Drosophila RNA polymerase II elongation factor DmS-II has homology to mouse S-II and sequence similarity to yeast PPR2

Promoter analysis of the Drosophila melanogaster gene encoding transcription elongation factor TFIIS

The promoter region of the Drosophila melanogaster TFIIS gene was characterized by transient expression assay. Serial deletion analysis of the promoter region showed that the promoter region between -112 and +113 is required for the efficient expression of the D. melanogaster TFIIS gene. The results also suggest that the DNA fragments between -112 and -54 and between +94 and +113 contain the vital elements for the expression. The importance of these fragments was further substantiated by the findings that the sequences in these fragments of the D. melanogaster TFIIS gene are conserved in the 5'-flanking regions of the Drosophila virilis TFIIS gene. The comparison of the nucleotide sequences in the 5'-flanking region of the D. melanogaster and D. virilis TFIIS genes revealed that the three regions, -85--59, +76-+126, and the vicinity of the transcription initiation site of the D. melanogaster TFIIS gene, are conserved. It is very interesting that the long downstream DNA between +76 and +126 is highly conserved with 90% identities between the two species. The downstream promoter region between +94 and +113 of the D. melanogaster TFIIS gene was further analyzed by transient expression and band mobility shift assays. The results obtained suggest that the region between +94 and +113 is probably recognized by nuclear factors and that the sequence (+98)AGTAAACAACAT(+109) seems to make a great contribution to promoter activity of the D. melanogaster TFIIS gene.

Participation of transcription elongation factor XSII-K1 in mesoderm-derived tissue development in Xenopus laevis

We isolated a cDNA clone for a novel member of the S-II family of transcription elongation factors from Xenopus laevis. This S-II, named XSII-K1, is assumed to be the Xenopus homologue of mouse SII-K1 that we reported previously (Taira, Y., Kubo, T., and Natori, S. (1998) Genes Cells 3, 289-296). Expression of the XSII-K1 gene was found to be restricted to mesoderm-derived tissues such as liver, kidney, and skeletal muscle. Contrary to the general S-II gene, expression of the XSII-K1 gene was not detected in embryos at stages earlier than 11. The animal cap assay revealed that activin A, but not basic fibroblast growth factor, induced expression of the XSII-K1 gene and that it participated in the expression of mesoderm-specific genes such as Xbra and Xalpha-actin. This is the first demonstration that the regulation at the level of transcription elongation is included in the development of mesoderm-derived tissues.

Ab initio gene finding in Drosophila genomic DNA

Ab initio gene identification in the genomic sequence of Drosophila melanogaster was obtained using (human gene predictor) and Fgenesh programs that have organism-specific parameters for human, Drosophila, plants, yeast, and nematode. We did not use information about cDNA/EST in most predictions to model a real situation for finding new genes because information about complete cDNA is often absent or based on very small partial fragments. We investigated the accuracy of gene prediction on different levels and designed several schemes to predict an unambiguous set of genes (annotation CGG1), a set of reliable exons (annotation CGG2), and the most complete set of exons (annotation CGG3). For 49 genes, protein products of which have clear homologs in protein databases, predictions were recomputed by Fgenesh+ program. The first annotation serves as the optimal computational description of new sequence to be presented in a database. Reliable exons from the second annotation serve as good candidates for selecting the PCR primers for experimental work for gene structure verification. Our results shows that we can identify approximately 90% of coding nucleotides with 20% false positives. At the exon level we accurately predicted 65% of exons and 89% including overlapping exons with 49% false positives. Optimizing accuracy of prediction, we designed a gene identification scheme using Fgenesh, which provided sensitivity (Sn) = 98% and specificity (Sp) = 86% at the base level, Sn = 81% (97% including overlapping exons) and Sp = 58% at the exon level and Sn = 72% and Sp = 39% at the gene level (estimating sensitivity on std1 set and specificity on std3 set). In general, these results showed that computational gene prediction can be a reliable tool for annotating new genomic sequences, giving accurate information on 90% of coding sequences with 14% false positives. However, exact gene prediction (especially at the gene level) needs additional improvement using gene prediction algorithms. The program was also tested for predicting genes of human Chromosome 22 (the last variant of Fgenesh can analyze the whole chromosome sequence). This analysis has demonstrated that the 88% of manually annotated exons in Chromosome 22 were among the ab initio predicted exons. The suite of gene identification programs is available through the WWW server of Computational Genomics Group at http://genomic.sanger.ac.uk/gf. html.

