Pre-mRNA splicing imprints mRNA in the nucleus with a novel RNA-binding protein that persists in the cytoplasm.

We describe a novel RNA binding protein, Y14, a predominantly nuclear nucleocytoplasmic shuttling protein. Interestingly, Y14 associates preferentially with mRNAs produced by splicing but not with pre-mRNAs, introns, or mRNAs produced from intronless cDNAs. Y14 associates with both nuclear mRNAs and newly exported cytoplasmic mRNAs. Splicing of a single intron is sufficient for Y14 association. Y14-containing nuclear complexes are different from general hnRNP complexes. They contain hnRNP proteins and several unique proteins including the mRNA export factor TAP. Thus, Y14 defines novel intermediates in the pathway of gene expression, postsplicing nuclear preexport mRNPs, and newly exported cytoplasmic mRNPs, whose composition is established by splicing. These findings suggest that pre-mRNA splicing imprints mRNA with a unique set of proteins that persists in the cytoplasm and thereby communicates the history of the transcript.

The survival motor neuron protein of Schizosacharomyces pombe. Conservation of survival motor neuron interaction domains in divergent organisms.

Spinal muscular atrophy is a common often lethal neurodegenerative disease resulting from deletions or mutations in the survival motor neuron gene (SMN). SMN is ubiquitously expressed in metazoan cells and plays a role in small nuclear ribonucleoprotein assembly and pre-mRNA splicing. Here we characterize the Schizosacharomyces pombe orthologue of SMN (yeast SMN (ySMN)). We report that the ySMN protein is essential for viability and localizes in both the cytoplasm and the nucleus. Like human SMN, we show that ySMN can oligomerize. Remarkably, ySMN interacts directly with human SMN and Sm proteins. The highly conserved carboxyl-terminal domain of ySMN is necessary for the evolutionarily conserved interactions of SMN and required for cell viability. We also demonstrate that the conserved amino-terminal region of ySMN is not required for SMN and Sm binding but is critical for the housekeeping function of SMN.

Gemin4. A novel component of the SMN complex that is found in both gems and nucleoli.

The survival of motor neurons (SMN) protein, the product of the neurodegenerative disease spinal muscular atrophy (SMA) gene, is localized both in the cytoplasm and in discrete nuclear bodies called gems. In both compartments SMN is part of a large complex that contains several proteins including Gemin2 (formerly SIP1) and the DEAD box protein Gemin3. In the cytoplasm, the SMN complex is associated with snRNP Sm core proteins and plays a critical role in spliceosomal snRNP assembly. In the nucleus, SMN is required for pre-mRNA splicing by serving in the regeneration of spliceosomes. These functions are likely impaired in cells of SMA patients because they have reduced levels of functional SMN. Here, we report the identification by nanoelectrospray mass spectrometry of a novel component of the SMN complex that we name Gemin4. Gemin4 is associated in vivo with the SMN complex through a direct interaction with Gemin3. The tight interaction of Gemin4 with Gemin3 suggests that it could serve as a cofactor of this DEAD box protein. Gemin4 also interacts directly with several of the Sm core proteins. Monoclonal antibodies against Gemin4 efficiently immunoprecipitate the spliceosomal U snRNAs U1 and U5 from Xenopus oocytes cytoplasm. Immunolocalization experiments show that Gemin4 is colocalized with SMN in the cytoplasm and in gems. Interestingly, Gemin4 is also detected in the nucleoli, suggesting that the SMN complex may also function in preribosomal RNA processing or ribosome assembly.

Gemin3: A novel DEAD box protein that interacts with SMN, the spinal muscular atrophy gene product, and is a component of gems.

