A test for intron function in the yeast actin gene

Specialization of actin isoforms derived from the loss of key interactions with regulatory factors

A paradox of eukaryotic cells is that while some species assemble a complex actin cytoskeleton from a single ortholog, other species utilize a greater diversity of actin isoforms. The physiological consequences of using different actin isoforms, and the molecular mechanisms by which highly conserved actin isoforms are segregated into distinct networks, are poorly known. Here, we sought to understand how a simple biological system, composed of a unique actin and a limited set of actin‐binding proteins, reacts to a switch to heterologous actin expression. Using yeast as a model system and biomimetic assays, we show that such perturbation causes drastic reorganization of the actin cytoskeleton. Our results indicate that defective interaction of a heterologous actin for important regulators of actin assembly limits certain actin assembly pathways while reinforcing others. Expression of two heterologous actin variants, each specialized in assembling a different network, rescues cytoskeletal organization and confers resistance to external perturbation. Hence, while species using a unique actin have homeostatic actin networks, actin assembly pathways in species using several actin isoforms may act more independently.

Excised linear introns regulate growth in yeast

Spliceosomal introns are ubiquitous non-coding RNAs that are typically destined for rapid debranching and degradation. Here we describe 34 excised introns in Saccharomyces cerevisiae that-despite being rapidly degraded in log-phase growth-accumulate as linear RNAs under either saturated-growth conditions or other stresses that cause prolonged inhibition of TORC1, which is a key integrator of growth signalling. Introns that become stabilized remain associated with components of the spliceosome and differ from other spliceosomal introns in having a short distance between their lariat branch point and 3' splice site, which is necessary and sufficient for their stabilization. Deletion of these unusual introns is disadvantageous in saturated conditions and causes aberrantly high growth rates in yeast that are chronically challenged with the TORC1 inhibitor rapamycin. The reintroduction of native or engineered stable introns suppresses this aberrant rapamycin response. Thus, excised introns function within the TOR growth-signalling network of S. cerevisiae and, more generally, excised spliceosomal introns can have biological functions.

Insights into the effects of disease-causing mutations in human actins

Mutations in all six actins in humans have now been shown to cause diseases. However, a number of factors have made it difficult to gain insight into how the changes in actin functions brought about by these pathogenic mutations result in the disease phenotype. These include the presence of multiple actins in the same cell, limited accessibility to pure mutant material, and complexities associated with the structures and their component cells that manifest the diseases. To try to circumvent these difficulties, investigators have turned to the use of model systems. This review describes these various approaches, the initial results obtained using them, and the insight they have provided into allosteric mechanisms that govern actin function. Although results so far have not explained a particular disease phenotype at the molecular level, they have provided valuable insight into actin function at the mechanistic level which can be utilized in the future to delineate the molecular bases of these different actinopathies.

Population genomics of intron splicing in 38 Saccharomyces cerevisiae genome sequences

Introns are a ubiquitous feature of eukaryotic genomes, and the dynamics of intron evolution between species has been extensively studied. However, comparatively few analyses have focused on the evolutionary forces shaping patterns of intron variation within species. To better understand the population genetic characteristics of introns, we performed an extensive population genetics analysis on key intron splice sequences obtained from 38 strains of Saccharomyces cerevisiae. As expected, we found that purifying selection is the dominant force governing intron splice sequence evolution in yeast, formally confirming that intron-containing alleles are a mutational liability. In addition, through extensive coalescent simulations, we obtain quantitative estimates of the strength of purifying selection (2N_es ≈ 19) and use diffusion approximations to provide insights into the evolutionary dynamics and sojourn times of newly arising splice sequence mutations in natural yeast populations. In contrast to previous functional studies, evolutionary analyses comparing the prevalence of introns in essential and nonessential genes suggest that introns in nonribosomal protein genes are functionally important and tend to be actively maintained in natural populations of S. cerevisiae. Finally, we demonstrate that heritable variation in splicing efficiency is common in intron-containing genes with splice sequence polymorphisms. More generally, our study highlights the advantages of population genomics analyses for exploring the forces that have generated extant patterns of genome variation and for illuminating basic biological processes.

