Negative Cofactor Research Articles

Alternative splicing of the conserved drug-resistant orthologue FpNcb2 is associated with its nuclear accumulation of products and full virulence of Fusarium pseudograminearum.

Negative cofactor 2 NC2β (Ncb2 or Dr1) is the beta subunit of a conserved heterodimeric regulator of transcription negative cofactor 2 (NC2) complex that has been identified as key regulator of drug resistance in model fungi. However, its role in plant pathogens is still unclear. We identified an NC2β orthologue, FpNcb2, in Fusarium pseudograminearum, which is not only a significant regulatory function in drug resistance, but also essential for growth, conidiation and penetration. Moreover, FpNcb2 undergoes alternative splicing which creates two mRNA isoforms. As a putative CCAAT binding protein, FpNcb2 concentrates in the nuclei, contributing to the expression of two spliced mRNA of FpNcb2 in hypha, conidiophores and conidia, with exception of FpNcb2ISOA in germlings. Expression of each spliced mRNA of FpNcb2 in Δfpncb2 mutant could full complement the defects on growth, conidiation and fungicides sensitivity to that of wild type. However, FpNcb2ISOA and FpNcb2ISOB have different effects on virulence. FpNcb2 acts as a regulator for the transcription of some genes encoding drug efflux and hydrolases. Our analysis showed the existence of alternative mRNA splicing in the NC2β orthologue, which is associated with protein subcellular localization and fungal virulence. The further elucidation of the target genes of NC2β will provide insights into the potential regulation mechanisms in the antifungal resistance and pathogenesis of F. pseudograminearum. © 2024 Society of Chemical Industry.

The Fallout of Catastrophic Technogenic Emissions of Toxic Gases Can Negatively Affect Covid-19 Clinical Course.

The coronavirus D-19 (Covid-19) pandemic has shaken almost every country in the world: as we stand, 6,3 million deaths from the infection have already been recorded, 167,000 and 380,000 of which are in Italy and the Russian Federation, respectively. In the first wave of the pandemic, Italy suffered an abnormally high death toll. A detailed analysis of available epidemiological data suggests that that rate was shockingly high in the Northern regions and in Lombardy, in particular, whilst in the southern region the situation was less dire. This inexplicably high mortality rate in conditions of a very well-developed health care system such as the one in Lombardy - recognized as one of the best in Italy - certainly cries for a convincing explanation. In 1976, the small city of Seveso, Lombardy, experienced a release of dioxin into the atmosphere after a massive technogenic accident. The immediate effects of the industrial disaster did not become apparent until a surge in the number of tumors in the affected population in the subsequent years. In this paper, we endeavor to prove our hypothesis that the release of dioxin was a negative cofactor that contributed to a worsening of the clinical course of COVID-19 in Lombardy.

TaDrAp1 and TaDrAp2, Partner Genes of a Transcription Repressor, Coordinate Plant Development and Drought Tolerance in Spelt and Bread Wheat.

Down-regulator associated protein, DrAp1, acts as a negative cofactor (NC2α) in a transcription repressor complex together with another subunit, down-regulator Dr1 (NC2β). In binding to promotors and regulating the initiation of transcription of various genes, DrAp1 plays a key role in plant transition to flowering and ultimately in seed production. TaDrAp1 and TaDrAp2 genes were identified, and their expression and genetic polymorphism were studied using bioinformatics, qPCR analyses, a 40K Single nucleotide polymorphism (SNP) microarray, and Amplifluor-like SNP genotyping in cultivars of bread wheat (Triticum aestivum L.) and breeding lines developed from a cross between spelt (T. spelta L.) and bread wheat. TaDrAp1 was highly expressed under non-stressed conditions, and at flowering, TaDrAp1 expression was negatively correlated with yield capacity. TaDrAp2 showed a consistently low level of mRNA production. Drought caused changes in the expression of both TaDrAp1 and TaDrAp2 genes in opposite directions, effectively increasing expression in lower yielding cultivars. The microarray 40K SNP assay and Amplifluor-like SNP marker, revealed clear scores and allele discriminations for TaDrAp1 and TaDrAp2 and TaRht-B1 genes. Alleles of two particular homeologs, TaDrAp1-B4 and TaDrAp2-B1, co-segregated with grain yield in nine selected breeding lines. This indicated an important regulatory role for both TaDrAp1 and TaDrAp2 genes in plant growth, ontogenesis, and drought tolerance in bread and spelt wheat.

