Splicing is required for rapid and efficient mRNA export in metazoans

Pre-mRNA splicing is among the last known nuclear events before export of mature mRNA to the cytoplasm. At present, it is not known whether splicing and mRNA export are biochemically coupled processes. In this study, we have injected pre-mRNAs containing a single intron or the same mRNAs lacking an intron (Deltai-mRNAs) into Xenopus oocyte nuclei. We find that the spliced mRNAs are exported much more rapidly and efficiently than the identical Deltai-mRNAs. Moreover, competition studies using excess Deltai-mRNA indicate that different factor(s) are involved in the inefficient export of Deltai-mRNA vs. the efficient export of spliced mRNA. Consistent with this conclusion, spliced mRNA and Deltai-mRNA, though identical in sequence, are assembled into different messenger ribonucleoprotein particles (mRNP) in vitro. Strikingly, the mRNA in the spliced mRNP, but not in the Deltai-mRNP, is exported rapidly and efficiently. We conclude that splicing generates a specific nucleoprotein complex that targets mRNA for export. Our results, revealing a link between splicing and efficient mRNA export, may explain the reports that an intron is required for efficient expression of many protein-coding genes in metazoans.

The RNA splicing factor hSlu7 is required for correct 3' splice-site choice

The production of correctly spliced messenger RNA requires two catalytic splicing steps. During step II, exon 1 attacks an adenine-guanine (AG) dinucleotide at the 3' splice site. This AG is usually located between 18 and 40 nucleotides downstream from the branch site, and closer AGs are skipped in favour of AGs located more optimally downstream. At present, little is understood about how the correct AG is distinguished from other AGs. Here we describe a metazoan splicing factor (hSlu7) that is required for selection of the correct AG. In the absence of hSlu7, use of the correct AG is suppressed and incorrect AGs are activated. We investigated this loss of fidelity by analysing spliceosomes assembled in the absence of hSlu7. These studies reveal that exon 1 is loosely associated with these spliceosomes. Thus, the improperly held exon cannot access the correct AG, but can attack other AGs indiscriminately. We conclude that hSlu7 is required to hold exon 1 tightly within the spliceosome for attack on a prespecified AG.

Resolution of the mammalian E complex and the ATP-dependent spliceosomal complexes on native agarose mini-gels

A great deal of progress in elucidating the mechanisms of spliceosome assembly has been achieved by analyzing the A, B, and C spliceosomal complexes on native polyacrylamide gels. In contrast, progress in understanding the earliest spliceosomal complex E has been hampered because this complex dissociates on native gels and is difficult to detect by other methods. Here we report conditions for resolving the spliceosomal complex E using a native horizontal agarose mini-gel system. This system also provides a simple alternative to polyacrylamide gels for resolving the ATP-dependent spliceosomal complexes.

Characterization of a protein complex containing spliceosomal proteins SAPs 49, 130, 145, and 155

SF3b is a U2 snRNP-associated protein complex essential for spliceosome assembly. Although evidence that SF3b contains the spliceosomal proteins SAPs 49, 130, 145, and 155 has accumulated, a protein-mediated association between all of these proteins has yet to be directly demonstrated. Here we report the isolation of a cDNA encoding SAP 130, which completes the cloning of the putative SF3b complex proteins. Using antibodies to SAP 130 and other putative SF3b components, we showed that SAPs 130, 145, and 155 are present in a protein complex in nuclear extracts and that these proteins associate with one another in purified U2 snRNP. Moreover, SAPs 155 and 130 interact with each other (directly or indirectly) within this complex, and SAPs 49 and 145 are known to interact directly with each other. Thus, together with prior work, our studies indicate that SAPs 49, 130, 145, and 155 are indeed components of SF3b. The Saccharomyces cerevisiae homologs of SAPs 49 and 145 are encoded by essential genes. We show here that the S. cerevisiae homologs of SAPs 130 and 155 (scSAP 130/RSE1 and scSAP 155, respectively) are also essential. Recently, the SF3b proteins were found in purified U12 snRNP, which functionally substitutes for U2 snRNP in the minor spliceosome. This high level of conservation, together with the prior observation that the SF3b proteins interact with pre-mRNA very close to the branch site, suggest that the SF3b complex plays a critical role near or at the spliceosome catalytic core.

