TFIIB-related factors in RNA polymerase I transcription

Analyzing the role of ferroptosis in ribosome-related bone marrow failure disorders: From pathophysiology to potential pharmacological exploitation

Within the last decade, the scientific community has witnessed the importance of ferroptosis as a novel cascade of molecular events leading to cellular decisions of death distinct from apoptosis and other known forms of cell death. Notably, such non- apoptotic and iron-dependent regulated cell death has been found to be intricately linked to several physiological processes as well as to the pathogenesis of various diseases. To this end, recent data support the notion that a potential molecular connection between ferroptosis and inherited bone marrow failure (IBMF) in individuals with ribosomopathies may exist. In this review, we suggest that in ribosome-related IBMFs the identified mutations in ribosomal proteins lead to changes in the ribosome composition of the hematopoietic progenitors, changes that seem to affect ribosomal function, thus enhancing the expression of some mRNAs subgroups while reducing the expression of others. These events lead to an imbalance inside the cell as some molecular pathways are promoted while others are inhibited. This disturbance is accompanied by ROS production and lipid peroxidation, while an additional finding in most of them is iron accumulation. Once lipid peroxidation and iron accumulation are the two main characteristics of ferroptosis, it is possible that this mechanism plays a key role in the manifestation of IBMF in this type of disease. If this molecular mechanism is further confirmed, new pharmacological targets such as ferroptosis inhibitors that are already exploited for the treatment of other diseases, could be utilized to improve the treatment of ribosomopathies.

A UTP3-dependent nucleolar translocation pathway facilitates pre-rRNA 5'ETS processing

The ribosome small subunit (SSU) is assembled by the SSU processome which contains approximately 70 non-ribosomal protein factors. Whilst the biochemical mechanisms of the SSU processome in 18S rRNA processing and maturation have been extensively studied, how SSU processome components enter the nucleolus has yet to be systematically investigated. Here, in examining the nucleolar localization of 50 human SSU processome components, we found that UTP3, together with another 24 proteins, enter the nucleolus autonomously. For the remaining 25 proteins we found that UTP3/SAS10 assists the nucleolar localization of five proteins (MPP10, UTP25, EMG1 and the two UTP-B components UTP12 and UTP13), likely through its interaction with nuclear importin α. This 'ferrying' function of UTP3 was then confirmed as conserved in the zebrafish. We also found that knockdown of human UTP3 impairs cleavage at the A0-site while loss-of-function of either utp3/sas10 or utp13/tbl3 in zebrafish causes the accumulation of aberrantly processed 5'ETS products, which highlights the crucial role of UTP3 in mediating 5'ETS processing. Mechanistically, we found that UTP3 facilitates the degradation of processed 5'ETS by recruiting the RNA exosome component EXOSC10 to the nucleolus. These findings lay the groundwork for studying the mechanism of cytoplasm-to-nucleolus trafficking of SSU processome components.

Synthesis of the ribosomal RNA precursor in human cells: mechanisms, factors and regulation

The ribosomal RNA precursor (pre-rRNA) comprises three of the four ribosomal RNAs and is synthesized by RNA polymerase (Pol) I. Here, we describe the mechanisms of Pol I transcription in human cells with a focus on recent insights gained from structure-function analyses. The comparison of Pol I-specific structural and functional features with those of other Pols and with the excessively studied yeast system distinguishes organism-specific from general traits. We explain the organization of the genomic rDNA loci in human cells, describe the Pol I transcription cycle regarding structural changes in the enzyme and the roles of human Pol I subunits, and depict human rDNA transcription factors and their function on a mechanistic level. We disentangle information gained by direct investigation from what had apparently been deduced from studies of the yeast enzymes. Finally, we provide information about how Pol I mutations may contribute to developmental diseases, and why Pol I is a target for new cancer treatment strategies, since increased rRNA synthesis was correlated with rapidly expanding cell populations.

