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

ARMC Subfamily: Structures, Functions, Evolutions, Interactions, and Diseases

Armadillo repeat-containing proteins (ARMCs) are widely distributed in eukaryotes and have important influences on cell adhesion, signal transduction, mitochondrial function regulation, tumorigenesis, and other processes. These proteins share a similar domain consisting of tandem repeats approximately 42 amino acids in length, and this domain constitutes a substantial platform for the binding between ARMCs and other proteins. An ARMC subfamily, including ARMC1∼10, ARMC12, and ARMCX1∼6, has received increasing attention. These proteins may have many terminal regions and play a critical role in various diseases. On the one hand, based on their similar central domain of tandem repeats, this ARMC subfamily may function similarly to other ARMCs. On the other hand, the unique domains on their terminals may cause these proteins to have different functions. Here, we focus on the ARMC subfamily (ARMC1∼10, ARMC12, and ARMCX1∼6), which is relatively conserved in vertebrates and highly conserved in mammals, particularly primates. We review the structures, biological functions, evolutions, interactions, and related diseases of the ARMC subfamily, which involve more than 30 diseases and 40 bypasses, including interactions and relationships between more than 100 proteins and signaling molecules. We look forward to obtaining a clearer understanding of the ARMC subfamily to facilitate further in-depth research and treatment of related diseases.

Transcription factor IIS cooperates with the E3 ligase UBR5 to ubiquitinate the CDK9 subunit of the positive transcription elongation factor B

Elongation of transcription by mammalian RNA polymerase II (RNAPII) is regulated by specific factors, including transcription factor IIS (TFIIS) and positive transcription elongation factor b (P-TEFb). We show that the E3 ubiquitin ligase UBR5 associates with the CDK9 subunit of positive transcription elongation factor b to mediate its polyubiquitination in human cells. TFIIS also binds UBR5 to stimulate CDK9 polyubiquitination. Co-localization of UBR5, CDK9, and TFIIS along specific regions of the γ fibrinogen (γFBG) gene indicates that a ternary complex involving these factors participates in the transcriptional regulation of this gene. In support of this notion, overexpression of TFIIS not only modifies the ubiquitination pattern of CDK9 in vivo but also increases the association of CDK9 with various regions of the γFBG gene. Notably, the TFIIS-mediated increase in CDK9 loading is obtained during both basal and activated transcription of the γFBG gene. This increased CDK9 binding is paralleled by an increase in the recruitment of RNAPII along the γFBG gene and the phosphorylation of the C-terminal domain of the RNAPII largest subunit RPB1 on Ser-2, a known target of CDK9. Together, these results identify UBR5 as a novel E3 ligase that regulates transcription and define an additional function of TFIIS in the regulation of CDK9.

Transcription initiation factor IID-interactive histone chaperone CIA-II implicated in mammalian spermatogenesis

Histones are thought to have specific roles in mammalian spermatogenesis, because several subtypes of histones emerge that are post-translationally modified during spermatogenesis. Though regular assembly of nucleosome is guaranteed by histone chaperones, their involvement in spermatogenesis is yet to be characterized. Here we identified a histone chaperone-related factor, which we designated as CCG1-interacting factor A-II (CIA-II), through interaction with bromodomains of TAFII250/CCG1, which is the largest subunit of human transcription initiation factor IID (TFIID). We found that human CIA-II (hCIA-II) localizes in HeLa nuclei and is highly expressed in testis and other proliferating cell-containing tissues. Expression of mouse CIA-II (mCIA-II) does not occur in the germ cell-lacking testes of adult WBB6F1-W/Wv mutant mice, indicating its expression in testis to be specific to germ cells. Fractionation of testicular germ cells revealed that mCIA-II transcripts accumulate in pachytene spermatocytes but not in spermatids. In addition, the mCIA-II transcripts in testis were present as early as 4 days after birth and decreased at 56 days after birth. These findings indicate that mCIA-II expression in testis is restricted to premeiotic to meiotic stages during spermatogenesis. Also, we found that hCIA-II interacts with histone H3 in vivo and with histones H3/H4 in vitro and that it facilitates supercoiling of circular DNA when it is incubated with core histones and topoisomerase I in vitro. These data suggest that CIA-II is a histone chaperone and is implicated in the regulation of mammalian spermatogenesis.