Identification of both shared and distinct proteins in the major and minor spliceosomes

In metazoans, two distinct spliceosomes catalyzing pre-messenger RNA splicing have been identified. Here, the human U11/U12 small nuclear ribonucleoprotein (snRNP), a subunit of the minor (U12-dependent) spliceosome, was isolated. Twenty U11/U12 proteins were identified, including subsets unique to the minor spliceosome or common to both spliceosomes. Common proteins include four U2 snRNP polypeptides that constitute the essential splicing factor SF3b. A 35-kilodalton U11-associated protein homologous to the U1 snRNP 70K protein was also identified. These data provide fundamental information about proteins of the minor spliceosome and shed light on its evolutionary relationship to the major spliceosome.

Identification of RNA-protein contacts within functional ribonucleoprotein complexes by RNA site-specific labeling and UV crosslinking

A variety of cellular processes are carried out by highly complex ribonucleoprotein (RNP) particles in which multiple RNA-RNA, RNA-protein, and protein-protein interactions occur. The spliceosome, which executes the nuclear pre-mRNA splicing reaction, is a particularly striking example of a complex RNP, containing a minimum of 50 distinct protein components as well as five small nuclear RNAs. In order to identify which among the numerous proteins may play critical roles in the splicing reaction, we have assembled spliceosomal complexes on pre-mRNA containing a single 32P-labeled nucleotide, isolated the complexes by gel filtration, and then carried out UV crosslinking. The combination of these three methods has allowed the identification of proteins that crosslink to critical sequence elements during each stage in spliceosome assembly. These methods should be generally applicable to the analysis of RNP complexes assembled in vitro.

Human step II splicing factor hSlu7 functions in restructuring the spliceosome between the catalytic steps of splicing

The spliceosome catalyzes pre-mRNA splicing in two steps. After catalytic step I, a major remodeling of the spliceosome occurs to establish the active site for step II. Here, we report the isolation of a cDNA encoding hSlu7, the human homolog of the yeast second step splicing factor Slu7. We show that hSlu7 associates with the spliceosome late in the splicing pathway, but at a stage prior to recognition of the 3' splice site for step II. In the absence of hSlu7, splicing is stalled between the catalytic steps in a novel complex, the CDeltahSlu7 complex. We provide evidence that this complex differs significantly in structure from the known spliceosomal complexes, yet is a functional intermediate between the catalytic steps of splicing. Together, our observations indicate that hSlu7 is required for a structural alteration of the spliceosome prior to the establishment of the catalytically active spliceosome for step II.

Association of guide RNA binding protein gBP21 with active RNA editing complexes in Trypanosoma brucei

RNA editing in Trypanosoma brucei mitochondria produces mature mRNAs by a series of enzyme-catalyzed reactions that specifically insert or delete uridylates in association with a macromolecular complex. Using a mitochondrial fraction enriched for in vitro RNA editing activity, we produced several monoclonal antibodies that are specific for a 21-kDa guide RNA (gRNA) binding protein initially identified by UV cross-linking. Immunofluorescence studies localize the protein to the mitochondrion, with a preference for the kinetoplast. The antibodies cause a supershift of previously identified gRNA-specific ribonucleoprotein complexes and immunoprecipitate in vitro RNA editing activities that insert and delete uridylates. The immunoprecipitated material also contains gRNA-specific endoribonuclease, terminal uridylyltransferase, and RNA ligase activities as well as gRNA and both edited and unedited mRNA. The immunoprecipitate contains numerous proteins, of which the 21-kDa protein, a 90-kDa protein, and novel 55- and 16-kDa proteins can be UV cross-linked to gRNA. These studies indicate that the 21-kDa protein associates with the ribonucleoprotein complex (or complexes) that catalyze RNA editing.