Pseudocercospora fijiensis Conidial Germination Is Dominated by Pathogenicity Factors and Effectors

Conidia play a vital role in the survival and rapid spread of fungi. Many biological processes of conidia, such as adhesion, signal transduction, the regulation of oxidative stress, and autophagy, have been well studied. In contrast, the contribution of pathogenicity factors during the development of conidia in fungal phytopathogens has been poorly investigated. To date, few reports have centered on the pathogenicity functions of fungal phytopathogen conidia. Pseudocercospora fijiensis is a hemibiotrophic fungus and the causal agent of the black Sigatoka disease in bananas and plantains. Here, a conidial transcriptome of P. fijiensis was characterized computationally. Carbohydrates, amino acids, and lipid metabolisms presented the highest number of annotations in Gene Ontology. Common conidial functions were found, but interestingly, pathogenicity factors and effectors were also identified. Upon analysis of the resulting proteins against the Pathogen-Host Interaction (PHI) database, 754 hits were identified. WideEffHunter and EffHunter effector predictors identified 618 effectors, 265 of them were shared with the PHI database. A total of 1107 conidial functions devoted to pathogenesis were found after our analysis. Regarding the conidial effectorome, it was found to comprise 40 canonical and 578 non-canonical effectors. Effectorome characterization revealed that RXLR, LysM, and Y/F/WxC are the largest effector families in the P. fijiensis conidial effectorome. Gene Ontology classification suggests that they are involved in many biological processes and metabolisms, expanding our current knowledge of fungal effectors.

Ribosome biogenesis factors-from names to functions

The assembly of ribosomal subunits is a highly orchestrated process that involves a huge cohort of accessory factors. Most eukaryotic ribosome biogenesis factors were first identified by genetic screens and proteomic approaches of pre-ribosomal particles in Saccharomyces cerevisiae. Later, research on human ribosome synthesis not only demonstrated that the requirement for many of these factors is conserved in evolution, but also revealed the involvement of additional players, reflecting a more complex assembly pathway in mammalian cells. Yet, it remained a challenge for the field to assign a function to many of the identified factors and to reveal their molecular mode of action. Over the past decade, structural, biochemical, and cellular studies have largely filled this gap in knowledge and led to a detailed understanding of the molecular role that many of the players have during the stepwise process of ribosome maturation. Such detailed knowledge of the function of ribosome biogenesis factors will be key to further understand and better treat diseases linked to disturbed ribosome assembly, including ribosomopathies, as well as different types of cancer.

Mechanism of RNA polymerase I selection by transcription factor UAF

Preribosomal RNA is selectively transcribed by RNA polymerase (Pol) I in eukaryotes. The yeast transcription factor upstream activating factor (UAF) represses Pol II transcription and mediates Pol I preinitiation complex (PIC) formation at the 35S ribosomal RNA gene. To visualize the molecular intermediates toward PIC formation, we determined the structure of UAF in complex with native promoter DNA and transcription factor TATA-box-binding protein (TBP). We found that UAF recognizes DNA using a hexameric histone-like scaffold with markedly different interactions compared with the nucleosome and the histone-fold-rich transcription factor IID (TFIID). In parallel, UAF positions TBP for Core Factor binding, which leads to Pol I recruitment, while sequestering it from DNA and Pol II/III-specific transcription factors. Our work thus reveals the structural basis of RNA Pol selection by a transcription factor.

Structure and function of the poxvirus transcription machinery

Members of the Poxviridae family are large double-stranded DNA viruses that replicate exclusively in the cytoplasm of their hosts. This goes in hand with a high level of independence from the host cell, which supports transcription and replication events only in the nucleus or in DNA-containing organelles. Consequently, virus specific, rather than cellular enzymes mediate most processes involving DNA replication and mRNA synthesis. Recent technological advances allowed a detailed functional and structural investigation of the transcription machinery of the prototypic poxvirus vaccinia. The DNA-dependent RNA polymerase (RNAP) at its core displays distinct similarities to eukaryotic RNAPs. Strong idiosyncrasies, however, are apparent for viral factors that are associated with the viral RNAP during mRNA production. We expect that future studies will unravel more key aspects of poxvirus gene expression, helping also the understanding of nuclear transcription mechanisms.

