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Charles N Cole

Publications and source records attributed to Charles N Cole.

9 recordsLinked to original sources
PubMed2006

The phylogenetic distribution of metazoan microRNAs: insights into evolutionary complexity and constraint.

How complex body plans evolved in animals such as fruit flies and vertebrates, as compared to the relatively simple jellyfish and sponges, is not known, given the similarity of developmental genetic repertoires shared by all these taxa. Here, we show that a core set of 18 microRNAs (miRNAs), non-coding RNA molecules that negatively regulate the expression of protein-coding genes, are found only in protostomes and deuterostomes and not in sponges or cnidarians. Because many of these miRNAs are expressed in specific tissues and/or organs, miRNA-mediated regulation could have played a fundamental evolutionary role in the origins of organs such as brain and heart--structures not found in cnidarians or sponges--and thus contributed greatly to the evolution of complex body plans. Furthermore, the continuous acquisition and fixation of miRNAs in various animal groups strongly correlates both with the hierarchy of metazoan relationships and with the non-random origination of metazoan morphological innovations through geologic time.

Animals↗
PubMed2006

Transport of messenger RNA from the nucleus to the cytoplasm.

All movement of molecules and macromolecules between the cytoplasm and the nucleus takes place through nuclear pore complexes (NPCs), very large macromolecular complexes that are the only channels connecting these compartments. mRNA export is mediated by multiple, highly conserved protein factors that couple steps of nuclear pre-mRNA biogenesis to mRNA transport. Mature messenger ribonucleoproteins (mRNPs) diffuse from sites of transcription to NPCs, although some active genes are positioned at the nuclear periphery where they interact physically with components of NPCs. As properly processed mRNPs translocate through the pore, certain mRNP proteins are removed, probably through the enzymatic action of the DEAD-box helicase Dbp5, which binds to Nup159 and Gle1, components of the cytoplasmic filaments of the NPC. Gle1 and the phosphoinositide IP6 activate Dbp5's ATPase activity in vitro and this could provide critical spatial regulation of Dbp5 activity in vivo.

Active Transport, Cell Nucleus↗
PubMed2005

Yeast poly(A)-binding protein, Pab1, and PAN, a poly(A) nuclease complex recruited by Pab1, connect mRNA biogenesis to export.

In eukaryotic cells, pre-mRNAs undergo extensive processing in the nucleus prior to export. Processing is subject to a quality-control mechanism that retains improperly processed transcripts at or near sites of transcription. A poly(A) tail added by the normal 3'-processing machinery is necessary but not sufficient for export. Retention depends on the exosome. In this study, we identify the poly(A)-binding protein, Pab1, and the poly(A) nuclease, PAN, as important factors that couple 3' processing to export. Pab1 contains a nonessential leucine-rich nuclear export signal and shuttles between the nucleus and the cytoplasm. It can exit the nucleus either as cargo of exportin 1 or bound to mRNA. Pab1 is essential but several bypass suppressors have been identified. Deletion of PAB1 from these bypass suppressor strains results in exosome-dependent retention at sites of transcription. Retention is also seen in cells lacking PAN, which Pab1 is thought to recruit and which may be responsible for the final step of mRNA biogenesis, trimming of the poly(A) tail to the length found on newly exported mRNAs. The studies presented here suggest that proper loading of Pab1 onto mRNAs and final trimming of the tail allows release from transcription sites and couples pre-mRNA processing to export.

Active Transport, Cell Nucleus↗
PubMed2004

Physical and genetic interactions link the yeast protein Zds1p with mRNA nuclear export.

Eukaryotic gene expression requires the export of mRNA from the nucleus to the cytoplasm. The DEAD box protein Dbp5p is an essential export factor conserved from yeast to man. A fraction of Dbp5p forms a complex with nucleoporins of the cytoplasmic filaments of the nuclear pore complex. Gfd1p was identified originally as a multicopy suppressor of the rat8-2 ts allele of DBP5. Here we reported that Dbp5p and Gfd1p interact with Zds1p, a protein previously identified as a multicopy suppressor in several yeast genetic screens. By using the two-hybrid system, we showed that Zds1p interacts in vivo with both Gfd1p and Dbp5p. In vitro binding experiments revealed that Gfd1p and Dbp5p bind directly to the C-terminal part of Zds1p. In addition, ZDS1 interacted genetically with mutant alleles of genes encoding key factors in mRNA export, including DBP5 and MEX67. Furthermore, deletion of ZDS1 or of both ZDS1 and the closely related ZDS2 exacerbated the poly(A)+ export defects shown by dbp5-2 and mex67-5 mutants. We proposed that Zds1p associates with the complex formed by Dbp5p, Gfd1p, and nucleoporins at the cytosolic fibrils of the nuclear pore complex and is required for optimal mRNA export.