WW domain-mediated interactions reveal a spliceosome-associated protein that binds a third class of proline-rich motif: the proline glycine and methionine-rich motif

Pre-mRNA splicing requires the bridging of the 5' and 3' ends of the intron. In yeast, this bridging involves interactions between the WW domains in the splicing factor PRP40 and a proline-rich domain in the branchpoint binding protein, BBP. Using a proline-rich domain derived from formin (a product of the murine limb deformity locus), we have identified a family of murine formin binding proteins (FBP's), each of which contains one or more of a special class of tyrosine-rich WW domains. Two of these WW domains, in the proteins FBP11 and FBP21, are strikingly similar to those found in the yeast splicing factor PRP40. We show that FBP21 is present in highly purified spliceosomal complex A, is associated with U2 snRNPs, and colocalizes with splicing factors in nuclear speckle domains. Moreover, FBP21 interacts directly with the U1 snRNP protein U1C, the core snRNP proteins SmB and SmB', and the branchpoint binding protein SF1/mBBP. Thus, FBP21 may play a role in cross-intron bridging of U1 and U2 snRNPs in the mammalian A complex.

A potential role for U2AF-SAP 155 interactions in recruiting U2 snRNP to the branch site

Base pairing between U2 snRNA and the branchpoint sequence (BPS) is essential for pre-mRNA splicing. Because the metazoan BPS is short and highly degenerate, this interaction alone is insufficient for specific binding of U2 snRNP. The splicing factor U2AF binds to the pyrimidine tract at the 3' splice site in the earliest spliceosomal complex, E, and is essential for U2 snRNP binding in the spliceosomal complex A. We show that the U2 snRNP protein SAP 155 UV cross-links to pre-mRNA on both sides of the BPS in the A complex. SAP 155's downstream cross-linking site is immediately adjacent to the U2AF binding site, and the two proteins interact directly in protein-protein interaction assays. Using UV cross-linking, together with functional analyses of pre-mRNAs containing duplicated BPSs, we show a direct correlation between BPS selection and UV cross-linking of SAP 155 on both sides of the BPS. Together, our data are consistent with a model in which U2AF binds to the pyrimidine tract in the E complex and then interacts with SAP 155 to recruit U2 snRNP to the BPS.

Cyclin E associates with components of the pre-mRNA splicing machinery in mammalian cells

Cyclin E-cdk2 is a critical regulator of cell cycle progression from G1 into S phase in mammalian cells. Despite this important function little is known about the downstream targets of this cyclin-kinase complex. Here we have identified components of the pre-mRNA processing machinery as potential targets of cyclin E-cdk2. Cyclin E-specific antibodies coprecipitated a number of cyclin E-associated proteins from cell lysates, among which are the spliceosome-associated proteins, SAP 114, SAP 145, and SAP 155, as well as the snRNP core proteins B' and B. The three SAPs are all subunits of the essential splicing factor SF3, a component of U2 snRNP. Cyclin E antibodies also specifically immunoprecipitated U2 snRNA and the spliceosome from splicing extracts. We demonstrate that SAP 155 serves as a substrate for cyclin E-cdk2 in vitro and that its phosphorylation in the cyclin E complex can be inhibited by the cdk-specific inhibitor p21. SAP 155 contains numerous cdk consensus phosphorylation sites in its N terminus and is phosphorylated prior to catalytic step II of the splicing pathway, suggesting a potential role for cdk regulation. These findings provide evidence that pre-mRNA splicing may be linked to the cell cycle machinery in mammalian cells.

Validating a measure of patient satisfaction with community nursing services

This study describes an attempt to develop and validate a measure of patient satisfaction with a district nursing service in a south-west London inner city borough. The patients were 126 house-bound elderly people living alone and dependent upon district nursing services. The patient satisfaction measure was derived from an earlier North American questionnaire assessing satisfaction with hospital nursing services. The results indicated that the measure chosen reflected multiple dimensions of patient satisfaction that were differentially sensitive to factors such as the degree of personalization of care and the impact of disruptions to the service. Scores on the questionnaire were also related in a systematic way with the number and type of spontaneous comments made about the service. Overall the results suggest that self-report questionnaire measures of satisfaction can be devised that are sensitive to variations in the style and level of community nursing offered to older house-bound people.

