Reexamining the polyadenylation signal: were we wrong about AAUAAA?

MacDonald, Clinton C.; Redondo, Jose Luis

doi:10.1016/s0303-7207(02)00044-8

Cited by 76 publications

(86 citation statements)

References 71 publications

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“…In addition, these data suggest that the poly(A) signal of the upstream gene is important for preventing premature transcriptional termination at the locus. Why eukaryotes have evolved the less common, noncanonical ATTAAA poly(A) signal is not known (23). Our data suggest one potential function for this polyA signal.…”

Section: Production Of Separate Cheb42a and Llz Transcripts Requires mentioning

confidence: 81%

Eukaryotic operon-like transcription of functionally related genes in Drosophila

Ben‐Shahar

Nannapaneni²,

Casavant³

et al. 2007

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

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Complex biological processes require coordinated function of many genes. One evolutionary solution to the problem of coordinately expressing functionally related genes in bacteria and nematodes is organization of genes in operons. Surprisingly, eukaryotic operons are considered rare outside the nematode lineage. In Drosophila melanogaster, we found lounge lizard (llz), which encodes a degenerin/ENaC cation channel, cotranscribed with CheB42a, a nonhomologous gene of unknown function residing <100 bp upstream. These two genes were transcribed from a single promoter as one primary transcript and were processed posttranscriptionally to generate individual mRNAs. The mechanism did not involve alternative splicing, and it differed from the trans splicing used in nematode operons. Both genes were expressed in the same tissues, and previous work suggested that both may be involved in courtship behavior. A bioinformatic approach identified numerous additional loci as potential Drosophila operons. These data reveal eukaryotic operon-like transcription of functionally related genes in Drosophila. The results also suggest that operon-based transcription may be more common in eukaryotes than previously appreciated.degenerin/epithelial Na ϩ channel ͉ fruit fly ͉ ion channels ͉ lounge lizard ͉ CheB42a D egenerin/epithelial Na ϩ channel (DEG/ENaC) proteins form non-voltage-gated cation channels. Their functions vary widely and include mechanosensation, nociception (sensing acidic stimuli), salt sensing, and detecting the peptidergic neurotransmitter FMRFamide (1-4). During our investigation of Drosophila melanogaster DEG/ENaC channels, we discovered a genomic locus containing a DEG/ENaC gene, which we named lounge lizard (llz, CG33349), and a nonhomologous gene of unknown function (CheB42a) (5) that appeared to be transcribed in the same direction with a predicted intergenic distance of Ͻ100 bp. The close proximity of these two genes and the lack of obvious promoter sequences in front of the downstream gene suggested that they might be cotranscribed from a single upstream promoter. This organization would resemble that of the nematode operon, an elegant evolutionary solution for coexpressing genes that are part of the same biochemical pathway or physiological process (6, 7).Although abundant in nematodes, operons are thought to be rare in other eukaryotes. This is despite eukaryote's complicated cellular physiology and the intricacy of their genomes, which might predict that operon-like transcription would solve some of the problem of coordinately regulating genes (8). With this background, we hypothesized that the CheB42a/llz locus might be transcribed as a eukaryotic operon, and, hence, the two genes might be functionally related.

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Section: Production Of Separate Cheb42a and Llz Transcripts Requires mentioning

confidence: 81%

Eukaryotic operon-like transcription of functionally related genes in Drosophila

Ben‐Shahar

Nannapaneni²,

Casavant³

et al. 2007

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

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“…Repeated attempts to extend the 5 -and 3 -UTRs did not yield additional sequence. While it is possible that we are still lacking untranslated sequence, it is also likely that the difference between the results of northern blot analysis and the length of isolated RACE clones is due to polyadenylation, because poly-A tails can be several hundred nucleotides in length (MacDonald & Redondo 2002). The majority of the P. motoro StAR transcript is 3 -UTR sequence, which contains three consensus polyadenlyation signals (beginning at 2125, 2130 and 3341 bp).…”

Section: Discussionmentioning

confidence: 99%

Cloning and characterization of cDNAs encoding steroidogenic acute regulatory protein from freshwater stingrays (Potamotrygon spp.)

Nunez¹,

Piermarini²,

Evans³

et al. 2005

Journal of Molecular Endocrinology

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The steroidogenic acute regulatory protein (StAR) is critical to the regulated synthesis of steroids in vertebrates. We have isolated cDNA sequences encoding StAR in the freshwater stingrays Potamotrygon hystrix and P. motoro. A single P. hystrix StAR transcript (3376 bp) and two overlapping P. motoro StAR transcripts (1272 and 3365 bp) were isolated. The P. hystrix and P. motoro StAR transcripts contain open reading frames encoding proteins of 284 amino acids that are 99% identical to each other and 56-64% identical to other StAR proteins. Pregnenolone synthesis by green monkey kidney (COS-1) cells transfected with an expression construct encoding a human cholesterol side chain cleavage/adrenodoxin reductase/adrenodoxin fusion protein was increased 16-fold by coexpression with a pCMV5/P. motoro StAR expression construct. Northern blot analysis revealed a single 4000 bp StAR transcript in the P. motoro interrenal gland, but RT-PCR indicates StAR mRNA is also expressed in the brain, gonads, atria, ventricle, gill (female only) and muscle (female only). Expression in extragonadal and extraadrenocortical tissues is an indication that StAR may be critical to processes other than steroidogenesis. The longest P. motoro StAR transcript contains a sequence with great similarity to short interspersed repetitive elements found in other elasmobranchs. This study is the first to isolate and characterize elasmobranch StAR cDNA sequences and to demonstrate the activity of a nonmammalian StAR protein in a heterologous expression system.