Deep (Meta)genomics and (Meta)transcriptome Analyses of Fungal and Bacteria Consortia From Aircraft Tanks and Kerosene Identify Key Genes in Fuel and Tank Corrosion

Microbial contamination of fuels, associated with a wide variety of bacteria and fungi, leads to decreased product quality and can compromise equipment performance by biofouling or microbiologically influenced corrosion. Detection and quantification of microorganisms are critical in monitoring fuel systems for an early detection of microbial contaminations. To address these challenges, we have analyzed six metagenomes, one transcriptome, and more than 1,200 fluid and swab samples taken from fuel tanks or kerosene. Our deep metagenome sequencing and binning approaches in combination with RNA-seq data and qPCR methods implied a metabolic symbiosis between fungi and bacteria. The most abundant bacteria were affiliated with α-, β-, and γ-Proteobacteria and the filamentous fungi Amorphotheca. We identified a high number of genes, which are related to kerosene degradation and biofilm formation. Surprisingly, a large number of genes coded enzymes involved in polymer degradation and potential bio-corrosion processes. Thereby, the transcriptionally most active microorganisms were affiliated with the genera Methylobacteria, Pseudomonas, Kocuria, Amorpotheka, Aspergillus, Fusarium, and Penicillium. Many not yet cultured bacteria and fungi appeared to contribute to the biofilm transcriptional activities. The largest numbers of transcripts were observed for dehydrogenase, oxygenase, and exopolysaccharide production, attachment and pili/flagella-associated proteins, efflux pumps, and secretion systems as well as lipase and esterase activity.

Evolution of Regulated Transcription

The genomes of all organisms abound with various cis-regulatory elements, which control gene activity. Transcriptional enhancers are a key group of such elements in eukaryotes and are DNA regions that form physical contacts with gene promoters and precisely orchestrate gene expression programs. Here, we follow gradual evolution of this regulatory system and discuss its features in different organisms. In eubacteria, an enhancer-like element is often a single regulatory element, is usually proximal to the core promoter, and is occupied by one or a few activators. Activation of gene expression in archaea is accompanied by the recruitment of an activator to several enhancer-like sites in the upstream promoter region. In eukaryotes, activation of expression is accompanied by the recruitment of activators to multiple enhancers, which may be distant from the core promoter, and the activators act through coactivators. The role of the general DNA architecture in transcription control increases in evolution. As a whole, it can be seen that enhancers of multicellular eukaryotes evolved from the corresponding prototypic enhancer-like regulatory elements with the gradually increasing genome size of organisms.

DNA binding preferences of S. cerevisiae RNA polymerase I Core Factor reveal a preference for the GC-minor groove and a conserved binding mechanism

In Saccharomyces cerevisiae, Core Factor (CF) is a key evolutionarily conserved transcription initiation factor that helps recruit RNA polymerase I (Pol I) to the ribosomal DNA (rDNA) promoter. Upregulated Pol I transcription has been linked to many cancers, and targeting Pol I is an attractive and emerging anti-cancer strategy. Using yeast as a model system, we characterized how CF binds to the Pol I promoter by electrophoretic mobility shift assays (EMSA). Synthetic DNA competitors along with anti-tumor drugs and nucleic acid stains that act as DNA groove blockers were used to discover the binding preference of yeast CF. Our results show that CF employs a unique binding mechanism where it prefers the GC-rich minor groove within the rDNA promoter. In addition, we show that yeast CF is able to bind to the human rDNA promoter sequence that is divergent in DNA sequence and demonstrate CF sensitivity to the human specific Pol I inhibitor, CX-5461. Finally, we show that the human Core Promoter Element (CPE) can functionally replace the yeast Core Element (CE) in vivo when aligned by conserved DNA structural features rather than DNA sequence. Together, these findings suggest that the yeast CF and the human ortholog Selectivity Factor 1 (SL1) use an evolutionarily conserved, structure-based mechanism to target DNA. Their shared mechanism may offer a new avenue in using yeast to explore current and future Pol I anti-cancer compounds.

Structure and Function of RNA Polymerases and the Transcription Machineries

In all living organisms, the flow of genetic information is a two-step process: first DNA is transcribed into RNA, which is subsequently used as template for protein synthesis during translation. In bacteria, archaea and eukaryotes, transcription is carried out by multi-subunit RNA polymerases (RNAPs) sharing a conserved architecture of the RNAP core. RNAPs catalyse the highly accurate polymerisation of RNA from NTP building blocks, utilising DNA as template, being assisted by transcription factors during the initiation, elongation and termination phase of transcription. The complexity of this highly dynamic process is reflected in the intricate network of protein-protein and protein-nucleic acid interactions in transcription complexes and the substantial conformational changes of the RNAP as it progresses through the transcription cycle.In this chapter, we will first briefly describe the early work that led to the discovery of multisubunit RNAPs. We will then discuss the three-dimensional organisation of RNAPs from the bacterial, archaeal and eukaryotic domains of life, highlighting the conserved nature, but also the domain-specific features of the transcriptional apparatus. Another section will focus on transcription factors and their role in regulating the RNA polymerase throughout the different phases of the transcription cycle. This includes a discussion of the molecular mechanisms and dynamic events that govern transcription initiation, elongation and termination.