Testicular Microlithiasis Is Associated with Impaired Spermatogenesis in Patients with Unexplained Infertility

Introduction: Testicular microlithiasis (TML) was shown to be associated with an increased risk of infertility. However, the association of TML with spermatogenesis in patients with unexplained infertility is still unknown. In this study, we therefore investigated the effect of TML on hormones and sperm parameters in a large cohort of infertile men without major factors for impaired fertility and azoospermic men serving for comparison. Methods: Over a period of 10 years, we retrospectively analyzed 2,914 patients who attended our centre with the diagnosis of unexplained infertility and sperm count >1 million/ejaculate, as well as 281 patients with unexplained azoospermia. From the 2,914 patients, we identified 218 patients with TML as revealed by ultrasound imaging. Further, 26 out of 281 azoospermic patients showed TML. Subsequently, we performed a thorough analysis of reproductive parameters and their association with TML. Results: The overall incidence of TML in patients with unexplained infertility and in unexplained azoospermic men was 7.5 and 9.3%, respectively. Patients with unexplained infertility and TML showed significantly smaller testicular volume, elevated FSH level, and lower sperm count and motility. Impaired spermatogenesis was not associated with the amount of microlithiasis, considered after classification into subgroups (<5 vs. ≥5 microliths/testis), and instead was associated with presence or absence of TML. TML in unexplained infertile azoospermic patients was not significantly associated neither with andrological reproductive parameters nor with sperm retrieval rate in microsurgical testicular sperm extraction. Discussion/Conclusion: TML itself, and not the number of microliths, is associated with impaired spermatogenesis in patients with unexplained infertility. The parameter TML alone is not sufficient to predict spermatogenic impairment in azoospermic patients. This study highlights the importance of ultrasound imaging in the clinical evaluation of infertile men, taking into account that TML is a negative co-factor for male fertility.

The negative cofactor 2 complex is a key regulator of drug resistance in Aspergillus fumigatus

The frequency of antifungal resistance, particularly to the azole class of ergosterol biosynthetic inhibitors, is a growing global health problem. Survival rates for those infected with resistant isolates are exceptionally low. Beyond modification of the drug target, our understanding of the molecular basis of azole resistance in the fungal pathogen Aspergillus fumigatus is limited. We reasoned that clinically relevant antifungal resistance could derive from transcriptional rewiring, promoting drug resistance without concomitant reductions in pathogenicity. Here we report a genome-wide annotation of transcriptional regulators in A. fumigatus and construction of a library of 484 transcription factor null mutants. We identify 12 regulators that have a demonstrable role in itraconazole susceptibility and show that loss of the negative cofactor 2 complex leads to resistance, not only to the azoles but also the salvage therapeutics amphotericin B and terbinafine without significantly affecting pathogenicity.

Analyzing the Dynamics of Single TBP-DNA-NC2 Complexes Using Hidden Markov Models

Single-pair Förster resonance energy transfer (spFRET) has become an important tool for investigating conformational dynamics in biological systems. To extract dynamic information from the spFRET traces measured with total internal reflection fluorescence microscopy, we extended the hidden Markov model (HMM) approach. In our extended HMM analysis, we incorporated the photon-shot noise from camera-based systems into the HMM. Thus, the variance in Förster resonance energy transfer (FRET) efficiency of the various states, which is typically a fitted parameter, is explicitly included in the analysis estimated from the number of detected photons. It is also possible to include an additional broadening of the FRET state, which would then only reflect the inherent flexibility of the dynamic biological systems. This approach is useful when comparing the dynamics of individual molecules for which the total intensities vary significantly. We used spFRET with the extended HMM analysis to investigate the dynamics of TATA-box-binding protein (TBP) on promoter DNA in the presence of negative cofactor 2 (NC2). We compared the dynamics of two promoters as well as DNAs of different length and labeling location. For the adenovirus major late promoter, four FRET states were observed; three states correspond to different conformations of the DNA in the TBP-DNA-NC2 complex and a four-state model in which the complex has shifted along the DNA. The HMM analysis revealed that the states are connected via a linear, four-well model. For the H2B promoter, more complex dynamics were observed. By clustering the FRET states detected with the HMM analysis, we could compare the general dynamics observed for the two promoter sequences. We observed that the dynamics from a stretched DNA conformation to a bent conformation for the two promoters were similar, whereas the bent conformation of the TBP-DNA-NC2 complex for the H2B promoter is approximately three times more stable than for the adenovirus major late promoter.