Gene structure and chromosome mapping of mouse transcription elongation factor S-II (Tcea1)

We report the organization and chromosome localization of the mouse transcription elongation factor S-II gene (Tcea1). This gene was found to be a single copy gene consisting of 10 exons spanning approximately 30kb. Its organization was the same as those of the mouse testis-specific S-II gene (Tcea2) and Xenopus general S-II gene (xTFIIS.oA), but different from that of the human S-II gene family. We also identified a processed pseudogene (Tcea1-ps1) with a sequence highly homologous to those of S-II cDNAs but containing a translation termination codon within its open reading frame. Linkage analysis showed that Tcea1 and Tcea1-ps1 are mapped on mouse chromosomes 1 and 15, respectively. Relationships between Tcea1 and S-II cDNAs isolated so far are discussed.

An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster: the Adh region

A contiguous sequence of nearly 3 Mb from the genome of Drosophila melanogaster has been sequenced from a series of overlapping P1 and BAC clones. This region covers 69 chromosome polytene bands on chromosome arm 2L, including the genetically well-characterized "Adh region." A computational analysis of the sequence predicts 218 protein-coding genes, 11 tRNAs, and 17 transposable element sequences. At least 38 of the protein-coding genes are arranged in clusters of from 2 to 6 closely related genes, suggesting extensive tandem duplication. The gene density is one protein-coding gene every 13 kb; the transposable element density is one element every 171 kb. Of 73 genes in this region identified by genetic analysis, 49 have been located on the sequence; P-element insertions have been mapped to 43 genes. Ninety-five (44%) of the known and predicted genes match a Drosophila EST, and 144 (66%) have clear similarities to proteins in other organisms. Genes known to have mutant phenotypes are more likely to be represented in cDNA libraries, and far more likely to have products similar to proteins of other organisms, than are genes with no known mutant phenotype. Over 650 chromosome aberration breakpoints map to this chromosome region, and their nonrandom distribution on the genetic map reflects variation in gene spacing on the DNA. This is the first large-scale analysis of the genome of D. melanogaster at the sequence level. In addition to the direct results obtained, this analysis has allowed us to develop and test methods that will be needed to interpret the complete sequence of the genome of this species. Before beginning a Hunt, it is wise to ask someone what you are looking for before you begin looking for it. Milne 1926

Molecular cloning of cDNA and tissue-specific expression of the gene for SII-K1, a novel transcription elongation factor SII

BACKGROUND

Transcription elongation factor SII has been shown to promote read-through by RNA polymerase II of pausing sites within various eukaryotic genes in vitro by inducing cleavage of the 3'-end of the nascent transcript in the ternary elongation complex. Recently, we showed that various mouse tissues contain multiple SII-related proteins. Of these, 'general SII' was ubiquitously expressed, whereas the others were expressed in a tissue-specific manner. We have identified testis-specific SII (SII-T1) and shown that it was expressed exclusively in spermatocytes.

RESULTS

A new SII cDNA clone (pSII-K1) was isolated from mouse kidney. This clone contained an open reading frame which encoded a protein consisting of 347 amino acid residues (SII-K1). A comparison of the amino acid sequences of SII-K1 with those of general SII and SII-T1 revealed that their amino- and carboxy-terminal regions were very similar, but that the sequence of the 95 internal residues (87/181) was unique to each. The recombinant SII-K1 produced in Escherichia coli stimulated RNA polymerase II as did general S-II. The gene for SII-K1 was found to be expressed strongly in the heart, liver, skeletal muscle and kidney, but not in other tissues examined. Contrary to the expression of the general SII gene, the SII-K1 gene was expressed only in 15- and 17-day-old embryos during mouse embryonic development.

CONCLUSIONS

We identified a novel member of SII family transcription elongation factor named SII-K1. This factor was expressed exclusively in the heart, liver, kidney and skeletal muscle. During mouse embryonic development, no significant expression of the SII-K1 gene was detected before the formation of these tissues.