Distinct Mechanisms of Transcription Initiation by RNA Polymerases I and II

RNA polymerases I and II (Pol I and Pol II) are the eukaryotic enzymes that catalyze DNA-dependent synthesis of ribosomal RNA and messenger RNA, respectively. Recent work shows that the transcribing forms of both enzymes are similar and the fundamental mechanisms of RNA chain elongation are conserved. However, the mechanisms of transcription initiation and its regulation differ between Pol I and Pol II. Recent structural studies of Pol I complexes with transcription initiation factors provided insights into how the polymerase recognizes its specific promoter DNA, how it may open DNA, and how initiation may be regulated. Comparison with the well-studied Pol II initiation system reveals a distinct architecture of the initiation complex and visualizes promoter- and gene-class-specific aspects of transcription initiation. On the basis of new structural studies, we derive a model of the Pol I transcription cycle and provide a molecular movie of Pol I transcription that can be used for teaching.

Reconstitution of RNA Polymerase I Upstream Activating Factor and the Roles of Histones H3 and H4 in Complex Assembly

RNA polymerase I (Pol I) transcription in Saccharomyces cerevisiae requires four separate factors that recruit Pol I to the promoter to form a pre-initiation complex. Upstream Activating Factor (UAF) is one of two multi-subunit complexes that regulate pre-initiation complex formation by binding to the ribosomal DNA promoter and by stimulating recruitment of downstream Pol I factors. UAF is composed of Rrn9, Rrn5, Rrn10, Uaf30, and histones H3 and H4. We developed a recombinant Escherichia coli-based system to coexpress and purify transcriptionally active UAF complex and to investigate the importance of each subunit in complex formation. We found that no single subunit is required for UAF assembly, including histones H3 and H4. We also demonstrate that histone H3 is able to interact with each UAF-specific subunit, and show that there are at least two copies of histone H3 and one copy of H4 present in the complex. Together, our results provide a new model suggesting that UAF contains a hybrid H3-H4 tetramer-like subcomplex.

Breaking the mold: structures of the RNA polymerase I transcription complex reveal a new path for initiation

While structures of the RNA polymerase (Pol) II initiation complex have been resolved and extensively studied, the Pol I initiation complex remained elusive. Here, we review the recent structural analyses of the yeast Pol I transcription initiation complex that reveal several unique and unexpected Pol I-specific properties.

Structural insights into transcription initiation by yeast RNA polymerase I

In eukaryotic cells, RNA polymerase I (Pol I) synthesizes precursor ribosomal RNA (pre‐rRNA) that is subsequently processed into mature rRNA. To initiate transcription, Pol I requires the assembly of a multi‐subunit pre‐initiation complex (PIC) at the ribosomal RNA promoter. In yeast, the minimal PIC includes Pol I, the transcription factor Rrn3, and Core Factor (CF) composed of subunits Rrn6, Rrn7, and Rrn11. Here, we present the cryo‐EM structure of the 18‐subunit yeast Pol I PIC bound to a transcription scaffold. The cryo‐EM map reveals an unexpected arrangement of the DNA and CF subunits relative to Pol I. The upstream DNA is positioned differently than in any previous structures of the Pol II PIC. Furthermore, the TFIIB‐related subunit Rrn7 also occupies a different location compared to the Pol II PIC although it uses similar interfaces as TFIIB to contact DNA. Our results show that although general features of eukaryotic transcription initiation are conserved, Pol I and Pol II use them differently in their respective transcription initiation complexes.

Structural mechanism of ATP-independent transcription initiation by RNA polymerase I

Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a structure of Saccharomyces cerevisiae Pol I-CF-DNA to 3.8 Å resolution using single-particle cryo-electron microscopy. The structure reveals a bipartite architecture of Core Factor and its recognition of the promoter from -27 to -16. Core Factor's intrinsic mobility correlates well with different conformational states of the Pol I cleft, in addition to the stabilization of either Rrn7 N-terminal domain near Pol I wall or the tandem winged helix domain of A49 at a partially overlapping location. Comparison of the three states in this study with the Pol II system suggests that a ratchet motion of the Core Factor-DNA sub-complex at upstream facilitates promoter melting in an ATP-independent manner, distinct from a DNA translocase actively threading the downstream DNA in the Pol II PIC.