The survival of motor neurons (SMN) gene is the disease gene of spinal muscular atrophy (SMA), a common motor neuron degenerative disease. The SMN protein is part of a complex containing several proteins, of which one, SIP1 (SMN interacting protein 1), has been characterized so far. The SMN complex is found in both the cytoplasm and in the nucleus, where it is concentrated in bodies called gems. In the cytoplasm, SMN and SIP1 interact with the Sm core proteins of spliceosomal small nuclear ribonucleoproteins (snRNPs), and they play a critical role in snRNP assembly. In the nucleus, SMN is required for pre-mRNA splicing, likely by serving in the regeneration of snRNPs. Here, we report the identification of another component of the SMN complex, a novel DEAD box putative RNA helicase, named Gemin3. Gemin3 interacts directly with SMN, as well as with SmB, SmD2, and SmD3. Immunolocalization studies using mAbs to Gemin3 show that it colocalizes with SMN in gems. Gemin3 binds SMN via its unique COOH-terminal domain, and SMN mutations found in some SMA patients strongly reduce this interaction. The presence of a DEAD box motif in Gemin3 suggests that it may provide the catalytic activity that plays a critical role in the function of the SMN complex on RNPs.

Expression of the mouse fibronectin gene and fibronectin-lacZ transgenes during somitogenesis.

Fibronectins (FNs) are essential for the proper development of embryonic mesenchymal tissues. A lacZ reporter gene has been fused to 4.9 kbp of DNA from the rat FN gene 5' flanking region, and this construct has been microinjected into fertilized mouse embryos to investigate the cis elements needed for the temporal and spatial regulation of FN in vivo. Histochemical staining of embryos for beta-galactosidase activity demonstrated that four independent lines shared a specific pattern of lacZ expression, reflecting the activity of the fibronectin sequences contained within the transgene. Specifically, somites stained positively for lacZ, but expression was spatially and temporally non-uniform, with higher levels in more caudal somites after a total of ca. 13 somite pairs had formed. This rostral-caudal gradient of lacZ expression in somites of embryos beyond this stage resembled the distribution of endogenous FN mRNA, as detected by whole mount in situ hybridization. The transgene was not expressed in the developing heart where endogenous FN mRNA was detected. Unexpectedly, highly localized staining was observed within the neural tube beginning at ca. E10-10.5, and two of the lines exhibited additional areas of staining due to the individual integration sites. Thus, the 4.9 kbp FN fragment appears to recapitulate closely the complex pattern of FN expression observed during somitogenesis. A smaller fragment of 0.9 kbp also directed lacZ expression in caudal somites at E9.5, suggesting that these sequences are sufficient to establish the spatio-temporal pattern.

Modulation of transcription of the rat fibronectin gene by cell density.

The fibronectin (FN) gene is under complex regulatory control in vitro and in vivo. Sequences from the rat FN gene directed efficient expression of a lacZ reporter gene product, beta-galactosidase, in NIH/3T3 mouse fibroblasts. Stable transfectants were generated to facilitate studies of gene regulation by cell growth state. The expression of FN-lacZ constructs increased approximately twofold when cultures attained confluence, relative to total protein. The magnitude of this increase correlates well with that observed for FN mRNA levels and protein synthesis rate. Fragments containing 4.9, 0.9, or 0.3 kbp upstream of the transcription start site are equally responsive to cell density and/or cell contact. Deletion of a cAMP-responsive element enhanced the response, suggesting a negative role for this sequence motif and demonstrating that the FN gene is regulated by cell density at the transcriptional level. The effect of high cell density is apparently different from decreased growth rate, as incubation with low serum did not result in increased expression of the lacZ reporter. Finally, conditioned medium from dense cells did not enhance reporter gene expression in sparse cells, suggesting that the density signal is not transmitted via a soluble factor.

Unexpected nuclear localization of a chimeric beta-galactosidase lacZ reporter gene product in mammalian cells.

A lacZ cassette was designed to include a synthetic amino terminus optimized for translation in eukaryotic cells, as well as multiple restriction sites for the insertion of heterologous regulatory elements both 5' and 3' of the reporter. The cassette was placed under the control of the metallothionein promoter in combination with the SV40 enhancer and this plasmid was introduced into mammalian cells. High levels of beta-galactosidase were observed in several cell types, demonstrating efficient expression of the reporter. Unexpectedly, most of the chromogenic reaction product appeared to be intra- or peri-nuclear, indicating that the enzyme is similarly localized. The synthetic amino terminus does not resemble known nuclear localization signals and thus may constitute a novel signal.