The inducible elongin A elongation activation domain: structure, function and interaction with the elongin BC complex

The elongin (SIII) complex strongly stimulates the rate of elongation by RNA polymerase II by suppressing transient pausing by polymerase at many sites along the DNA. Elongin (SIII) is composed of a transcriptionally active A subunit and two small regulatory B and C subunits, which bind stably to each other to form a binary complex that interacts with elongin A and strongly induces its transcriptional activity. The elongin (SIII) complex is a potential target for negative regulation by the von Hippel-Lindau (VHL) tumor suppressor protein, which is capable of binding stably to the elongin BC complex and preventing it from activating elongin A. Here, we identify an elongin A domain sufficient for activation of elongation and demonstrate that it is a novel type of inducible activator that targets the RNA polymerase II elongation complex and is evolutionarily conserved in species as distantly related as Caenorhabditis elegans and man. In addition, we demonstrate that both the elongin A elongation activation domain and the VHL tumor suppressor protein interact with the elongin BC complex through a conserved elongin BC binding site motif that is essential for induction of elongin A activity by elongin BC and for tumor suppression by the VHL protein.

Genes encoding isoforms of transcription elongation factor TFIIS in Xenopus and the use of multiple unusual RNA processing signals

We have identified cDNAs encoding three related forms of transcription elongation factor TFIIS (S-II) in Xenopus laevis ovary. Comparison of Xenopus and mammalian sequences identifies likely diagnostic amino acids that distinguish classes of vertebrate TFIIS. The diversity of TFIIS polypeptides in Xenopus is due partly to the presence of two diverged genes in this tetraploid genome. We isolated genomic clones containing one of the genes, xTFIIS.oA, and, unlike a previously described vertebrate TFIIS gene, found that it contains introns. Alternative splicing at a CAG/CAG motif containing the 3' splice site of intron 4 produces the third form of xTFIIS, which differs from one of the others simply in lacking Ser109. Intron 6 of xTFIIS.oA contains splice and branch site consensus sequences conforming to those of the minor class of AT-AC introns and this was confirmed for the homeologous xTFIIS.oB gene by genomic PCR. Other unusual but functional variants of RNA processing signals were found in xTFIIS genes at the 5' splice site of intron 8 and the polyadenylation hexanucleotides. Utilization of multiple unusual processing signals may make the generation of mature xTFIIS.o mRNAs inefficient and the possible regulatory consequences of this are discussed.

Spermatocyte-specific expression of the gene for mouse testis-specific transcription elongation factor S-II

Previously, we characterized a rat cDNA for testis-specific transcription elongation factor S-II (SII-T1) (Q. Xu et al., J. Biol. Chem. 269, 3100-3103 (1994)). Here, we isolated a 335-bp fragment of the cDNA for mouse SII-T1, and used it to examine the expression of the SII-T1 gene in the testis by in situ hybridization. The results indicated that the SII-T1 gene is expressed exclusively in spermatocytes, showing no appreciable expression in spermatogonia, spermatids, or Leydig cells. RT-PCR experiments using testis RNA from W/Wv mutant mice also suggested that SII-T1 is a specific transcription elongation factor essential for spermatogenesis.

Isolation and characterization of the Schizosaccharomyces pombe gene encoding transcript elongation factor TFIIS

A gene designated tfs1 has been isolated from Schizosaccharomyces pombe based on its similarity to genes encoding transcription elongation factor TFIIS. The nucleotide sequence of the tfs1 gene predicts a polypeptide with similarity to mammalian. Drosophila and Saccharomyces cerevisiae TFIIS. A haploid Sz. pombe strain with tfs1 deleted from the genome is viable. Thus, tfs1 is not essential for viability. However, deletion of tfs1 results in slow growth and increased sensitivity to the drug 6-azauracil, a phenotype similar to that of a S. cerevisiae strain deleted for the gene encoding TFIIS. The DNA sequence of tfs1 has been deposited in GenBank under Accession Number U20526.