Identification of Conidiogenesis-Associated Genes in Colletotrichum gloeosporioides by Agrobacterium tumefaciens-Mediated Transformation

The Colletotrichum gloeosporioides is one of the most significant pathogens leading to huge economic losses. To infect plants and cause disease dissemination, the fungus elaborates to produce asexual spores called conidia, which are long-lived and highly resistant to environmental stresses. Here, we report a large-scale, systematic genome-wide screening of conidiogenesis-associated genes via conidiation assays, and high-efficiency TAIL-PCRs. Of 10,210 independent transformants tested, 59 mutants exhibited significant variation in conidial production. The T-DNA right flanking sequences of 11 conidiation-related transformants were further identified, and the obtained sequences were aligned to the genome sequence to uncover the novel loci of sporogenesis. When considering together, this study provided a large number of conidial production-variation mutants and the conidiation-related genes, which will be a valuable resource for characterizing the molecular mechanisms of conidial formation in the fungus.

Specialization versus conservation: How Pol I and Pol III use the conserved architecture of the pre-initiation complex for specialized transcription

Here, we discuss the overall architecture of the RNA polymerase I (Pol I) and III (Pol III) core enzymes and their associated general transcription factors in the context of models of the Pol I and Pol III pre-initiation complexes, thereby highlighting potential functional adaptations of the Pol I and Pol III enzymes to their respective transcription tasks. Several new insights demonstrate the great degree of specialization of each of the eukaryotic RNA polymerases that is only beginning to be revealed as the structural and functional characterization of all eukaryotic RNA polymerases and their pre-initiation complexes progresses.

Dynein Light Chain LC8 Is Required for RNA Polymerase I-Mediated Transcription in Trypanosoma brucei, Facilitating Assembly and Promoter Binding of Class I Transcription Factor A

Dynein light chain LC8 is highly conserved among eukaryotes and has both dynein-dependent and dynein-independent functions. Interestingly, LC8 was identified as a subunit of the class I transcription factor A (CITFA), which is essential for transcription by RNA polymerase I (Pol I) in the parasite Trypanosoma brucei. Given that LC8 has never been identified with a basal transcription factor and that T. brucei relies on RNA Pol I for expressing the variant surface glycoprotein (VSG), the key protein in antigenic variation, we investigated the CITFA-specific role of LC8. Depletion of LC8 from mammalian-infective bloodstream trypanosomes affected cell cycle progression, reduced the abundances of rRNA and VSG mRNA, and resulted in rapid cell death. Sedimentation analysis, coimmunoprecipitation of recombinant proteins, and bioinformatic analysis revealed an LC8 binding site near the N terminus of the subunit CITFA2. Mutation of this site prevented the formation of a CITFA2-LC8 heterotetramer and, in vivo, was lethal, affecting assembly of a functional CITFA complex. Gel shift assays and UV cross-linking experiments identified CITFA2 as a promoter-binding CITFA subunit. Accordingly, silencing of LC8 or CITFA2 resulted in a loss of CITFA from RNA Pol I promoters. Hence, we discovered an LC8 interaction that, unprecedentedly, has a basal function in transcription.

The σ enigma: bacterial σ factors, archaeal TFB and eukaryotic TFIIB are homologs

Structural comparisons of initiating RNA polymerase complexes and structure-based amino acid sequence alignments of general transcription initiation factors (eukaryotic TFIIB, archaeal TFB and bacterial σ factors) show that these proteins are homologs. TFIIB and TFB each have two-five-helix cyclin-like repeats (CLRs) that include a C-terminal helix-turn-helix (HTH) motif (CLR/HTH domains). Four homologous HTH motifs are present in bacterial σ factors that are relics of CLR/HTH domains. Sequence similarities clarify models for σ factor and TFB/TFIIB evolution and function and suggest models for promoter evolution. Commitment to alternate modes for transcription initiation appears to be a major driver of the divergence of bacteria and archaea.

