Structure-function analysis of fission yeast Hus1-Rad1-Rad9 checkpoint complex

Hus1, Rad1, and Rad9 are three evolutionarily conserved proteins required for checkpoint control in fission yeast. These proteins are known to form a stable complex in vivo. Recently, computational studies have predicted structural similarity between the individual proteins of Hus1-Rad1-Rad9 complex and the replication processivity factor proliferating cell nuclear antigen (PCNA). This has led to the proposal that the Hus1-Rad1-Rad9 complex may form a PCNA-like ring structure, and could function as a sliding clamp during checkpoint control. In the present study, we have attempted to test the predictions of this model by asking whether the PCNA alignment identifies functionally important residues or explains mutant phenotypes of hus1, rad1, or rad9 alleles. Although some of our results are consistent with the PCNA alignment, others indicate that the Hus1-Rad1-Rad9 complex possesses unique structural and functional features.

Mouse Hus1, a homolog of the Schizosaccharomyces pombe hus1+ cell cycle checkpoint gene

Cell cycle checkpoints are regulatory mechanisms that arrest the cell cycle or initiate programmed cell death when critical events such as DNA replication fail to be completed or when DNA or spindle damage occurs. In fission yeast, cell cycle checkpoint responses to DNA replication blocks and DNA damage require the hus1+ gene. Mammalian homologs of hus1+ were recently identified, and here we report a detailed analysis of mouse Hus1. An approximately 4.2-kb full-length cDNA encoding the 32-kDa mouse Hus1 protein was isolated. The genomic structure and exon-intron boundary sequences of the gene were determined, and mouse Hus1 was found to consist of nine exons. Mouse Hus1 was mapped to the proximal end of chromosome 11 and is therefore a candidate gene for the mouse mutation germ cell deficient, which maps to the same genomic region. Finally, mouse Hus1 was found to be expressed in a variety of adult tissues and at several stages of embryonic development.

Use of gap repair in fission yeast to obtain novel alleles of specific genes

We have adapted a method for making libraries of mutations in any specific gene for use in the fission yeast Schizosaccharomyces pombe . This elegant and simple method consists of PCR amplification of the gene of interest, followed by co-transformation of fission yeast with the PCR fragment and a linearized plasmid vector prepared such that the ends of the vector share DNA sequence with the ends of the PCR fragment. Homologous recombination between the vector and the PCR fragment occurs at a high frequency and results in a collection of yeast transformants, most harboring a mutated allele of the original gene within the vector of choice. This library can then be screened or selected for phenotypes of interest.

Hus1p, a conserved fission yeast checkpoint protein, interacts with Rad1p and is phosphorylated in response to DNA damage

The hus1+ gene is one of six fission yeast genes, termed the checkpoint rad genes, which are essential for both the S-M and DNA damage checkpoints. Classical genetics suggests that these genes are required for activation of the PI-3 kinase-related (PIK-R) protein, Rad3p. Using a dominant negative allele of hus1+, we have demonstrated a genetic interaction between hus1+ and another checkpoint rad gene, rad1+. Hus1p and Rad1p form a stable complex in wild-type fission yeast, and the formation of this complex is dependent on a third checkpoint rad gene, rad9+, suggesting that these three proteins may exist in a discrete complex in the absence of checkpoint activation. Hus1p is phosphorylated in response to DNA damage, and this requires rad3+ and each of the other checkpoint rad genes. Although there is no gene related to hus1+ in the Saccharomyces cerevisiae genome, we have identified closely related mouse and human genes, suggesting that aspects of the checkpoint control mechanism are conserved between fission yeast and higher eukaryotes.

Molecular analysis of hus1+, a fission yeast gene required for S-M and DNA damage checkpoints

The structure of hus1+, a Schizosaccharomyces pombe gene required for S-M and DNA damage checkpoints, has been determined. Expression of hus1+ requires splicing of five exons, including a microexon that is only 13 nucleotides long. hus1+ is predicted to encode a 33 kDa protein with no similarity to sequences in any database, including the entire S. cerevisiae genome. Yeast strains disrupted for the hus1+ gene are viable but checkpoint-defective. Polyclonal antibodies were raised against bacterially expressed Hus1 protein, and used to study Hus1 regulation. Hus1 protein levels are not affected by S-phase arrest, and are not altered by mutations in other checkpoint genes, suggesting that Hus1 is not regulated at the transcriptional or translational levels.