Carbohydrate-related nutritional and genetic risks of obesity for indigenous northerners

By the end of the 2010-s the prevalence of obesity among the indigenous people of the North approached to the all-Russia one and the speed of the spread of other metabolic disorders exceeded the average all-country levels. Aim of this review is to analyze data on the increase in consumption and variety of sugars coupled with a genetic specificity of regulation of saccharidase activity and their possible impact on the matters. Results. It have been shown that the traditional protein-lipid-based northern type diet has substantially changed and now contains a high proportion of carbohydrates. The carbohydrate per capita consumption among the indigenous people of the North has reached the all-Russia average level (40 kg per year) which exceeds the European average of 36.2 kg per year. The variety of food disaccharides has also considerably increased. The daily consumption of sucrose, at the beginning of the 20th century it was the only sugar contained in the store-bought foods, increased from 30 g in the 1930s to 63-65 g in the 1990s. In addition, the proportion of sucrose dropped to 60-70 per cent, while the contribution of other disaccharides (lactose, trehalose) reached 30-40 per cent. Daily starch consumption has also increased and got close to the national average (males 228.5 g, females 157.5 g per day). Such a diet in itself increases the risk of metabolic disorders and obesity. The high prevalence of the genotypes that determine reduced levels or inability to produce sucrase-isomaltase, lactase, trehalase, salivary and pancreatic amylases among northerners becomes a negative cofactor. The evolutionary driven and embodied in genotype reduced ability of the indigenous Arctic people to digest complex carbohydrates is in a conflict with the growing consumption of sugars and starchy foods in modern conditions. The northern people have a high proportion of carriers of the AG deletion in SI gene (3.5-14.3% against 0.05-0.2% among Europeans) which determines malabsorption of sucrose. The CC/LCT genotype (96.6% in northerners, 36-49% in Russians) presumes lactose intolerance and is associated with the risk of childhood obesity. The occurrence of A allele in the rs2276064 locus of TREH gene (trehalose intolerance; 31.3-58.9% in northerners, 1.9% in Europeans) increases the probability of the onset of type 2 diabetes mellitus. According to preliminary estimates, 28-52% of the northerners completely lost AMY gene that precludes or drastically reduces the ability to digest starch. A reduction in the number of copies of AMY gene (the average number of copies AMY2A - 4, in, in northerners it is 1.0-1.4) is associated with overweight and obesity. Conclusion. The analysis shows that, in the case of the modern indigenous northerners, nutritional and genetic risks of metabolic disorders accumulate.

Role of canine circovirus in dogs with acute haemorrhagic diarrhoea

Canine circovirus (CanineCV) has been detected in some dogs with severe haemorrhagic diarrhoea, but its pathogenic role is unclear. This study evaluated a suspected association between the presence of CanineCV...

Reversal of platinum drug resistance by the histone deacetylase inhibitor belinostat

ObjectivesTo investigate and elucidate the mechanism for the potentiation of cisplatin anticancer activity by belinostat in platinum (Pt)-resistant lung cancer cells. Materials and methodsCombination of cisplatin and belinostat was investigated in two pairs of parental and cisplatin-resistant non-small cell lung cancer (NSCLC) cell lines. The Pt-resistant cell models exhibited overexpression of the efflux transporter ABCC2 and enhanced DNA repair capacity. Cellular accumulation of cisplatin and extent of DNA platination were measured by inductively coupled plasma optical emission spectrometer. Expression of Pt transporters and DNA repair gene were determined by quantitative real-time PCR. Inhibition of ABCC2 transport activity was examined by flow cytometric assay. Regulation of ABCC2 at the promoter level was studied by chromatin immunoprecipitation assay. Results and conclusionIn Pt-resistant lung cancer cells, belinostat apparently circumvent the resistance through inhibition of both ABCC2 and DNA repair-mediated mechanisms. The combination of belinostat and cisplatin were found to display synergistic cytotoxic effect in cisplatin-resistant lung cancer cell lines when the two drugs were added concomitantly or when belinostat was given before cisplatin. Upon the concomitant administration of belinostat, cellular accumulation of cisplatin and formation of DNA-Pt adducts were found to be increased whereas expression levels of the efflux transporter ABCC2 and the DNA repair gene ERCC1 were inhibited in Pt-resistant cells. Belinostat-mediated downregulation of ABCC2 was associated with an increase association of a transcriptional repressor (negative cofactor 2) but reduced association of a transcriptional activator (TFIIB) to the ABCC2 promoter. The data advocates the use of belinostat as a novel drug resistance reversal agent for use in combination cancer chemotherapeutic regimens.