Elongation by RNA polymerase II: structure-function relationship

RNA polymerase II is the eukaryotic enzyme that transcribes all the mRNA in the cell. Complex mechanisms of transcription and its regulation underlie basic functions including differentiation and morphogenesis. Recent evidence indicates the process of RNA chain elongation as a key step in transcription control. Elongation was therefore expected and found to be linked to human diseases. For these reasons, major efforts in determining the structures of RNA polymerases from yeast and bacteria, at rest and as active enzymes, were undertaken. These studies have revealed much information regarding the processes involved in transcription. Eukaryotic RNA polymerases and their homologous bacterial counterparts are flexible enzymes with domains that separate DNA and RNA, prevent the escape of nucleic acids during transcription, allow for extended pausing or "arrest" during elongation, allow for translocation of the DNA and more. Structural studies of RNA polymerases are described below within the context of the process of transcription elongation, its regulation and function.

Promoting elongation with transcript cleavage stimulatory factors

Transcript elongation by RNA polymerase is a dynamic process, capable of responding to a number of intrinsic and extrinsic signals. A number of elongation factors have been identified that enhance the rate or efficiency of transcription. One such class of factors facilitates RNA polymerase transcription through blocks to elongation by stimulating the polymerase to cleave the nascent RNA transcript within the elongation complex. These cleavage factors are represented by the Gre factors from prokaryotes, and TFIIS and TFIIS-like factors found in archaea and eukaryotes. High-resolution structures of RNA polymerases and the cleavage factors in conjunction with biochemical investigations and genetic analyses have provided insights into the mechanism of action of these elongation factors. However, there are yet many unanswered questions regarding the regulation of these factors and their effects on target genes.

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.

The Euplotes crassus conjugation-specific conN1 gene encodes a transcription elongation factor TFIIS-like protein

The Euplotes crassus macronuclear DNA molecule containing the conjugation-specific conN1 gene has been sequenced, along with a cDNA clone. The results indicate that the conN1 gene encodes a protein similar to the transcription elongation factor TFIIS proteins identified in other eukaryotes.

TFIIAalpha/beta-like factor is encoded by a germ cell-specific gene whose expression is up-regulated with other general transcription factors during spermatogenesis in the mouse

TFIIAalpha/beta-like factor (ALF) is a testis-specific counterpart of the large subunit of human general transcription factor TFIIA. Northern analysis shows that ALF mRNA first appears in mouse testis at Postnatal Day 14. Similarly, expression of the general transcription factors TBP, TRF2, TFIIAalpha/beta, TFIIAgamma, and TFIIIB(90) is also increased beginning at Postnatal Day 14, suggesting that there is a coordinated induction of many general transcription factors during male germ cell differentiation. Analysis of male germ cells separated by Staput sedimentation shows that ALF is present in pachytene spermatocytes and haploid spermatids. In addition, in situ hybridization experiments with adult mouse testis shows that ALF is present in haploid spermatids. Searches of the human genome sequence database using the basic local alignment search tool reveal that the ALF and TFIIAalpha/beta(GTF2A1) genes are both composed of nine exons, whereas the TFIIAgamma (GTF2A2) gene is composed of five exons. Furthermore, nucleotide and amino acid comparisons among human and mouse ALF, TFIIAalpha/beta, and TFIIAgamma cDNA sequences show that ALF has diverged more rapidly than either TFIIAalpha/beta or TFIIAgamma. Finally, the ALF and SBLF (Stoned B-Like Factor) sequences present in the chimeric SALF cDNA are both present on human chromosome 2, and an analysis of the corresponding genes suggests a model for the formation of SALF.