Isolation and characterization of a cDNA encoding a new type of human transcription elongation factor S-II

We report the isolation of a cDNA encoding a new type of transcription factor S-II, termed h-SII-T1, from a human library. The mRNA corresponding to the clone is highly expressed in testis and ovary. Comparison of the deduced amino acid (aa) sequence with those of other S-II molecules shows that (i) the C-terminal zinc finger (Zf) domain is highly conserved, and (ii) the central segment is most similar to that of the rat testis-specific S-II. Further analyses of the hS-II-T1 aa sequence indicate that its N-terminal sequence exhibits similarity to eubacterial sigma 54. The significance of tissue-specific S-II molecules for the regulation of transcription elongation is discussed.

Isolation and characterization of the gene encoding the Drosophila melanogaster transcriptional elongation factor, TFIIS

We have characterized a genomic clone encoding the Drosophila melanogaster transcriptional elongation factor, TFIIS. The coding region of the TFIIS gene is interrupted by a short intron. The potential promoter region, deduced from the determination of the transcription start point (tsp), lacks distinct TATAAA or CCAAT box consensus sequences. Southern analysis and the in situ hybridization to chromosomes suggests that it is single-copy gene which is localized to the 35B region on the left arm of the second chromosome.

Identification of a decay in transcription potential that results in elongation factor dependence of RNA polymerase II

The rate of RNA elongation by RNA polymerase II (pol II) is affected by DNA sequences called intrinsic arrest sites. Efficient transcription through these sites requires elongation factor SII. In addition to the sequence-specific features of the DNA, we show that the acquisition of SII-dependence is a function of its "dwell-time" at an arrest site. This temperature-dependent decay in elongation potential appears irreversible, implying that factor-dependent and factor-independent elongation complexes are not mutually interconvertible at this position. TFIIF and NH4Cl are known to increase the elongation rate of pol II. Both agents preempt arrest, consistent with the idea that elongation dwell time influences the process. TFIIF and SII act upon different steps in a complementary way to prevent or resolve arrest, respectively. They are probably instrumental in facilitating the efficient transcription of large eukaryotic genes in vivo.

Structure-function relationship of yeast S-II in terms of stimulation of RNA polymerase II, arrest relief, and suppression of 6-azauracil sensitivity

The yeast S-II null mutant is viable, but the mutation induces sensitivity to 6-azauracil. To examine whether the region needed for stimulation of RNA polymerase II and that for suppression of 6-azauracil sensitivity in the S-II molecule could be separated, we constructed various deletion mutants of S-II and expressed them in the null mutant using the GAL1 promoter to see if the mutant proteins suppressed 6-azauracil sensitivity. We also expressed these constructs in Escherichia coli, purified the mutant proteins to homogeneity, and examined if they stimulated RNA polymerase II. We found that a mutant protein lacking the first 147 amino acid residues suppressed 6-azauracil sensitivity but that removal of 2 additional residues completely abolished the suppression. A mutant protein lacking the first 141 residues had activity to stimulate RNA polymerase II, whereas removal of 10 additional residues completely abolished this activity. We also examined arrest-relief activity of these mutant proteins and found that there is a good correlation between RNA polymerase II-stimulating activity and arrest-relief activity. Therefore, at least the last 168 residues of S-II are sufficient for expressing these three activities.

Self-splicing group I introns in eukaryotic viruses

We report the occurrence of self-splicing group I introns in viruses that infect the eukaryotic green alga Chlorella. The introns contained all the conserved features of primary sequence and secondary structure previously described for the group IB introns. The Chlorella viral introns (approximately 400 nt) self-spliced in vitro, yielding the typical group I intron splicing intermediates and products. Contrasting to eukaryotic nuclear group I introns, all of which are located in the rRNA genes, these introns were inserted in genes encoding proteins. In one case, the exons encoded a protein showing significant homology to the eukaryotic transcription factor SII (TFIIS), which may be important for viral gene expression. In another case, the gene for the open reading frame (ORF) of a 14.2 kDa polypeptide with unknown functions contained the intron. Scattered distribution of these introns among the viral species and their structural similarity to the group I introns of algae and protists indicated horizontal intron transmission. These eukaryotic viral introns offer an opportunity to understand how group I introns reach organisms of different phylogenetic kingdoms.