Cognitive deficits, psychopathology, and psychosocial functioning in bipolar mood disorder

The objective of this study was to study the relationship of poor functioning, cognition, and psychopathology in bipolar mood disorder. The authors assessed 36 patients with bipolar mood disorder (23 VA, 13 community) for the presence of psychopathology, cognitive deficits, and psychosocial impairment. The authors assessed psychopathology using screening and follow-up questions based on the schedule for affective disorder and schizophrenia, lifetime version (SADS-L), schedule for the assessment for negative symptoms (SANS), and schedule for the assessment of positive symptoms (SAPS), and psychosensory features using the "Profile of Psychomotor Symptoms." They tested cognitive functioning in the following domains: 1) general intelligence and language, 2) verbal and visual memory, and 3) visuospatial functioning. They also assessed psychosocial functioning using a structured scale to assess maladjustment and an impairment rating scale. Patients with bipolar disorder showed significant impairment compared to age equivalent normals in several cognitive domains. Anhedonia was related to memory deficits. Memory deficits were also associated with poor psychosocial functioning. This study demonstrates that nondemented, asymptomatic patients with bipolar disorder exhibit substantial cognitive deficits that are associated with poor functioning, and anhedonia and avolition best predict this outcome.

Sexually transmitted diseases are common in women attending Jamaican family planning clinics and appropriate detection tools are lacking

OBJECTIVES

To assess sexually transmitted diseases (STD) among women attending Jamaican family planning clinics and to evaluate decision models as alternatives to STD laboratory diagnosis.

METHODS

Women attending two family planning clinics in Kingston were interviewed and tested for syphilis seroreactivity using toluidine red unheated serum test and Treponema pallidum haemagglutination, for gonorrhoea using culture, for chlamydial infection using enzyme linked immunoassay, and for trichomoniasis using culture. Urine was tested with leucocyte esterase dipstick (LED). The women were treated based upon a clinical algorithm. Computer simulations explored the use of risk inclusive decision models for detection of cervical infection and/or trichomoniasis.

RESULTS

Among 767 women, 206 (26.9%) had at least one STD. The prevalence of gonorrhoea was 2.7%; chlamydial infection 12.2%; gonococcal and/or chlamydial cervical infection 14.1%; trichomoniasis 11.5%; syphilis seroreactivity 5.9%. The clinical algorithm was 3.7% sensitive and 96.7% specific in detecting cervical infection. Detection of cervical infection and/or trichomoniasis was 63.5% sensitive and 60.6% specific using LED and 57.7% sensitive and 46.2% specific using the risk inclusive algorithm employed in Jamaican STD clinics. Either cervical friability or LED (+) or family planning clinic attender less than 25 years old with more than one sexual partner in the past year was 72.5% sensitive and 53.3% specific. The positive predictive values of the STD clinic algorithm, LED, and two developed decision models ranged from 25.0% to 33.4% to detect cervical infection and/or trichomoniasis in these women.

CONCLUSION

STDs were quite prevalent in these mainly asymptomatic family planning clinic attenders. None of the evaluated decision models can be considered a good alternative to case detection using laboratory diagnosis. Appropriate detection tools are needed. In the meantime, available STD control strategies should be maximised, such as promotion of condom use; adequate treatment of symptomatic STD patients and partners; and education of women and men.

Phosphorylation of spliceosomal protein SAP 155 coupled with splicing catalysis

The U2 snRNP component SAP 155 contacts pre-mRNA on both sides of the branch site early in spliceosome assembly and is therefore positioned near or at the spliceosome catalytic center. We have isolated a cDNA encoding human SAP 155 and identified its highly related Saccharomyces cerevisiae homolog (50% identity). The carboxy-terminal two-thirds of SAP 155 shows the highest conservation and is remarkably similar to the regulatory subunit A of the phosphatase PP2A. Significantly, SAP 155 is phosphorylated concomitant with or just after catalytic step one, making this the first example of a protein modification tightly regulated with splicing catalysis.

Osteopontin stimulates a subpopulation of quiescent human prostate epithelial cells with high proliferative potential to divide in vitro

BACKGROUND

Osteopontin (OPN) is a secreted extracellular matrix (ECM) protein found in bone, as well as associated with epithelial cells. The main objective of these studies was to test in vitro the hypothesis that interaction with OPN stimulates proliferation of a quiescent subpopulation of prostate epithelial cells with high proliferative potential.