Defects in the NC2 repressor affect both canonical and non-coding RNA polymerase II transcription initiation in yeast.

BackgroundThe formation of the pre-initiation complex in eukaryotic genes is a key step in transcription initiation. The TATA-binding protein (TBP) is a universal component of all pre-initiation complexes for all kinds of RNA polymerase II (RNA pol II) genes, including those with a TATA or a TATA-like element, both those that encode proteins and those that transcribe non-coding RNAs. Mot1 and the negative cofactor 2 (NC2) complex are regulators of TBP, and it has been shown that depletion of these factors in yeast leads to defects in the control of transcription initiation that alter cryptic transcription levels in selected yeast loci.ResultsIn order to cast light on the molecular functions of NC2, we performed genome-wide studies in conditional mutants in yeast NC2 essential subunits Ydr1 and Bur6. Our analyses show a generally increased level of cryptic transcription in all kinds of genes upon depletion of NC2 subunits, and that each kind of gene (canonical or ncRNAs, TATA or TATA-like) shows some differences in the cryptic transcription pattern for each NC2 mutant.ConclusionsWe conclude that NC2 plays a general role in transcription initiation in RNA polymerase II genes that is related with its known TBP interchange function from free to promoter bound states. Therefore, loss of the NC2 function provokes increases in cryptic transcription throughout the yeast genome. Our results also suggest functional differences between NC2 subunits Ydr1 and Bur6.

Structural basis for recognition and remodeling of the TBP:DNA:NC2 complex by Mot1.

Swi2/Snf2 ATPases remodel substrates such as nucleosomes and transcription complexes to control a wide range of DNA-associated processes, but detailed structural information on the ATP-dependent remodeling reactions is largely absent. The single subunit remodeler Mot1 (modifier of transcription 1) dissociates TATA box-binding protein (TBP):DNA complexes, offering a useful system to address the structural mechanisms of Swi2/Snf2 ATPases. Here, we report the crystal structure of the N-terminal domain of Mot1 in complex with TBP, DNA, and the transcription regulator negative cofactor 2 (NC2). Our data show that Mot1 reduces DNA:NC2 interactions and unbends DNA as compared to the TBP:DNA:NC2 state, suggesting that Mot1 primes TBP:NC2 displacement in an ATP-independent manner. Electron microscopy and cross-linking data suggest that the Swi2/Snf2 domain of Mot1 associates with the upstream DNA and the histone fold of NC2, thereby revealing parallels to some nucleosome remodelers. This study provides a structural framework for how a Swi2/Snf2 ATPase interacts with its substrate DNA:protein complex.

Taspase1 processing alters TFIIA cofactor properties in the regulation of TFIID

TFIIA is an important positive regulator of TFIID, the primary promoter recognition factor of the basal RNA polymerase II transcription machinery. TFIIA antagonises negative TFIID regulators such as negative cofactor 2 (NC2), promotes specific binding of the TBP subunit of TFIID to TATA core promoter sequence elements and stimulates the interaction of TBP-associated factors (TAFs) in the TFIID complex with core promoter elements located downstream of TATA, such as the initiator element (INR). Metazoan TFIIA consists of 3 subunits, TFIIAα (35 kDa), β (19 kDa) and γ (12 kDa). TFIIAα and β subunits are encoded by a single gene and result from site-specific cleavage of a 55 kDa TFIIA(α/β) precursor protein by the protease Taspase1. Metazoan cells have been shown to contain variable amounts of TFIIA (55/12 kDa) and Taspase1-processed TFIIA (35/19/12 kDa) depending on cell type, suggesting distinct gene-specific roles of unprocessed and Taspase1-processed TFIIA. How precisely Taspase1 processing affects TFIIA functions is not understood. Here we report that Taspase1 processing alters TFIIA interactions with TFIID and the conformation of TFIID/TFIIA promoter complexes. We further show that Taspase1 processing induces increased sensitivity of TFIID/TFIIA complexes to the repressor NC2, which is counteracted by the presence of an INR core promoter element. Our results provide first evidence that Taspase1 processing affects TFIIA regulation of TFIID and suggest that Taspase1 processing of TFIIA is required to establish INR-selective core promoter activity in the presence of NC2.