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“…The efficacy of this approach has been demonstrated in the recent stream of publications revisiting the poly(A) cis-elements in different organisms in which such signal models were established based on conventional genetic analysis. Although still prominent, the status of the canonical AAUAAA pattern in mammals has been challenged (MacDonald and Redondo, 2002 [w] The online version of this article contains Web-only data. Article, publication date, and citation information can be found at www.plantphysiol.org/cgi…”

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confidence: 99%

“…The efficacy of this approach has been demonstrated in the recent stream of publications revisiting the poly(A) cis-elements in different organisms in which such signal models were established based on conventional genetic analysis. Although still prominent, the status of the canonical AAUAAA pattern in mammals has been challenged (MacDonald and Redondo, 2002). The most detailed information comes from the analysis of yeast poly(A) signals (Graber et al, 1999b(Graber et al, , 2002Van Helden et al, 2000) in which a large number of variants of efficiency elements were found at the same position as AAUAAA.…”

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confidence: 99%

Compilation of mRNA Polyadenylation Signals in Arabidopsis Revealed a New Signal Element and Potential Secondary Structures

et al. 2005

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Using a novel program, SignalSleuth, and a database containing authenticated polyadenylation [poly(A)] sites, we analyzed the composition of mRNA poly(A) signals in Arabidopsis (Arabidopsis thaliana), and reevaluated previously described cis-elements within the 3#-untranslated (UTR) regions, including near upstream elements and far upstream elements. As predicted, there are absences of high-consensus signal patterns. The AAUAAA signal topped the near upstream elements patterns and was found within the predicted location to only approximately 10% of 3#-UTRs. More importantly, we identified a new set, named cleavage elements, of poly(A) signals flanking both sides of the cleavage site. These cis-elements were not previously revealed by conventional mutagenesis and are contemplated as a cluster of signals for cleavage site recognition. Moreover, a singlenucleotide profile scan on the 3#-UTR regions unveiled a distinct arrangement of alternate stretches of U and A nucleotides, which led to a prediction of the formation of secondary structures. Using an RNA secondary structure prediction program, mFold, we identified three main types of secondary structures on the sequences analyzed. Surprisingly, these observed secondary structures were all interrupted in previously constructed mutations in these regions. These results will enable us to revise the current model of plant poly(A) signals and to develop tools to predict 3#-ends for gene annotation.Messenger RNA polyadenylation is a crucial step during the maturation of most eukaryotic mRNA, in which a polyadenine [poly(A)] tract is added to the cleaved 3#-end of a precursor mRNA (pre-mRNA) posttranscriptionally. Such a modification of mRNA has been shown to affect its stability, translatability, and nuclear-to-cytoplasmic export (Zhao et al., 1999). The posttranscriptional processing of mRNA is an event that has also been found tightly coupled with splicing and transcription termination (Proudfoot et al., 2002;Proudfoot, 2004). Thus, it is an essential processing event and the integral part of gene expression.The polyadenylation process requires two major components: the cis-elements or poly(A) signals of the pre-mRNA, and the trans-acting factors that carry out the cleavage and addition of the poly(A) tail at the 3#-end. These trans-acting factors are a complex of about 25 to 30 proteins involved in signal recognition, cleavage, and polyadenylation (Proudfoot, 2004). These proteins seem to be conserved among eukaryotic organisms. However, the poly(A) signals have been found to differ widely among yeast (Saccharomyces cerevisiae), animals, and plants in terms of signal locations and sequence content. The highly conserved AAUAAA element in mammals becomes a minor signal in plant and yeast genes, and the ubiquitous downstream elements of mammalian pre-mRNAs are nowhere to be found in yeast and plants. The latter two possess an enhancing element located far upstream of the cleavage site (Zhao et al., 1999).Previous understanding of these signal elements was derived mostly...

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Reexamining the polyadenylation signal: were we wrong about AAUAAA?

Cited by 76 publications

References 71 publications

Eukaryotic operon-like transcription of functionally related genes in Drosophila

Eukaryotic operon-like transcription of functionally related genes in Drosophila

Cloning and characterization of cDNAs encoding steroidogenic acute regulatory protein from freshwater stingrays (Potamotrygon spp.)

Compilation of mRNA Polyadenylation Signals in Arabidopsis Revealed a New Signal Element and Potential Secondary Structures

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