. However, from many pre-mRNAs, multiple mature mRNAs are generated from a single gene by alternative splicing (AS), where different combinations of splice sites are used. Both CS and AS are critical to the proper expression of intron-containing genes. Recent transcriptome-wide analysis of AS using high-throughput sequencing indicates that pre-mRNAs from up to 42% of introncontaining genes in Arabidopsis (Arabidopsis thaliana; Filichkin et al., 2010) and about 48% in rice (Oryza sativa; Lu et al., 2010) are alternatively spliced, whereas about 95% of human genes are alternatively spliced (Pan et al., 2008). In addition to pre-mRNAs, some primary microRNAs (pri-miRNAs) are also subject to CS and AS (Hirsch et al., 2006;Szarzynska et al., 2009;Mica et al., 2010). AS increases the protein-coding capacity of a genome and generates functionally different proteins from the same gene (Reddy, 2007). AS results in protein isoforms with loss or gain of function and altered subcellular localization, protein stability, and/or posttranslational modifications. Furthermore, AS plays an important role in gene regulation through regulated unproductive splicing and translation, leading to RNA degradation by mRNA surveillance mechanisms, differential recruitment of mRNAs to ribosomes, or translatability of splice variants (Kurihara et al., 2009;Licatalosi and Darnell, 2010;Palusa and Reddy, 2010). Numerous spliceosomal proteins either promote or suppress splicing by interacting with splicing regulatory elements on the pre-mRNAs. In recent years, the localization and dynamics of some splicing regulators in plants have been analyzed using a variety of approaches. This review summarizes the current status of research in this area, with emphasis on RNAbinding proteins (RBPs) that are involved in splicing regulation, discusses open questions, and presents some approaches to address these questions. SPLICING REGULATORSpre-mRNAs splicing takes place cotranscriptionally in the spliceosome, a large multicomponent complex composed of small nuclear RNAs (snRNAs) and about 170 proteins, many of which are involved in the regulation of splicing (Wahl et al., 2009;Valadkhan and Jaladat, 2010). The composition of the human and yeast spliceosome has been analyzed in great detail (Wahl et al., 2009); however, information on plant splicing has been scarce, as no in vitro assembly of a functional plant spliceosome has been possible to date. A detailed search for Arabidopsis orthologs of the human spliceosome proteome revealed that most splicing factors are present in the Arabidopsis genome, indicating a similar complexity (Barta et al., 2011). Interestingly, m...

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AtCyp59 is a multidomain cyclophilin from Arabidopsis thaliana that interacts with SR proteins and the C-terminal domain of the RNA polymerase II

Cited by 72 publications

References 58 publications

A Redox 2-Cys Mechanism Regulates the Catalytic Activity of Divergent Cyclophilins

A Redox 2-Cys Mechanism Regulates the Catalytic Activity of Divergent Cyclophilins

Complexity of the Alternative Splicing Landscape in Plants

Localization and Dynamics of Nuclear Speckles in Plants

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