Fluorescently labeled recombinant RNAP system to probe archaeal transcription initiation

The transcriptional apparatus is one of the most complex cellular machineries and in order to fully appreciate the behavior of these protein-nucleic acid assemblies one has to understand the molecular details of the system. In addition to classical biochemical and structural studies, fluorescence-based techniques turned out as an important--and sometimes the critical--tool to obtain information about the molecular mechanisms of transcription. Fluorescence is not only a multi-modal parameter that can report on molecular interactions, environment and oligomerization status. Measured on the single-molecule level it also informs about the heterogeneity of the system and gives access to distances and distance changes in the molecular relevant nanometer regime. A pre-requisite for fluorescence-based measurements is the site-specific incorporation of one or multiple fluorescent dyes. In this respect, the archaeal transcription system is ideally suited as it is available in a fully recombinant form and thus allows for site-specific modification via sophisticated labeling schemes. The application of fluorescence based approaches to the archaeal transcription apparatus changed our understanding of the molecular mechanisms and dynamics that drive archaeal transcription and unraveled the architecture of transcriptional complexes not amenable to structural interrogation.

Nuclear PI3K signaling in cell growth and tumorigenesis

The PI3K/Akt signaling pathway is a major driving force in a variety of cellular functions. Dysregulation of this pathway has been implicated in many human diseases including cancer. While the activity of the cytoplasmic PI3K/Akt pathway has been extensively studied, the functions of these molecules and their effector proteins within the nucleus are poorly understood. Harboring key cellular processes such as DNA replication and repair as well as nascent messenger RNA transcription, the nucleus provides a unique compartmental environment for protein–protein and protein–DNA/RNA interactions required for cell survival, growth, and proliferation. Here we summarize recent advances made toward elucidating the nuclear PI3K/Akt signaling cascade and its key components within the nucleus as they pertain to cell growth and tumorigenesis. This review covers the spatial and temporal localization of the major nuclear kinases having PI3K activities and the counteracting phosphatases as well as the role of nuclear PI3K/Akt signaling in mRNA processing and exportation, DNA replication and repair, ribosome biogenesis, cell survival, and tumorigenesis.

Architecture of the Saccharomyces cerevisiae RNA polymerase I Core Factor complex

Core Factor (CF) is a conserved RNA polymerase (Pol) I general transcription factor and is comprised of Rrn6, Rrn11, and the TFIIB-related subunit Rrn7. CF binds TBP, Pol I, and the regulatory factors Rrn3 and UAF. We used chemical crosslinking-mass spectrometry (CXMS) to determine the molecular architecture of CF and its interactions with TBP. The CF subunits assemble through an interconnected network of interactions between five structural domains that are conserved in orthologous subunits of the human Pol I factor SL1. The crosslinking-derived model was validated through a series of genetic and biochemical assays. Our combined results show the architecture of CF and the functions of the CF subunits in assembly of the complex. We extend these findings to model how CF assembles into the Pol I preinitiation complex, providing new insight into the roles of CF, TBP and Rrn3.

RNA polymerase III accurately initiates transcription from RNA polymerase II promoters in vitro

In eukaryotes, there are three major RNA polymerases (Pol) in the nucleus, which are commonly described as transcribing non-overlapping subsets of genes. Structural studies have highlighted a conserved core shared among all three transcription systems. Initiation of human Pol III from TATA box-containing Pol II promoters under conditions with impaired Pol II transcription activity have been described previously. RNA polymerase III and Pol II were found to co-localize at the promoters of the c-myc gene and the RPPH1 sRNA in vivo. Here, I report that Pol III can, like Pol II, initiate transcription from most tested Pol II core promoters when assayed with crude human nuclear extracts (HSK, SNF, or Dignam). Both polymerases often initiate from the same transcription start site, and depend on a TATA box or AT-rich region but not the downstream promoter element (DPE) or the motif ten element (MTE). Moderate (∼2-fold) changes in the ratio of DNA template to nuclear extract were sufficient to change Pol II-mediated transcription to a mixture of Pol II- and Pol III-, or to a solely Pol III-dependent initiation of transcription from Pol II promoters. Polymerase specificity is thus not fixed but a variable that depends on the properties of the promoter and the transcription conditions. These findings provide functional evidence for a close similarity between the Pol II and Pol III transcription complexes, and additionally explain previous controversies in the literature.