Structural basis for the species-specific activity of TFIIS

Many proteins involved in eukaryotic transcription are similar in function and in sequence between organisms. Despite the sequence similarities, there are many factors that do not function across species. For example, transcript elongation factor TFIIS is highly conserved among eukaryotes, and yet the TFIIS protein from Saccharomyces cerevisiae cannot function with mammalian RNA polymerase II and vice versa. To determine the reason for this species specificity, chimeras were constructed linking three structurally independent regions of the TFIIS proteins from yeast and human cells. Two independently folding domains, II and III, have been examined previously using NMR (). Yeast domain II alone is able to bind yeast RNA polymerase II with the same affinity as the full-length TFIIS protein, and this domain was expected to confer the species selectivity. Domain III has previously been shown to be readily exchanged between mammalian and yeast factors. However, the results presented here indicate that domain II is insufficient to confer species selectivity, and a primary determinant lies in a 30-amino acid highly conserved linker region connecting domain II with domain III. These 30 amino acids may physically orient domains II and III to support functional interactions between TFIIS and RNA polymerase II.

Identification, cloning, expression, and biochemical characterization of the testis-specific RNA polymerase II elongation factor ELL3

The human ELL gene, which is a frequent target for translocation in acute myeloid leukemia, was initially isolated from rat liver nuclei and found to be an RNA polymerase II elongation factor. Based on homology to ELL, we later cloned ELL2 and demonstrated that it can also increase the catalytic rate of transcription elongation by RNA polymerase II. To better understand the role of ELL proteins in the regulation of transcription by RNA polymerase II, we have initiated a search for proteins related to ELLs. In this report, we describe the molecular cloning, expression, and characterization of ELL3, a novel RNA polymerase II elongation factor approximately 50% similar to both ELL and ELL2. Our transcriptional studies have demonstrated that ELL3 can also increase the catalytic rate of transcription elongation by RNA polymerase II. The C-terminal domain of ELL, which we recently demonstrated to be required and sufficient for the immortalization of myeloid progenitor cells, shares strong similarities to the C-terminal domain of ELL3. ELL3 was localized by immunofluorescence to the nucleus of cells, and Northern analysis indicated that ELL3 is a testis-specific RNA polymerase II elongation factor.

Genetic interactions between TFIIS and the Swi-Snf chromatin-remodeling complex

The eukaryotic transcript elongation factor TFIIS enables RNA polymerase II to read through blocks to elongation in vitro and interacts genetically with a variety of components of the transcription machinery in vivo. In Saccharomyces cerevisiae, the gene encoding TFIIS (PPR2) is not essential, and disruption strains exhibit only mild phenotypes and an increased sensitivity to 6-azauracil. The nonessential nature of TFIIS encouraged the use of a synthetic lethal screen to elucidate the in vivo roles of TFIIS as well as provide more information on other factors involved in the regulation of transcript elongation. Several genes were identified that are necessary for either cell survival or robust growth when the gene encoding TFIIS has been disrupted. These include UBP3, KEX2, STT4, and SWI2/SNF2. SWI1 and SNF5 disruptions were also synthetically lethal with ppr2Delta, suggesting that the reduced ability to remodel chromatin confers the synthetic phenotype. The synthetic phenotypes show marked osmosensitivity and cytoskeletal defects, including a terminal hyperelongated bud phenotype with the Swi-Snf complex. These results suggest that genes important in osmoregulation, cell membrane synthesis and integrity, and cell division may require the Swi-Snf complex and TFIIS for efficient transcription. The detection of these genetic interactions provides another functional link between the Swi-Snf complex and the elongation machinery.

Transcription elongation factor SII

RNA chain elongation by RNA polymerase II (pol II) is a complex and regulated process which is coordinated with capping, splicing, and polyadenylation of the primary transcript. Numerous elongation factors that enable pol II to transcribe faster and/or more efficiently have been purified. SII is one such factor. It helps pol II bypass specific blocks to elongation that are encountered during transcript elongation. SII was first identified biochemically on the basis of its ability to enable pol II to synthesize long transcripts. ((1)) Both the high resolution structure of SII and the details of its novel mechanism of action have been refined through mutagenesis and sophisticated in vitro assays. SII engages transcribing pol II and assists it in bypassing blocks to elongation by stimulating a cryptic, nascent RNA cleavage activity intrinsic to RNA polymerase. The nuclease activity can also result in removal of misincorporated bases from RNA. Molecular genetic experiments in yeast suggest that SII is generally involved in mRNA synthesis in vivo and that it is one type of a growing collection of elongation factors that regulate pol II. In vertebrates, a family of related SII genes has been identified; some of its members are expressed in a tissue-specific manner. The principal challenge now is to understand the isoform-specific functional differences and the biology of regulation exerted by the SII family of proteins on target genes, particularly in multicellular organisms.

