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Elliott, Barbara J.; Dattaroy, Tomal; Meeks-Midkiff, Lisa R.; Forbes, Kevin P.; Hunt, Arthur G.

doi:10.1023/a:1022035219500

Cited by 16 publications

(4 citation statements)

References 25 publications

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“…This protein would be a key component of the CPSF complex that acts together with CstF in 3Ј end formation. AtCPSF100 interacts with PolyA polymerase (41) and is essential for embryonic development (29). The esp5 allele (G12E) obtained from our screen did not have a strong effect on plant development or morphology, and it is likely to encode a protein with partial loss of function.…”

Section: Resultsmentioning

confidence: 82%

Defective RNA processing enhances RNA silencing and influences flowering ofArabidopsis

Herr

Molnár

Jones

et al. 2006

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

178

187

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Many eukaryotic cells use RNA-directed silencing mechanisms to protect against viruses and transposons and to suppress endogenous gene expression at the posttranscriptional level. RNA silencing also is implicated in epigenetic mechanisms affecting chromosome structure and transcriptional gene silencing. Here, we describe enhanced silencing phenotype (esp) mutants in Arabidopsis thaliana that reveal how proteins associated with RNA processing and 3 end formation can influence RNA silencing. These proteins were a putative DEAH RNA helicase homologue of the yeast PRP2 RNA splicing cofactor and homologues of mRNA 3 end formation proteins CstF64, symplekin͞PTA1, and CPSF100. The last two proteins physically associated with the flowering time regulator FY in the 3 end formation complex AtCPSF. The phenotypes of the 3 end formation esp mutants include impaired termination of the transgene transcripts, early flowering, and enhanced silencing of the FCA-␤ mRNA. Based on these findings, we propose that the ESP-containing 3 end formation complexes prevent transgene and endogenous mRNAs from entering RNA-silencing pathways. According to this proposal, in the absence of these ESP proteins, these RNAs have aberrant 3 termini. The aberrant RNAs would enter the RNA silencing pathways because they are converted into dsRNA by RNA-dependent RNA polymerases.aberrant RNA ͉ polyadenylation ͉ siRNAs ͉ epigenetics ͉ RNA polymerase

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Section: Resultsmentioning

confidence: 82%

Defective RNA processing enhances RNA silencing and influences flowering ofArabidopsis

Herr

Molnár

Jones

et al. 2006

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

178

187

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“…In mammals and yeast, PAP is coordinated with the cleaved pre-mRNA by the CPSF subcomplex, and several protein-protein interactions between CPSF subunits and PAP have been reported; however, these do not include direct contacts between CPSF73 and PAP. Among other polyadenylation complex subunits that do engage in direct interactions with PAP are Fip1 [ 47 – 51 ], CPSF160 [ 52 ], CPSF100 [ 53 , 54 ], and CFIm25 [ 49 , 55 ]. Curiously, clear-cut orthologs of these proteins were not found in the three apicomplexan genomes studied here.…”

Section: Discussionmentioning

confidence: 99%

Characterization of mRNA polyadenylation in the apicomplexa

2018

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Messenger RNA polyadenylation is a universal aspect of gene expression in eukaryotes. In well-established model organisms, this process is mediated by a conserved complex of 15–20 subunits. To better understand this process in apicomplexans, a group of unicellular parasites that causes serious disease in humans and livestock, a computational and high throughput sequencing study of the polyadenylation complex and poly(A) sites in several species was conducted. BLAST-based searches for orthologs of the human polyadenylation complex yielded clear matches to only two—poly(A) polymerase and CPSF73—of the 19 proteins used as queries in this analysis. As the human subunits that recognize the AAUAAA polyadenylation signal (PAS) were not immediately obvious, a computational analysis of sequences adjacent to experimentally-determined apicomplexan poly(A) sites was conducted. The results of this study showed that there exists in apicomplexans an A-rich region that corresponds in position to the AAUAAA PAS. The set of experimentally-determined sites in one species, Sarcocystis neurona, was further analyzed to evaluate the extent and significance of alternative poly(A) site choice in this organism. The results showed that almost 80% of S. neurona genes possess more than one poly(A) site, and that more than 780 sites showed differential usage in the two developmental stages–extracellular merozoites and intracellular schizonts–studied. These sites affected more than 450 genes, and included a disproportionate number of genes that encode membrane transporters and ribosomal proteins. Taken together, these results reveal that apicomplexan species seem to possess a poly(A) signal analogous to AAUAAA even though genes that may encode obvious counterparts of the AAUAAA-recognizing proteins are absent in these organisms. They also indicate that, as is the case in other eukaryotes, alternative polyadenylation is a widespread phenomenon in S. neurona that has the potential to impact growth and development.