Active Transport, Cell Nucleus↗
PubMed2004

The nuclear pore complex and the DEAD box protein Rat8p/Dbp5p have nonessential features which appear to facilitate mRNA export following heat shock.

Nuclear pore complexes (NPCs) play an essential role in RNA export. Nucleoporins required for mRNA export in Saccharomyces cerevisiae are found in the Nup84p and Nup82p subcomplexes of the NPC. The Nup82p subcomplex contains Nup82p, Rat7p/Nup159p, Nsp1p, Gle1p/Rss1p, and Rip1p/Nup42p and is found only on the cytoplasmic face of NPCs. Both Rat7p and Gle1p contain binding sites for Rat8p/Dbp5p, an essential DEAD box protein and putative RNA helicase. Rip1p interacts directly with Gle1p and is the only protein known to be essential for mRNA export after heat shock but not under normal growth conditions. We report that in cells lacking Rip1p, both Gle1p and Rat8p dissociate from NPCs following heat shock at 42 degrees C. Rat8p but not Gle1p was retained at NPCs if rip1Delta cells were first shifted to 37 degrees C and then to 42 degrees C, and this was correlated with preserving mRNA export in heat-shocked rip1Delta cells. Export following ethanol shock was less dependent on the presence of Rip1p. Exposure to 10% ethanol led to dissociation of Rat8p from NPCs in both wild-type and rip1Delta cells. Following this treatment, Rat8p was primarily nuclear in wild-type cells but primarily cytoplasmic in rip1Delta cells. We also determined that efficient export of heat shock mRNA after heat shock depends upon a novel 6-amino-acid element within Rat8p. This motif is not required under normal growth conditions or following ethanol shock. These studies suggest that the molecular mechanism responsible for the defect in export of heat shock mRNAs in heat-shocked rip1Delta cells is dissociation of Rat8p from NPCs. These studies also suggest that both nuclear pores and Rat8p have features not required for mRNA export in growing cells but which enhance the ability of mRNAs to be exported following heat shock.

Anti-Infective Agents, Local↗
PubMed2003

An early function during transcription for the yeast mRNA export factor Dbp5p/Rat8p suggested by its genetic and physical interactions with transcription factor IIH components.

The yeast DEAD-box protein Dbp5p/Rat8p is an essential factor for mRNA export and shuttles between the nucleus and the cytoplasm. It is concentrated at the cytoplasmic fibrils of the nuclear pore complex where it interacts with several nucleoporins. On the basis of this localization, it has been suggested that it might participate in a terminal step of RNA export, the release from the mRNA of proteins that accompany the mRNA during translocation through nuclear pores. In this report, we present evidence linking Dbp5p to transcription. Two different screens identified genetic interactions between DBP5 and genes involved in early transcription events, initiation and promoter clearance. Mutations of transcription proteins expected to impair transcription act as suppressors of dbp5 mutants, whereas those that may act to increase transcription are synthetically lethal with dbp5 mutations. We also show that growth and mRNA export in dbp5 mutant strains are dependent on the carboxy-terminal domain of the RNA pol II largest subunit. Finally, we show that Dbp5p associates physically with components of transcription factor IIH. Because these interactions affect not only growth but also mRNA export, they are likely to reflect a functional relationship between Dbp5p and the transcription machinery. Together, our results suggest a nuclear role for Dbp5 during the early steps of transcription.

Active Transport, Cell Nucleus↗
PubMed2003

Rpb4p, a subunit of RNA polymerase II, mediates mRNA export during stress.

Changes in gene expression represent a major mechanism by which cells respond to stress. We and other investigators have previously shown that the yeast RNA polymerase II subunit Rpb4p is required for transcription under various stress conditions, but not under optimal growth conditions. Here we show that, in addition to its role in transcription, Rpb4p is also required for mRNA export, but only when cells are exposed to stress conditions. The roles of Rpb4p in transcription and in mRNA export can be uncoupled genetically by specific mutations in Rpb4p. Both functions of Rpb4p are required to maintain cell viability during stress. We propose that Rpb4p participates in the cellular responses to stress at the interface of the transcription and the export machineries.

Amino Acid Sequence↗