Structural studies of Mot1 and NC2 in transcription initiation process

Regulation of protein–nucleic acid interactions plays a key role in various cellular processes. The SNF2/SWI2 protein family forms a large and diverse class of proteins and multiprotein assemblies, which use energy derived from ATP hydrolysis to disrupt or modify protein-DNA interactions. They possess a conserved helicase-like domain accompanied by protein-specific targeting and regulation regions. The SNF2/SWI2 family member Mot1 (Modifier of transcription 1, also known as BTAF1) is a single polypeptide ATP-dependent remodeler. Mot1 acts directly on TBP (TATA-box binding protein) regulating RNA polymerase II preinitiation complex formation in the first stages. Global distribution of TBP on promoter regions is also modulated by NC2 (Negative Cofactor 2). It has been suggested that Mot1 and NC2 can co occupy the same promoter sites influencing the assembly of the transcription machinery simultaneously. Our understanding of the molecular mechanism of SWI2/SNF2 family ATPases is very limited. Previously, we have reported the crystal structure of the complex of Encephalitozoon cuniculi N terminal domain of Mot1 (Mot1NTD) with its substrate, TBP [1]. Here we present the crystal structure of the TBP NC2 Mot1NTD complex bound to a promoter DNA fragment at 3.9Å resolution. In our studies we have applied a combined structural biology approach using crystallography, electron microscopy reconstructions and chemical cross-linking. We probed the conformational changes of the complex during the ATP hydrolysis cycle and unveiled the structural basis of the Mot1–NC2 interplay. Our findings greatly contribute not only to our limited understanding of Mot1 action, but all SNF2/SWI2 family remodeling enzymes.

Ethanol is a Significant Cofactor in HAART Induced Hepatotoxicity

Highly Active Antiretroviral Therapy (HAART) has significantly increased life expectancy of HIV patients; however, there are major side effects which include lipodystrophy and hepatotoxicity. Alcohol abuse is highly prevalent in HIV patients and can be a significant negative cofactor in HAART‐hepatotoxicity. Hence, the mechanisms underlying HAART and alcohol induced hepatotoxicity were investigated. Specifically, effects of HAART drugs (azidothymidine, and Indinavir sulphate) in combination with alcohol were examined both in vitro and in vivo. Individually, alcohol and AZT caused cytotoxicity in H4IIEC3 (a rat hepatoma) cells which was significantly increased in combination. These data indicate that alcohol can induce and further enhance HAART‐cytotoxicity.Assessment of Alcohol and HAART drug interaction and hepatotoxicity using an animal model of chronic alcohol feeding showed increased visceral adiposity compared to pair‐fed animals, suggesting disturbances in lipid metabolism. Lipodystrophy was seen as hepatic macro and microvesicular steatosis, elevated triglycerides and free fatty acids. These animals also exhibited increased inflammation and hepatic neutrophil infiltration. Overall, our data demonstrate that alcohol exacerbates HAART hepatotoxicity, and act as a significant cofactor in the development of hepatic steatosis and liver injury.

Administration of genetic expression by multi-task proteins and long-range action

Administration of genetic expression by multi-task proteins and long-range action

Phosphoinositide isoforms determine compartment-specific ion channel activity

Phosphoinositides serve as address labels for recruiting peripheral cytoplasmic proteins to specific subcellular compartments, and as endogenous factors for modulating the activity of integral membrane proteins. Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P(2)) is a plasma-membrane (PM)-specific phosphoinositide and a positive cofactor required for the activity of most PM channels and transporters. This requirement for phosphoinositide cofactors has been proposed to prevent PM channel/transporter activity during passage through the biosynthetic/secretory and endocytic pathways. To determine whether intracellularly localized channels are similarly "inactivated" at the PM, we studied PIP(2) modulation of intracellular TRPML1 channels. TRPML1 channels are primarily localized in lysosomes, but can also be detected temporarily in the PM upon lysosomal exocytosis. By directly patch-clamping isolated lysosomes, we previously found that lysosomal, but not PM-localized, TRPML1 is active with PI(3,5)P(2), a lysosome-specific PIP(2), as the underlying positive cofactor. Here we found that "silent" PM-localized TRPML1 could be activated by depleting PI(4,5)P(2) levels and/or by adding PI(3,5)P(2) to inside-out membrane patches. Unlike PM channels, surface-expressed TRPML1 underwent a unique and characteristic run-up upon patch excision, and was potently inhibited by a low micromolar concentration of PI(4,5)P(2). Conversely, depletion of PI(4,5)P(2) by either depolarization-induced activation or chemically induced translocation of 5'-phosphatase potentiated whole-cell TRPML1 currents. PI(3,5)P(2) activation and PI(4,5)P(2) inhibition of TRPML1 were mediated by distinct basic amino acid residues in a common PIP(2)-interacting domain. Thus, PI(4,5)P(2) may serve as a negative cofactor for intracellular channels such as TRPML1. Based on these results, we propose that phosphoinositide regulation sets compartment-specific activity codes for membrane channels and transporters.