Mutations on the DNA binding surface of TBP discriminate between yeast TATA and TATA-less gene transcription

Most RNA polymerase (Pol) II promoters lack a TATA element, yet nearly all Pol II transcription requires TATA binding protein (TBP). While the TBP-TATA interaction is critical for transcription at TATA-containing promoters, it has been unclear whether TBP sequence-specific DNA contacts are required for transcription at TATA-less genes. Transcription factor IID (TFIID), the TBP-containing coactivator that functions at most TATA-less genes, recognizes short sequence-specific promoter elements in metazoans, but analogous promoter elements have not been identified in Saccharomyces cerevisiae. We generated a set of mutations in the yeast TBP DNA binding surface and found that most support growth of yeast. Both in vivo and in vitro, many of these mutations are specifically defective for transcription of two TATA-containing genes with only minor defects in transcription of two TATA-less, TFIID-dependent genes. TBP binds several TATA-less promoters with apparent high affinity, but our results suggest that this binding is not important for transcription activity. Our results are consistent with the model that sequence-specific TBP-DNA contacts are not important at yeast TATA-less genes and suggest that other general transcription factors or coactivator subunits are responsible for recognition of TATA-less promoters. Our results also explain why yeast TBP derivatives defective for TATA binding appear defective in activated transcription.

More pieces to the puzzle: recent structural insights into class II transcription initiation

Class II transcription initiation is a highly regulated process and requires the assembly of a pre-initiation complex (PIC) containing DNA template, RNA polymerase II (RNAPII), general transcription factors (GTFs) TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH and Mediator. RNAPII, TFIID, TFIIH and Mediator are large multiprotein complexes, each containing 10 and more subunits. Altogether, the PIC is made up of about 60 polypeptides with a combined molecular weight of close to 4MDa. Recent structural studies of key PIC components have significantly advanced our understanding of transcription initiation. TFIID was shown to bind promoter DNA in a reorganized state. The architecture of a core-TFIID complex was elucidated. Crystal structures of the TATA-binding protein (TBP) bound to TBP-associated factor 1 (TAF1), RNAPII-TFIIB complexes and the Mediator head module were solved. The overall architectures of large PIC assemblies from human and yeast have been determined by electron microscopy (EM). Here we review these latest structural insights into the architecture and assembly of the PIC, which reveal exciting new mechanistic details of transcription initiation.

Structural insights into transcription initiation by RNA polymerase II

Transcriptional regulation is one of the most important steps in control of cell identity, growth, differentiation, and development. Many signaling pathways controlling these processes ultimately target the core transcription machinery that, for protein coding genes, consists of RNA polymerase II (Pol II) and the general transcription factors (GTFs). New studies on the structure and mechanism of the core assembly and how it interfaces with promoter DNA and coactivator complexes have given tremendous insight into early steps in the initiation process, genome-wide binding, and mechanisms conserved for all nuclear and archaeal Pols. Here, we review recent developments in dissecting the architecture of the Pol II core machinery with a focus on early and regulated steps in transcription initiation.

Emergence and expansion of TFIIB-like factors in the plant kingdom

Many gene families in higher plants have expanded in number, giving rise to diverse protein paralogs with specialized biochemical functions. For instance, plant general transcription factors such as TFIIB have expanded in number and in some cases perform specialized transcriptional functions in the plant cell. To date, no comprehensive genome-wide identification of the TFIIB gene family has been conducted in the plant kingdom. To determine the extent of TFIIB expansion in plants, I used the remote homology program HHPred to search for TFIIB homologs in the plant kingdom and performed a comprehensive analysis of eukaryotic TFIIB gene families. I discovered that higher plants encode more than 10 different TFIIB-like proteins. In particular, Arabidopsis thaliana encodes 14 different TFIIB-like proteins and predicted domain architectures of the newly identified TFIIB-like proteins revealed that they have unique modular domain structures that are divergent in sequence and size. Phylogenetic analysis of selected eukaryotic organisms showed that most life forms encode three major TFIIB subfamilies that include TFIIB, Brf, Rrn7/TAF1B/MEE12 subfamilies, while all plants and some algae species encode one or two additional TFIIB-related protein subfamilies. A subset of A. thaliana GTFs have also expanded in number, indicating that GTF diversification and expansion is a general phenomenon in higher plants. Together, these findings were used to generate a model for the evolutionary history of TFIIB-like proteins in eukaryotes.