The sequence, and its evolutionary implications, of a Thermococcus celer protein associated with transcription

Through random search, a gene from Thermococcus celer has been identified and sequenced that appears to encode a transcription-associated protein (110 amino acid residues). The sequence has clear homology to approximately the last half of an open reading frame reported previously for Sulfolobus acidocaldarius [Langer, D. & Zillig, W. (1993) Nucleic Acids Res. 21, 2251]. The protein translations of these two archaeal genes in turn are homologs of a small subunit found in eukaryotic RNA polymerase I (A12.2) and the counterpart of this from RNA polymerase II (B12.6). Homology is also seen with the eukaryotic transcription factor TFIIS, but it involves only the terminal 45 amino acids of the archaeal proteins. Evolutionary implications of these homologies are discussed.

RNA cleavage and chain elongation by Escherichia coli DNA-dependent RNA polymerase in a binary enzyme.RNA complex

In the absence of DNA, Escherichia coli RNA polymerase (EC 2.7.7.6) can bind RNA to form an equimolar binary complex with the concomitant release of the sigma factor. We show now that E. coli RNA polymerase binds at a region near the 3' terminus of the RNA and that an RNA in such RNA.RNA polymerase complexes undergoes reactions previously thought to be unique to nascent RNA in ternary complexes with DNA. These include GreA/GreB-dependent cleavage of the RNA and elongation by 3'-terminal addition of NMP from NTP. Both of these reactions are inhibited by rifampicin. Hence, by several criteria, the RNA in binary complexes is bound to the polymerase in a manner quite similar to that in ternary complexes. These findings can be explained by a model for the RNA polymerase ternary complex in which the RNA is bound at the 3' terminus through two protein binding sites located up to 10 nt apart. In this model, the stability of RNA binding to the polymerase in the ternary complex is due primarily to its interaction with the protein.

Characterization of the gene encoding the human transcriptional elongation factor TFIIS

The transcriptional elongation factor TFIIS causes stimulation of RNA polymerase II elongation and readthrough of some of the elongation blocks. We present cloning and sequence characterization of the human TFIIS gene and a pseudogene. The intron-less organization of both of these genes indicates that previously identified cDNAs which suggested the presence of an intron were the products of cloning artifacts. The gene is organized in an uninterrupted ORF which codes for 301 amino acids, whereas the pseudogene lacks an ORF able to code for a full-length protein. The potential promoter for the gene has two putative GC-box-type consensus sequences, two CCAAT-box consensus sequences, and is bounded by a human Alu sequence. Two potential transcriptional termination signal sequences downstream from the consensus polyadenylation signal are proposed.

A human gene encoding a putative basic helix-loop-helix phosphoprotein whose mRNA increases rapidly in cycloheximide-treated blood mononuclear cells

G0S8 is a member of a set of putative G0/G1 switch regulatory genes (G0S genes) selected by screening cDNA libraries prepared from blood mononuclear cells cultured for 2 hr with lectin and cycloheximide. Comparison of a full-length cDNA sequence with the corresponding genomic sequence reveals an open reading frame of 211 amino acids, distributed across 5 exons. The 24-kD protein has a basic domain preceding a potential helix-loop-helix domain which contains a QTK motif found about 60 amino acids from the carboxyl terminus in the loop region of several helix-loop-helix proteins. There are potential phosphorylation sites for protein kinase C, creatine kinase II, and protein tyrosine kinases and regions of sequence similarity to helix-loop-helix proteins, tyrosine phosphatases, and RNA and DNA polymerases. The genomic sequence contains a CpG island, suggesting expression in the germ line. Potential binding sites for transcription factors are present in the 5' flank and introns; these include Zif268/NGFI-A/EGR1/G0S30, NGFI-B, Ap1, and factors that react with retroviral long terminal repeats (LTRs). There are several potential interferon response elements and a serum response element in the 3' flank overlapping a region of similarity to a cytomegalovirus immediate-early gene enhancer. Many of these motifs are found in immediate-early G0/G1 switch genes; however, we were unable to demonstrate an increase in G0S8 mRNA in response to lectin alone. Sequence similarities are noted between G0S8 and a variety of genes involved in the immune system, in the regulation of retroviruses, and in the cell cycle.