RAP30/74 (transcription factor IIF) is required for promoter escape by RNA polymerase II

RNA polymerase II-associating proteins (RAP30 and RAP74) are subunits of the transcription factor called variously RAP30/74, TFIIF, beta gamma, and FC. This factor is required for accurate transcription by RNA polymerase II, in addition to other basal transcription factors. Using recombinant human RAP30 and RAP74, the functions of these subunits have been tested separately during the initiation and elongation phases of transcription. RAP30 is required to form a Sarkosyl-resistant complex at 0.25% Sarkosyl, so RAP30 is required for initiation. RAP74, however, stimulates transcription when added after Sarkosyl, indicating that RAP74 is dispensable for initiation. The same result is obtained using a pulse-chase protocol in which accurately initiated RNA is labeled during a short pulse, followed by a chase with excess unlabeled nucleoside triphosphates. RAP30 is required in order to label the transcript during the pulse, but RAP74 is not. RAP74 must be added during the chase, however, in order to obtain a short runoff transcript. The following conclusions can be drawn from these experiments: 1) RAP30 is an initiation factor; 2) RAP74 is not required for ATP hydrolysis in initiation, which precedes phosphodiester bond formation; 3) RAP74 is not required for template strand separation; 4) RAP74 is not required to initiate phosphodiester bond formation; and 5) RAP74 is required for very early elongation.

Production of human RAP30 and RAP74 in bacterial cells

RAP30 and RAP74 are subunits of RAP30/74 (TFIIF), a general initiation and elongation factor for transcription by RNA polymerase II. Complementary DNA (cDNA) clones have previously been reported encoding human RAP30 and RAP74. Here we report expression of these cDNAs using a T7 RNA polymerase system in Escherichia coli. Production of human RAP30 was very efficient using the expression vector pET11d. RAP30 accumulated within inclusion bodies and was solubilized using guanidine hydrochloride. After removal of the denaturant, RAP30 was soluble and active in accurate transcription. Approximately 44 mg of highly purified and soluble RAP30 was obtained from a 1-liter culture of cells. Production of RAP74 was more problematic, because a mixture of full length RAP74 and RAP74 fragments was produced in E. coli. Most RAP74 fragments were shortened by deletion of the COOH-terminus of the protein and probably resulted from premature translation termination. RAP74 was most successfully produced using a pET23d construct, in which the RAP74 peptide was fused to a short polyhistidine stretch at its COOH-terminus. Addition of the polyhistidine sequence allowed purification using a Ni2+ affinity resin. Full length RAP74 carrying this polyhistidine extension was purified in a single step by Ni2+ affinity chromatography in 4 M urea; the yield of RAP74 was approximately 3 mg from a 1-liter culture of cells. RAP74 derivatized with a polyhistidine stretch at its NH2-terminus, on the other hand, remained contaminated with RAP74 fragments after Ni2+ affinity chromatography.(ABSTRACT TRUNCATED AT 250 WORDS)

A cDNA encoding RAP74, a general initiation factor for transcription by RNA polymerase II

RAP30/74 (also known as TFIIF, beta gamma and FC is one of several general factors required for initiation by RNA polymerase II. The small RAP30 subunit of RAP30/74 binds directly to polymerase and appears structurally and functionally homologous to bacterial sigma factors in their RNA polymerase-binding region. RAP30/74 or recombinant RAP30 suppresses nonspecific binding of RNA polymerase II to DNA and is required for RNA polymerase II to assemble stably into a preinitiation complex containing promoter DNA and the general factors TFIID, TFIIA and TFIIB; both RAP30 and RAP74 are physical components of the preinitiation complex. A complementary DNA encoding human RAP30 has been isolated, and here we report the isolation of a cDNA encoding human RAP74. RAP30 and RAP74 produced in Escherichia coli can be used in place of natural human RAP30/74 to direct accurate transcription initiation by RNA polymerase II in vitro.