Introns regulate RNA and protein abundance in yeast

The purpose of introns in the architecturally simple genome of Saccharomyces cerevisiae is not well understood. To assay the functional relevance of introns, a series of computational analyses and several detailed deletion studies were completed on the intronic genes of S. cerevisiae. Mining existing data from genomewide studies on yeast revealed that intron-containing genes produce more RNA and more protein and are more likely to be haplo-insufficient than nonintronic genes. These observations for all intronic genes held true for distinct subsets of genes including ribosomal, nonribosomal, duplicated, and nonduplicated. Corroborating the result of computational analyses, deletion of introns from three essential genes decreased cellular RNA levels and caused measurable growth defects. These data provide evidence that introns improve transcriptional and translational yield and are required for competitive growth of yeast.

GSH1, which encodes gamma-glutamylcysteine synthetase, is a target gene for yAP-1 transcriptional regulation

Changes in gene dosage of the YAP1 gene, encoding the yAP-1 transcriptional regulatory protein, cause profound alterations in cellular drug and metal resistance. Previous studies on yAP-1 action in yeast cells have used the AP-1 response element (ARE) from simian virus 40 as an artificial site for yAP-1-mediated transcriptional activation. No authentic yeast target sites for control of gene expression by yAP-1 are known. Here we show that the GSH1 gene, encoding gamma-glutamylcysteine synthetase, is transcriptionally responsive to the yAP-1 protein. GSH1 encodes the rate-limiting step in yeast glutathione biosynthesis and contains within its promoter region a DNA element that matches the ARE in 11 of 12 positions. The GSH1 yAP-1 response element (YRE) was recognized by yAP-1 protein in vitro. Northern (RNA) blot analysis showed that GSH1 mRNA levels were responsive to YAP1 gene dosage. A site-directed mutation in the YRE that blocked yAP-1 binding in vitro prevented the mutant GSH1 promoter from responding to elevation in YAP1 gene dosage. A delta gsh1 mutant strain was constructed and unable to grow in the absence of exogenous glutathione. A mutant GSH1 gene lacking the YRE was unable to confer normal cadmium tolerance, although other yAP-1-mediated phenotypes remained normal. Thus, GSH1 is one of several genes that are transcriptionally controlled by yAP-1 and influence drug resistance.

GSH1, which encodes gamma-glutamylcysteine synthetase, is a target gene for yAP-1 transcriptional regulation

Changes in gene dosage of the YAP1 gene, encoding the yAP-1 transcriptional regulatory protein, cause profound alterations in cellular drug and metal resistance. Previous studies on yAP-1 action in yeast cells have used the AP-1 response element (ARE) from simian virus 40 as an artificial site for yAP-1-mediated transcriptional activation. No authentic yeast target sites for control of gene expression by yAP-1 are known. Here we show that the GSH1 gene, encoding gamma-glutamylcysteine synthetase, is transcriptionally responsive to the yAP-1 protein. GSH1 encodes the rate-limiting step in yeast glutathione biosynthesis and contains within its promoter region a DNA element that matches the ARE in 11 of 12 positions. The GSH1 yAP-1 response element (YRE) was recognized by yAP-1 protein in vitro. Northern (RNA) blot analysis showed that GSH1 mRNA levels were responsive to YAP1 gene dosage. A site-directed mutation in the YRE that blocked yAP-1 binding in vitro prevented the mutant GSH1 promoter from responding to elevation in YAP1 gene dosage. A delta gsh1 mutant strain was constructed and unable to grow in the absence of exogenous glutathione. A mutant GSH1 gene lacking the YRE was unable to confer normal cadmium tolerance, although other yAP-1-mediated phenotypes remained normal. Thus, GSH1 is one of several genes that are transcriptionally controlled by yAP-1 and influence drug resistance.