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“…3 Insertions in two of these (encoding homologs of CPSF100 and CPSF73, respectively) lead to embryo lethality (27,28). The Arabidopsis CPSF100 protein interacts with at least one of the four PAPs (29), an interaction that seems to be unique to the plant polyadenylation machinery. There is a degree of novelty in the properties of the Arabidopsis homologs of the CstF subunits, in that one of the three proteins (AtCstF50) does not interact with AtCstF77 (30), in contrast to what has been shown in the mammalian complex (31).…”

mentioning

confidence: 99%

An Arabidopsis Fip1 Homolog Interacts with RNA and Provides Conceptual Links with a Number of Other Polyadenylation Factor Subunits

Forbes

Addepalli

Hunt

2006

Journal of Biological Chemistry

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The protein Fip1 is an important subunit of the eukaryotic polyadenylation apparatus, since it provides a bridge of sorts between poly(A) polymerase, other subunits of the polyadenylation apparatus, and the substrate RNA. In this study, a previously unreported Arabidopsis The polyadenylation of messenger RNAs in the nucleus is an important step in the biogenesis of mRNAs in eukaryotes. This RNA processing reaction adds an essential cis element, the poly(A) tail, to the 3Ј-end of a processed pre-mRNA. This process is also coupled with many other steps in mRNA biogenesis (1). Thus, some polyadenylation factors are associated with transcription factors and recruit parts of the polyadenylation apparatus to the transcription initiation complex (2). Polyadenylation is linked to pre-mRNA splicing in a number of ways. For example, interactions between the polyadenylation and splicing machineries are important for the definition of 3Ј-terminal exons in animal cells (3, 4). Other interactions help to modulate different processing fates for pre-mRNAs, thus contributing to the scope of alternative splicing and polyadenylation in eukaryotes. The polyadenylation apparatus interacts with the C-terminal domain of the large subunit of RNA polymerase II (5-9) and with factors that play roles in transcription termination (10); these interactions suggest a central role for 3Ј-end processing in the termination of transcription by RNA polymerase II and subsequent recycling of polymerase II for new rounds of initiation.Polyadenylation is mediated by a multifactor complex in yeast and mammals. This complex recognizes the polyadenylation signal in the pre-mRNA, cleaves the pre-mRNA at a site that is defined by the cis elements, and adds a defined tract of poly(A) to the processed pre-mRNA. In mammals, the factors involved in this process have been classified according to chromatographic and biochemical behaviors, and termed cleavage and polyadenylation specificity factor (CPSF), 2 cleavage-stimulatory factor (CstF), and cleavage factors I and II (CFIm and CFIIm, respectively) (1). Each of these factors in turn consists of several distinct subunits. With the exception of CFIm (the two subunits of which are not obviously apparent in the yeast proteome), yeast possesses a similar array of polyadenylation factor subunits that form a somewhat different set of chromatographically distinct factors, namely cleavage and polyadenylation factor and cleavage factor I (1). Interestingly, the enzyme that adds poly(A) (poly(A) polymerase, or PAP) is part of the cleavage and polyadenylation factor in yeast nuclear extracts but fractionates largely as a separate protein in mammalian extracts. Whereas there are differences in the chromatographic behaviors of the complexes in mammals and yeast, most of the functions of the individual subunits seem to be similar. Besides the PAPs, this includes RNA binding by CPSF160, CPSF30, and CstF64 and their yeast counterparts (Yhh1p, Yth1p, and Rna15p, respectively) (11-17) and bridging between factors (CstF77 and it...

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Untitled

Cited by 16 publications

References 25 publications

Defective RNA processing enhances RNA silencing and influences flowering ofArabidopsis

Defective RNA processing enhances RNA silencing and influences flowering ofArabidopsis

Characterization of mRNA polyadenylation in the apicomplexa

An Arabidopsis Fip1 Homolog Interacts with RNA and Provides Conceptual Links with a Number of Other Polyadenylation Factor Subunits

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