Template end-to-end transposition by RNA polymerase II

On 5'-template strand protruding templates, promoter-initiated run-off transcription by RNA polymerase II generates discrete, 15-16-nucleotide (nt) longer than expected products whose production is abrogated by elongation factor SII (Parsons, M. A., Sinden, R. R., and Izban, M. G. (1998) J. Biol. Chem. 273, 26998-27008). We demonstrate that template terminal complexes produce these RNAs and that transcript extension is a general and salt-sensitive (250 mM) feature of run-off transcription. On 5'-overhung templates the extended run-off transcripts appear to be retained within an RNA-DNA-enzyme ternary complex, and SII facilitates resumption of transcript elongation via a dinucleotide truncation intermediate. Moreover, on one of the 5-overhung templates, the initially extended complexes spontaneously resumed transcript extension and were uniquely resistant to salt (250 mM) challenge. However, SII did not facilitate this long distance extension on all template ends. Run-off transcripts on a blunt-ended template were initially extended by 2-11 nt (roughly in 2-nt increments); SII addition either before or after extension resulted in the accumulation of a 4-5-nt extension product. Based on these findings, we propose that the initial and continuously extended RNAs reflect intermediates and successful completion of template end-to-end transposition (template switching) by RNA polymerase II, respectively. Both the template end sequence and structure influenced the success of such an event.

Genomic characterization of a testis-specific TFIIS (TCEA2) gene

There is a family of genes encoding TFIIS-related proteins in human cells. We have focused upon the genomic organization of one family member expressed primarily in the testis. This gene encodes a transcription elongation factor similar to but distinct from that encoded by a previously reported TFIIS gene. Also in contrast to the previously reported TFIIS gene, the testis gene contains introns. All exon-intron junction sequences match the consensus GT/AG rule. The gene consists of seven exons and six introns with a total size of approximately 7 kb. The nucleotide sequence of the 5 flanking region of the testis TFIIS gene contains several potential regulatory factor-binding sites, not all of which are present in the TFIIS gene, whose expression is nearly ubiquitous. Elucidation of the full structure of the testis TFIIS gene should be useful for determining its chromosomal localization and its potential role in the regulation of gene expression in human tissues.

Transcript cleavage in an RNA polymerase I elongation complex. Evidence for a dissociable activity similar to but distinct from TFIIS

Stalled Xenopus RNA polymerase I (pol I) elongation complexes bearing a 52-nucleotide RNA were prepared by promoter-initiated transcription in the absence of UTP. When such complexes were isolated and incubated in the presence of Mg2+, the associated RNA was shortened from the 3'-end, and mono- and dinucleotides were released. Shortened transcripts were still associated with the DNA and were quantitatively reelongated upon addition of NTPs. The cleavage activity could be removed from the pol I-ternary complex with buffers containing 0.25% Sarkosyl. These findings indicate that a factor with characteristics similar to elongation factor TFIIS is associated with the pol I elongation complex. However, addition of recombinant Xenopus TFIIS to Sarkosyl-washed pol I elongation complexes had no effect, whereas it showed the expected effects in control reactions with identically prepared pol II elongation complexes. The results thus suggest the existence of a pol I-specific cleavage/elongation factor. I also report the sequence of a novel type of Xenopus TFIIS. The predicted amino acid sequences of the present and previously identified Xenopus TFIIS are less than 65% conserved. Thus, like mammalian species, Xenopus has at least two highly divergent forms of TFIIS.

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.