The intron of the yeast actin gene contains the promoter for an antisense RNA

Using Northern blot analysis we have detected an approximately 840 nucleotide-long RNA which is complementary to the 5' leader sequence and the first ten nucleotides of the coding sequence of the yeast actin (ACT1) messenger RNA. We have determined two transcription start sites for this actin antisense RNA (ASR1), both within the ACT1 intron, at about 80 and 90 nucleotides downstream from the 5' splice site. Analysis of a cDNA clone showed that this RNA species overlaps the entire trailer sequence and approximately 20 nucleotides of the coding sequence of the nearby yeast YPT1 gene.

Importance of introns for expression of mouse ribosomal protein gene rpL32

The importance of intronic sequences for expression of the mouse ribosomal protein gene rpL32 was evaluated by transfection experiments with a series of mutant constructs in which one or more of the three rpL32 introns was totally or partially deleted. When transiently transfected into monkey kidney (COS) cells or stably transfected into mouse L cells, a mutant that lacked all three introns was completely inactive. Constructs that contained intron 1, either alone or in combination with another intron, were expressed as efficiently as was the normal intact rpL32 gene. Constructs that lacked intron 1 but contained another spliceable intron, even one from a foreign gene, were expressed at about 10 to 20% of the maximum level. These results indicated that intron 1 contains an element that increases the level of expression by 5- to 10-fold. A comparison of internal deletion mutants localized the element to within the first 27 base pairs of intron 1. Nuclear run-on experiments with stably transfected COS cells demonstrated that this element functions at the transcriptional level. The element was inactive when translocated to a position upstream of the transcriptional start site or to a position within intron 3, which indicated that it does not have the properties of a typical enhancer. From these and other results, we conclude that introns have both a general and a specific role in rpL32 expression. The general role, which can be satisfied by any spliceable intron, is to ensure an efficient yield of RNA transcripts. The specific role is uniquely attributable to intron 1, which contains a transcriptional regulatory element near its 5' end.

Control of gene expression by artificial introns in Saccharomyces cerevisiae

Artificial yeast introns that show cold-sensitive splicing have been constructed. These conditional introns can be inserted into a target gene as an "intron cassette" without disrupting the coding information, allowing expression of the gene to be cold sensitive. Insertion of these intron cassettes rendered the yeast URA3 gene cold sensitive in its expression. The advantage of this intron-mediated control system is that any gene can be converted to a controllable gene by simple insertion of an intron.

Importance of introns for expression of mouse ribosomal protein gene rpL32

The importance of intronic sequences for expression of the mouse ribosomal protein gene rpL32 was evaluated by transfection experiments with a series of mutant constructs in which one or more of the three rpL32 introns was totally or partially deleted. When transiently transfected into monkey kidney (COS) cells or stably transfected into mouse L cells, a mutant that lacked all three introns was completely inactive. Constructs that contained intron 1, either alone or in combination with another intron, were expressed as efficiently as was the normal intact rpL32 gene. Constructs that lacked intron 1 but contained another spliceable intron, even one from a foreign gene, were expressed at about 10 to 20% of the maximum level. These results indicated that intron 1 contains an element that increases the level of expression by 5- to 10-fold. A comparison of internal deletion mutants localized the element to within the first 27 base pairs of intron 1. Nuclear run-on experiments with stably transfected COS cells demonstrated that this element functions at the transcriptional level. The element was inactive when translocated to a position upstream of the transcriptional start site or to a position within intron 3, which indicated that it does not have the properties of a typical enhancer. From these and other results, we conclude that introns have both a general and a specific role in rpL32 expression. The general role, which can be satisfied by any spliceable intron, is to ensure an efficient yield of RNA transcripts. The specific role is uniquely attributable to intron 1, which contains a transcriptional regulatory element near its 5' end.