Analysis of the nucleotide sequence of a 43 kbp segment of the genome of variola virus India-1967 strain

Sequencing and computer analysis of the nucleotide sequence of the variola virus strain India-1967 (VAR) genome segment (43069 bp) from the region of HindIII C, E, R, Q, K, H DNA fragments has been carried out. Forty-three potential open reading frames (ORFs) have been identified, and the polypeptides encoded by them have been compared with the analogous proteins of vaccinia virus strain Copenhagen (COP). ORF E7R of VAR is much shorter than the COP analog. The other polypeptides coded by the potential ORFs of VAR are highly conserved in comparison with COP. Possible functions of the predicted viral polypeptides are discussed.

Sequence of a 7.8 kb segment on the left arm of yeast chromosome XI reveals four open reading frames, including the CAP1 gene, an intron-containing gene and a gene encoding a homolog to the mammalian UOG-1 gene

We report here the DNA sequence of a segment of chromosome XI of Saccharomyces cerevisiae extending over 7.8 kb. The segment contains four long open reading frames, YKL150, YKL153, YKL155 and YKL156, YKL155 corresponds to the CAP1 gene. YKL153 contains an intron and shows an extremely biased codon usage suggestive of a highly expressed protein. YKL156 is a homolog to UOG-1, an open reading frame associated with the cDNA clone of the mammalian growth/differentiation factor 1. YKL150 reveals common motifs to both the RNA polymerase II elongation factor of Drosophila melanogaster and to the yeast PPR2 gene product.

Transcription termination

Chromosomes are organized into units of expression that are bounded by sites where transcription of DNA sequences into RNA is initiated and terminated. To allow for efficient stepwise assembly of complete transcripts, the transcribing enzyme (RNA polymerase) makes a stable complex with the DNA template until it reaches the terminator. Three general mechanisms of transcription termination have been recognized: one is by a spontaneous dissociation of the RNA at a sequence segment where RNA polymerase does not maintain its usual stable interaction with the nascent chain; another involves the action of a protein (rho factor in bacteria) on the nascent RNA to mediate its dissociation; and a third involves an action triggered by a protein that binds to the DNA at a sequence that is just downstream of the termination stop point. Transcription termination is important in the regulation of gene expression both by modulating the relative levels of various genes within a single unit of expression and by controlling continuation of transcription in response to a metabolic or regulatory signal.

Genetic interaction between transcription elongation factor TFIIS and RNA polymerase II

Little is known about the regions of RNA polymerase II (RNAPII) that are involved in the process of transcript elongation and interaction with elongation factors. One elongation factor, TFIIS, stimulates transcript elongation by binding to RNAPII and facilitating its passage through intrinsic pausing sites in vitro. In Saccharomyces cerevisiae, TFIIS is encoded by the PPR2 gene. Deletion of PPR2 from the yeast genome is not lethal but renders cells sensitive to the uracil analog 6-azauracil (6AU). Here, we show that mutations conferring 6AU sensitivity can also be isolated in the gene encoding the largest subunit of S. cerevisiae RNAPII (RPO21). A screen for mutations in RPO21 that confer 6AU sensitivity identified seven mutations that had been generated by either linker-insertion or random chemical mutagenesis. All seven mutational alterations are clustered within one region of the largest subunit that is conserved among eukaryotic RNAPII. The finding that six of the seven rpo21 mutants failed to grow at elevated temperature underscores the importance of this region for the functional and/or structural integrity of RNAPII. We found that the 6AU sensitivity of the rpo21 mutants can be suppressed by increasing the dosage of the wild-type PPR2 gene, presumably as a result of overexpression of TFIIS. These results are consistent with the proposal that in the rpo21 mutants, the formation of the RNAPII-TFIIS complex is rate limiting for the passage of the mutant enzyme through pausing sites. In addition to implicating a region of the largest subunit of RNAPII in the process of transcript elongation, our observations provide in vivo evidence that TFIIS is involved in transcription by RNAPII.