METHODS

To simulate conditions that restrict proliferation and inhibit terminal differentiation of basal cells in vivo, control cultures grew on substrate coated with collagen (CO) or fibronectin (FN), in medium containing low levels of growth factors.

RESULTS

Under growth-restricting conditions, most prostate epithelial cells with high proliferative potential, seeded in control secondary cultures, were quiescent within the time frame of the studies, as indicated by the small number of large colonies in these cultures. Growing prostate epithelial cells (PR) under the same growth-restricting conditions, but on substrate coated with OPN instead of CO or FN, stimulated proliferation of a subpopulation of single cells with high proliferative ability as indicated by: 1) dose-dependent increase in the percentage of single cells incorporating bromodeoxyuridine, i.e., proliferating PR; and 2) subsequent dose-dependent increase in the percentage of large colonies. The OPN effect was not merely due to preferential attachment to OPN, because PR attachment to OPN, CO, or FN was identical. PR attachment to OPN was inhibited in the presence of GRGDTP or an antibody against the integrin subunit alphav, but not in the presence of an RGES peptide or a nonspecific IgG.

CONCLUSIONS

Integrin-mediated OPN/PR interaction stimulates proliferation of a quiescent subpopulation of prostate epithelial cells with high proliferative potential, possibly stem cells.

The role of stably committed and uncommitted cells in establishing tissues of the somite

Somites are blocks of embryonic mesoderm tissue that give rise to skeletal muscle, cartilage, and other connective tissues. The development of different tissues within the somite is influenced by adjacent structures, in particular, the neural tube and notochord. Results of experiments performed in vivo and in vitro suggest that somites contain populations of cells stably programmed to undergo either skeletal myogenesis or chondrogenesis and a population uncommitted to either pathway. The fate of the uncommitted cells would depend on a transfer of information from the committed cells. Communication between committed and uncommitted cells is regulated by cell and tissue interactions that either activate or inhibit this process.

Human homologs of yeast prp16 and prp17 reveal conservation of the mechanism for catalytic step II of pre-mRNA splicing

Pre-mRNA splicing takes place in two catalytic steps. The second step is poorly understood, especially in mammals. In yeast, the splicing factors, Prps 16, 17, 18 and Slu7 function exclusively in step II. Here we report the isolation of cDNAs encoding human Prps 16 and 17 which are 41 and 36% identical to their yeast counterparts. The Prp16 gene is essential in yeast, and we show that a chimeric yeast-human Prp16 protein rescues a yeast Prp16 knockout strain. Immunodepletion of hPrp16 from splicing extracts specifically blocks step II, and the activity can be fully restored with recombinant hPrp16. Moreover, both hPrps 16 and 17 associate with the spliceosome late in the splicing pathway. Mutations at the 3' splice site that specifically block step II do not affect the association of hPrps 16 and 17 with the spliceosome, indicating that these factors may function at a stage of step II prior to recognition of the 3' splice site. Recently, the human homologs of Prp18 and Slu7 were identified. The observation that humans contain homologs of all four known step II proteins in yeast indicates that the mechanism for catalytic step II is highly conserved.

Effects of reducing dietary saturated fatty acids on plasma lipids and lipoproteins in healthy subjects: the DELTA Study, protocol 1