Thymidylate synthase gene expression is stimulated by some (but not all) introns

We previously described the construction of an intronless mouse thymidylate synthase (TS) minigene that has the normal 5' and 3' flanking regions of the gene linked to full length TS cDNA. Transfection of the minigene into ts- hamster V79 cells led to low level expression of normal mouse TS mRNA and protein. In the present study we analyzed the effect of introns on the expression of the TS minigene in transient transfection assays. Inclusion of introns 5 and 6 at their normal locations in the coding region led to an 8-9-fold stimulation of the level of TS and TS mRNA. Almost all of introns 5 and 6 could be deleted without diminishing the stimulatory effect. Inclusion of intron 3 also stimulated the expression of the minigene, although to a lesser extent than introns 5 and 6. However, inclusion of intron 4 had no stimulatory effect. Analysis of minigenes that contained various combinations of introns revealed that the stimulatory effects of the introns were not additive.

Identification of an orthologous mammalian cytokeratin gene. High degree of intron sequence conservation during evolution of human cytokeratin 10

Among the human acidic (type I) cytokeratins, components 10 and 11 are especially interesting, as they are under various kinds of expression control. They are synthesized in the suprabasal cell layers of certain stratified epithelia, notably epidermis, in an endogenous differentiation program; they are expressed in certain epithelial tumours but not in others; they can appear de novo in certain pathological situations such as in squamous metaplasias; and their expression in vivo and in vitro is under positive influence of extracellular calcium concentrations and is reduced in the presence of vitamin A or other retinoids. To provide a basis for studies of the various regulatory elements, we have isolated the human gene encoding cytokeratin 10, using a cDNA probe derived from the corresponding bovine gene, and have sequenced the mRNA coding region as well as adjacent regions approximately 1500 bases 5' upstream and 1000 bases 3' downstream. The eight exons encode a polypeptide 59,535 Mr, i.e. somewhat larger than the corresponding bovine and murine proteins. The deduced amino acid sequences display a high degree of homology, which is not restricted to the exons and the 5' and 3' adjacent regions but, surprisingly, is also evident in the seven introns, some of which contain extended sequence elements with 70% identical nucleotides and more, i.e. similar to the homology in the adjacent exons. This exceptionally high level of conservation of intron sequences is discussed in relation to the recently accumulating evidence of the occurrence of intron sequences important in the regulation of the expression of members of other multigene families during development.

Testing for intron function in the essential Saccharomyces cerevisiae tRNA(SerUCG) gene

The gene sup61+, which codes for the essential Saccharomyces cerevisiae tRNA(SerUCG), is the only single-copy tRNA gene in this organism know to contain an intron. To assess the role of this intron in tRNA gene expression, an intron-deleted sup61+ gene was constructed in vitro and introduced into the yeast genome. Isogenic intron- and intron+ strains were found to be indistinguishable by criteria that include growth rates, ability to undergo meiosis, levels of mature tRNA(SerUCG) transcribed in vivo, and the suppressor efficiency of amber- and ochre-specific alleles of this gene.

The intron requirement for immunoglobulin gene expression is dependent upon the promoter

Transfection assays were used to assess the need for an intron in order to obtain expression of cytoplasmic immunoglobulin mu mRNA. An intron is required when transcription is driven by an immunoglobulin promoter/enhancer combination, although this requirement is not specific for a particular intron. However, this need for an intron is dependent upon the promoter used. Whilst an intron is required in the case of immunoglobulin or beta-globin promoters, it is not in the case of cytomegalovirus or heat-shock promoters. The data point to a connection between the promoter and RNA processing or export.

Introns are inconsequential to efficient formation of cellular thymidine kinase mRNA in mouse L cells

TK mRNA levels were determined in mouse L cells transformed with intron deletion mutations of the chicken TK gene. Whether normalized per cell, per integrated gene, or per internal control signal, intron deletion did not diminish the efficiency of TK mRNA formation in transformed L cells. The results demonstrated that introns are not required for efficient biogenesis of cellular mRNA in transformed mouse L cells.