Genetic interaction between transcription elongation factor TFIIS and RNA polymerase II

Little is known about the regions of RNA polymerase II (RNAPII) that are involved in the process of transcript elongation and interaction with elongation factors. One elongation factor, TFIIS, stimulates transcript elongation by binding to RNAPII and facilitating its passage through intrinsic pausing sites in vitro. In Saccharomyces cerevisiae, TFIIS is encoded by the PPR2 gene. Deletion of PPR2 from the yeast genome is not lethal but renders cells sensitive to the uracil analog 6-azauracil (6AU). Here, we show that mutations conferring 6AU sensitivity can also be isolated in the gene encoding the largest subunit of S. cerevisiae RNAPII (RPO21). A screen for mutations in RPO21 that confer 6AU sensitivity identified seven mutations that had been generated by either linker-insertion or random chemical mutagenesis. All seven mutational alterations are clustered within one region of the largest subunit that is conserved among eukaryotic RNAPII. The finding that six of the seven rpo21 mutants failed to grow at elevated temperature underscores the importance of this region for the functional and/or structural integrity of RNAPII. We found that the 6AU sensitivity of the rpo21 mutants can be suppressed by increasing the dosage of the wild-type PPR2 gene, presumably as a result of overexpression of TFIIS. These results are consistent with the proposal that in the rpo21 mutants, the formation of the RNAPII-TFIIS complex is rate limiting for the passage of the mutant enzyme through pausing sites. In addition to implicating a region of the largest subunit of RNAPII in the process of transcript elongation, our observations provide in vivo evidence that TFIIS is involved in transcription by RNAPII.

The RNA polymerase II elongation complex. Factor-dependent transcription elongation involves nascent RNA cleavage

Regulation of transcription elongation is an important mechanism in controlling eukaryotic gene expression. SII is an RNA polymerase II-binding protein that stimulates transcription elongation and also activates nascent transcript cleavage by RNA polymerase II in elongation complexes in vitro (Reines, D. (1992) J. Biol. Chem. 267, 3795-3800). Here we show that SII-dependent in vitro transcription through an arrest site in a human gene is preceded by nascent transcript cleavage. RNA cleavage appeared to be an obligatory step in the SII activation process. Recombinant SII activated cleavage while a truncated derivative lacking polymerase binding activity did not. Cleavage was not restricted to an elongation complex arrested at this particular site, showing that nascent RNA hydrolysis is a general property of RNA polymerase II elongation complexes. These data support a model whereby SII stimulates elongation via a ribonuclease activity of the elongation complex.

Characterization of a HeLa cDNA clone encoding the human SII protein, an elongation factor for RNA polymerase II

We present the cloning and sequence characterization of a HeLa cDNA encoding the SII transcription elongation factor. This cDNA clone is distinct from those previously isolated from a human kidney cDNA library [Yoo et al., Nucleic Acids Res. 19 (1991) 1073-1079]. Southern analysis suggests that more than one gene may exist for SII in the human genome. A comparison of deduced amino acid sequences for SII-related proteins from a variety of eukaryotes demonstrates very high similarity, especially within the C-terminal domain.

Stability of Drosophila RNA polymerase II elongation complexes in vitro

We show that nuclear extract from Drosophila Kc cells supports efficient elongation by RNA polymerase II initiated from the actin 5C promoter. The addition of 0.3% Sarkosyl, 1 mg of heparin per ml, or 250 mM KCl immediately after initiation has two effects. First, the elongation rate is reduced 80 to 90% as a result of the inhibition of elongation factors. Second, there is an increase in the amount of long runoff RNA, suggesting that there is an early block to elongation that is relieved by the disruptive reagents. Consistent with the first effect, we find that the ability of factor 5 (TFIIF) to stimulate the elongation rate is inhibited by the disruptive agents when assayed in a defined system containing pure RNA polymerase II and a dC-tailed template. The disruptive agents also inhibit the ability of DmS-II to suppress transcriptional pausing but only slightly reduce the ability of DmS-II to increase the elongation rate twofold. The pause sites encountered by RNA polymerase II after initiation at a promoter and subsequent treatment with the disruptive reagents are also recognized by pure polymerase transcribing a dC-tailed template. It has been suggested that 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole inhibits RNA polymerase II during elongation, but we find that the purine nucleoside analog has no effect on elongation complexes containing RNA over 500 nucleotides in length or on the action of factor 5 or DmS-II in the defined system.