A Protective Strategy against Hyperinflammatory Responses Requiring the Nontranscriptional Actions of GPS2

The association between hyperinflammatory states and numerous diseases is widely recognized, but our understanding of the molecular strategies that have evolved to prevent uncontrolled activation of inflammatory responses remains incomplete. Here, we report a critical, nontranscriptional role of GPS2 as a guardian against hyperstimulation of the TNF-α-induced gene program. GPS2 cytoplasmic actions are required to specifically modulate RIP1 ubiquitylation and JNK activation by inhibiting TRAF2/Ubc13 enzymatic activity. In vivo relevance of GPS2 anti-inflammatory role is confirmed by inhibition of TNF-α target genes in macrophages and by improved insulin signaling in the adipose tissue of aP2-GPS2 transgenic mice. As the nontranscriptional role is complemented by GPS2 functioning as positive and negative cofactor for nuclear receptors, in vivo overexpression also results in elevated circulating level of Resistin and development of hepatic steatosis. Together, these studies define GPS2 as a molecular guardian required for precise control of inflammatory responses involved in immunity and homeostasis.

Unraveling the Dynamics of TBP-NC2 with Hidden Markov Modeling

One of the early steps in initiation of transcription is the binding of the TATA box Binding Protein (TBP) to a core-promoter TATA Box. After binding, the transcription complex is assembled in cooperation with our general transcription factors. The binding of TBP to DNA is also a prime target for regulating gene transcription and many cofactors can interact with TBP at this initial stage.In a recent publication (Schluesche et al), we showed that the binding of the Negative Cofactor 2 (NC2) leads to dynamic behavior of the TBP-NC2 complex along the DNA using single-pair Forster Resonance Energy Transfer (spFRET). To extract detailed kinetic information from the single molecule experiments, we have adapted a Hidden Markov Model to analyze the spFRET data collected using a EMCCD camera. With add of the HMM analysis, it is possible to determine how many states are available which transitions are possible, providing new insights into the origins of these different states.We performed measurements on four DNA strands, two containing the AdML promoter with identical labeling but different DNA lengths and two containing the H2B promoter with labels at two different positions on the DNA. Results of the AdML promoter showed the high reproducibility of the analysis method. Four FRET states were clearly observable. For the H2B promoter, many more states were observable in the HMM analysis showing a high complexity of dynamics but yet very similar patterns as observed for the AdML promoter.Schluesche et al 2007 NSMB 14:1196-1201

Basal core promoters control the equilibrium between negative cofactor 2 and preinitiation complexes in human cells.

Genome-wide mapping of the human TFIIB and NC2 transcription factor binding sites reveals insights into the formation of the pre-initiation complex.

The Yeast RNA Polymerase II-associated Factor Iwr1p Is Involved in the Basal and Regulated Transcription of Specific Genes

RNA polymerase II (RNA pol II) is a multisubunit enzyme that requires many auxiliary factors for its activity. Over the years, these factors have been identified using both biochemical and genetic approaches. Recently, the systematic characterization of protein complexes by tandem affinity purification and mass spectroscopy has allowed the identification of new components of well established complexes, including the RNA pol II holoenzyme. Using this approach, a novel and highly conserved factor, Iwr1p, that physically interacts with most of the RNA pol II subunits has been described in yeast. Here we show that Iwr1p genetically interacts with components of the basal transcription machinery and plays a role in both basal and regulated transcription. We report that mutation of the IWR1 gene is able to bypass the otherwise essential requirement for the transcriptional regulator negative cofactor 2, which occurs with different components of the basal transcription machinery, including TFIIA and subunits of the mediator complex. Deletion of the IWR1 gene leads to an altered expression of specific genes, including phosphate-responsive genes and SUC2. Our results show that Iwr1p is a nucleocytoplasmic shuttling protein and suggest that Iwr1p acts early in the formation of the pre-initiation complex by mediating the interaction of certain activators with the basal transcription apparatus.