Introns increase transcriptional efficiency in transgenic mice

Experiments were designed to test the effect of introns on gene expression in transgenic mice. Four different pairs of gene constructs, which were identical except that one member of each pair lacked all introns, were compared for expression of mRNA after introduction into the murine germ line by microinjection of fertilized eggs. The expression of two chimeric genes, made by fusing either the mouse metallothionein I or the rat elastase 1 promoter/enhancer to the rat growth hormone gene, was assayed in fetal liver or pancreas, respectively, while two natural genes, an oligonucleotide-marked mouse metallothionein I gene and the human beta-globin gene, were assayed in fetal liver. In each case there was, on average, 10- to 100-fold more mRNA produced from the intron-containing construct. Moreover, mRNA levels were proportional to the relative rates of transcription that were measured in isolated nuclei. However, when the expression of the two mouse metallothionein I gene-based constructs was tested after transfection into cultured cells, little difference was observed. These observations suggest that introns play a role in facilitating transcription of microinjected genes and that this effect may be manifest only on genes exposed to developmental influences.

Interpreting the behavior of enzymes: purpose or pedigree?

To interpret the growing body of data describing the structural, physical, and chemical behaviors of biological macromolecules, some understanding must be developed to relate these behaviors to the evolutionary processes that created them. Behaviors that are the products of natural selection reflect biological function and offer clues to the underlying chemical principles. Nonselected behaviors reflect historical accident and random drift. This review considers experimental data relevant to distinguishing between nonfunctional and functional behaviors in biological macromolecules. In the first segment, tools are developed for building functional and historical models to explain macromolecular behavior. These tools are then used with recent experimental data to develop a general outline of the relationship between structure, behavior, and natural selection in proteins and nucleic acids. In segments published elsewhere, specific functional and historical models for three properties of enzymes--kinetics, stereospecificity, and specificity for cofactor structures--are examined. Functional models appear most suitable for explaining the kinetic behavior of proteins. A mixture of functional and historical models appears necessary to understand the stereospecificity of enzyme reactions. Specificity for cofactor structures appears best understood in light of purely historical models based on a hypothesis of an early form of life exclusively using RNA catalysis.

Introns are inconsequential to efficient formation of cellular thymidine kinase mRNA in mouse L cells

TK mRNA levels were determined in mouse L cells transformed with intron deletion mutations of the chicken TK gene. Whether normalized per cell, per integrated gene, or per internal control signal, intron deletion did not diminish the efficiency of TK mRNA formation in transformed L cells. The results demonstrated that introns are not required for efficient biogenesis of cellular mRNA in transformed mouse L cells.

The Drosophila sgs3 gene: an in-vivo test of intron function

An intronless Drosophila melanogaster sgs3 "glue" gene from the Formosa strain was constructed and inserted by P element transformation into a strain carrying an sgs3 variant that produces a larger mRNA and protein. By comparing both the RNAs and proteins produced by the two alleles we show that the intron has no detectable effect on sgs3 expression.

Effect of intron mutations on processing and function of Saccharomyces cerevisiae SUP53 tRNA in vitro and in vivo

The Saccharomyces cerevisiae leucine-inserting amber suppressor tRNA gene SUP53 (a tRNALeu3 allele) was used to investigate the relationship between precursor tRNA structure and mature tRNA function. This gene encodes a pre-tRNA which contains a 32-base intron. The mature tRNASUP53 contains a 5-methylcytosine modification of the anticodon wobble base. Mutations were made in the SUP53 intron. These mutant genes were transcribed in an S. cerevisiae nuclear extract preparation. In this extract, primary tRNA gene transcripts are end-processed and base modified after addition of cofactors. The base modifications made in vitro were examined, and the mutant pre-tRNAs were analyzed for their ability to serve as substrates for partially purified S. cerevisiae tRNA endonuclease and ligase. Finally, the suppressor function of these mutant tRNA genes was assayed after their integration into the S. cerevisiae genome. Mutant analysis showed that the totally intact precursor tRNA, rather than any specific sequence or structure of the intron, was necessary for efficient nonsense suppression by tRNASUP53. Less efficient suppressor activity correlated with the absence of the 5-methylcytosine modification. Most of the intron-altered precursor tRNAs were successfully spliced in vitro, indicating that modifications are not critical for recognition by the tRNA endonuclease and ligase.