Stability of Drosophila RNA polymerase II elongation complexes in vitro

We show that nuclear extract from Drosophila Kc cells supports efficient elongation by RNA polymerase II initiated from the actin 5C promoter. The addition of 0.3% Sarkosyl, 1 mg of heparin per ml, or 250 mM KCl immediately after initiation has two effects. First, the elongation rate is reduced 80 to 90% as a result of the inhibition of elongation factors. Second, there is an increase in the amount of long runoff RNA, suggesting that there is an early block to elongation that is relieved by the disruptive reagents. Consistent with the first effect, we find that the ability of factor 5 (TFIIF) to stimulate the elongation rate is inhibited by the disruptive agents when assayed in a defined system containing pure RNA polymerase II and a dC-tailed template. The disruptive agents also inhibit the ability of DmS-II to suppress transcriptional pausing but only slightly reduce the ability of DmS-II to increase the elongation rate twofold. The pause sites encountered by RNA polymerase II after initiation at a promoter and subsequent treatment with the disruptive reagents are also recognized by pure polymerase transcribing a dC-tailed template. It has been suggested that 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole inhibits RNA polymerase II during elongation, but we find that the purine nucleoside analog has no effect on elongation complexes containing RNA over 500 nucleotides in length or on the action of factor 5 or DmS-II in the defined system.

Genes homologous to ubiquitin-conjugating proteins and eukaryotic transcription factor SII in African swine fever virus

The nucleotide sequence of the 6004-bp EcoRI I fragment of African swine fever virus DNA has been determined. Translation of the sequence revealed eight closely spaced open reading frames (ORFs), three of them reading rightward and five leftward. Northern blot hybridization analysis indicated that ORFs I73R and I78R were transcribed early in infection, whereas ORFs I177L, I196L, and I329L were expressed at late times. Transcripts for ORFs I215L, I226R, and I243L were detected at low levels in early RNA and at higher levels in late RNA. The intergenic regions between genes I73R/I329L and I78R/I215L were characterized by the presence of direct repeats in tandem. Direct repetitions were also found within ORF I196L. The protein encoded by ORF I329L contained a putative cleavable signal peptide and an internal transmembrane domain, and that encoded by ORF I177L had an amino-terminal hydrophobic region with the characteristics of a "start-stop" sequence. ORF I243L encoded a protein similar to the eukaryotic elongation factor SII. The protein encoded by ORF I215L was homologous to the family of ubiquitin-conjugating proteins.

Stimulation of transcript elongation requires both the zinc finger and RNA polymerase II binding domains of human TFIIS

The eukaryotic transcriptional factor TFIIS enhances transcript elongation by RNA polymerase II. Here we describe two functional domains in the 280 amino acid human TFIIS protein: residues within positions 100-230 are required for binding to polymerase, and residues 230-280, which form a zinc finger, are required in conjunction with the polymerase binding region for transcriptional stimulation. Interestingly, a mutant TFIIS with only the polymerase binding domain actually inhibits transcription, whereas a mutant in which the polymerase binding and zinc finger domains are separated by an octapeptide is only weakly active. The zinc finger itself has no effect on transcription, but in contrast to the wild-type protein, it binds to oligonucleotides. These findings suggest that TFIIS may interact with RNA polymerase II such that the normally masked zinc finger can specifically contact nucleotides in the transcription elongation zone at a position juxtaposed to the polymerization site.

Cloning, expression and characterization of the human transcription elongation factor, TFIIS

The cDNA for the human elongation factor, TFIIS, has been cloned and expressed in E. coli with the T7 expression system. This 280-amino acid TFIIS protein is shorter by 21 residues than that of the mouse. The missing 21 residues are located in the amino-terminal region, which is not thought to be required for transcriptional stimulation. Apart from this gap, human and mouse proteins reveal 96% overall identity and 98.5% sequence similarity if conservative substitutions are taken into account. The bacterially expressed human protein and the purified calf thymus proteins are indistinguishable in their ability to stimulate transcript elongation by purified RNA polymerase II. Estimation of the native molecular size of the human protein in solution indicates that it exists as a dimer.