Few well-controlled diet studies have investigated the effects of reducing dietary saturated fatty acid (SFA) intake in premenopausal and postmenopausal women or in blacks. We conducted a multicenter, randomized, crossover-design trial of the effects of reducing dietary SFA on plasma lipids and lipoproteins in 103 healthy adults 22 to 67 years old. There were 46 men and 57 women, of whom 26 were black, 18 were postmenopausal women, and 16 were men > or =40 years old. All meals and snacks, except Saturday dinner, were prepared and served by the research centers. The study was designed to compare three diets: an average American diet (AAD), a Step 1 diet, and a low-SFA (Low-Sat) diet. Dietary cholesterol was constant. Diet composition was validated and monitored by a central laboratory. Each diet was consumed for 8 weeks, and blood samples were obtained during weeks 5 through 8. The compositions of the three diets were as follows: AAD, 34.3% kcal fat and 15.0% kcal SFA; Step 1, 28.6% kcal fat and 9.0% kcal SFA; and Low-Sat, 25.3% kcal fat and 6.1% kcal SFA. Each diet provided approximately 275 mg cholesterol/d. Compared with AAD, plasma total cholesterol in the whole group fell 5% on Step 1 and 9% on Low-Sat. LDL cholesterol was 7% lower on Step 1 and 11% lower on Low-Sat than on the AAD (both P<.01). Similar responses were seen in each subgroup. HDL cholesterol fell 7% on Step 1 and 11% on Low-Sat (both P<.01). Reductions in HDL cholesterol were seen in all subgroups except blacks and older men. Plasma triglyceride levels increased approximately 9% between AAD and Step 1 but did not increase further from Step 1 to Low-Sat. Changes in triglyceride levels were not significant in most subgroups. Surprisingly, plasma Lp(a) concentrations increased in a stepwise fashion as SFA was reduced. In a well-controlled feeding study, stepwise reductions in SFA resulted in parallel reductions in plasma total and LDL cholesterol levels. Diet effects were remarkably similar in several subgroups of men and women and in blacks. The reductions in total and LDL cholesterol achieved in these different subgroups indicate that diet can have a significant impact on risk for atherosclerotic cardiovascular disease in the total population.

ApoE genotype does not predict lipid response to changes in dietary saturated fatty acids in a heterogeneous normolipidemic population. The DELTA Research Group. Dietary Effects on Lipoproteins and Thrombogenic Activity

Recent studies have suggested that variations in apoE genotypes may influence the magnitude of plasma lipid changes in response to dietary interventions. We examined the ability of apoE genotype to predict plasma lipid response to reductions in percent of calories from total fat (TF) and saturated fat (SF) in a normolipidemic study population (n = 103) heterogeneous with respect to age, gender, race, and menopausal status. Three diets, an average American diet (34.3% TF, 15.0% SF), an AHA Step 1 diet (28.6% TF, 9.0% SF), and a low saturated fat (Low-Sat) diet (25.3% TF, 6.1% SF) were each fed for a period of 8 weeks in a three-way crossover design. Cholesterol was kept constant at 275 mg/d; monounsaturated and polyunsaturated fat were kept constant at approximately 13% and 6.5% of calories, respectively. Fasting lipid levels were measured during each of the final 4 weeks of each diet period. Participants were grouped by apoE genotype: E2 (E2/2, E2/3, E2/4); E3 (E3/3); E4 (E3/4, E4/4). Relative to the average American diet, both the Step 1 and Low-Sat diets significantly reduced total cholesterol, LDL cholesterol, and HDL cholesterol in all three apoE genotype groups. No evidence of a significant diet by genotype interaction, however, could be identified for any of the measured lipid and lipoprotein end points. Additional analysis of the data within individual population subgroup (men and women, blacks and whites) likewise provided no evidence of a significant diet by genotype interaction. Thus, in a heterogeneous, normolipidemic study population, apoE genotype does not predict the magnitude of lipid response to reductions in dietary saturated fat.

Management of palatally impacted canines: the findings of a collaborative study

The impacted palatal canine requires a combination of both surgical and orthodontic management. Two types of approach are commonly used: simple exposure, or exposure with bracketing at the time of surgery. In this study 104 consecutively treated patients with palatally impacted canines were examined at two centres, one at which the ectopic tooth was surgically exposed alone and the other where an orthodontic bracket was bonded to facilitate early traction, and the flap replaced. The aim was to compare the outcome and complication rate for each type of procedure. In 30.7 per cent of all cases exposed and bracketed a second surgical intervention was required, compared with 15.3 per cent in the simple exposure group. Bracketing, though effective, is a more costly and time-consuming procedure, and it is suggested that simple exposure provides an equally efficient and predictable method of managing the palatally impacted canine with obvious clinical and financial benefits. The long-term periodontal status of the teeth which have been exposed in these two ways, however, needs further investigation.