Introns as relict retrotransposons: implications for the evolutionary origin of eukaryotic mRNA splicing mechanisms

A model is presented for the evolutionary origin of intron sequences within eukaryotic protein-coding genes. We propose that introns are the vestiges of transposable elements and, specifically, that they represent a novel class of retrovirus-like transposons. The attraction of the retrotransposon model is that it gives the RNA splicing mechanism a central role in the evolution of introns. There is a growing body of evidence to suggest that several aspects of splicing are intron-encoded. Consequently, it is reasonable to look for evolutionary explanations of the splicing mechanism in the context of the evolution of the intron sequences themselves. According to this model the ancestral intron genomes were replicated into RNA copies simply because of their insertion within transcriptionally active regions of the host genome. Splicing was necessary not only to minimize their negative effects on host gene expression, but also, and perhaps more importantly, to generate new copies of the intron genome free of flanking exon sequences. These spliced intron copies were then available for reverse transcription and reinsertion elsewhere in the genome. Thus, splicing can be seen as an essential step in the intron replication cycle. Most modern introns have probably lost the majority of their original genetic content and may be considered as degenerate evolutionary relicts. An exception to this degeneracy is the set of splicing signals which must be retained because of its continued importance to host cell survival.(ABSTRACT TRUNCATED AT 250 WORDS)

Effect of intron mutations on processing and function of Saccharomyces cerevisiae SUP53 tRNA in vitro and in vivo

The Saccharomyces cerevisiae leucine-inserting amber suppressor tRNA gene SUP53 (a tRNALeu3 allele) was used to investigate the relationship between precursor tRNA structure and mature tRNA function. This gene encodes a pre-tRNA which contains a 32-base intron. The mature tRNASUP53 contains a 5-methylcytosine modification of the anticodon wobble base. Mutations were made in the SUP53 intron. These mutant genes were transcribed in an S. cerevisiae nuclear extract preparation. In this extract, primary tRNA gene transcripts are end-processed and base modified after addition of cofactors. The base modifications made in vitro were examined, and the mutant pre-tRNAs were analyzed for their ability to serve as substrates for partially purified S. cerevisiae tRNA endonuclease and ligase. Finally, the suppressor function of these mutant tRNA genes was assayed after their integration into the S. cerevisiae genome. Mutant analysis showed that the totally intact precursor tRNA, rather than any specific sequence or structure of the intron, was necessary for efficient nonsense suppression by tRNASUP53. Less efficient suppressor activity correlated with the absence of the 5-methylcytosine modification. Most of the intron-altered precursor tRNAs were successfully spliced in vitro, indicating that modifications are not critical for recognition by the tRNA endonuclease and ligase.

A point mutation in the conserved hexanucleotide at a yeast 5' splice junction uncouples recognition, cleavage, and ligation

We have constructed an actin-HIS4 gene fusion, such that expression of HIS4 requires proper splicing of the actin intron. Using this chimeric gene in an in vivo screen for splicing mutations, we have isolated a G to A transition in the fifth position of the yeast 5' consensus sequence/GTAPyGT. This mutation still allows the junction to be recognized by the splicing machinery, albeit inefficiently. Surprisingly, the fidelity of the 5' endonucleolytic cleavage is also reduced. This results in an incorrect cleavage 6 nucleotides 5' of the 5' junction, at the dinucleotide/AT. Cleavage at this abnormal site does not lead to the production of mature mRNA, although this species appears to be in a lariat structure. The behavior of this mutant argues that recognition of the 5' junction and subsequent cleavage are separable events and, furthermore, that requirements for 3' endonucleolytic cleavage may be more complex than previously imagined.