Gpn2 and Rba50 Directly Participate in the Assembly of the Rpb3 Subcomplex in the Biogenesis of RNA Polymerase II

Subcellular localization shapes the fate of RNA polymerase III

RNA polymerase III (Pol III) plays a vital role in transcription and as a viral-DNA sensor, but how it is assembled and distributed within cells remains poorly understood. Here, we show that Pol III is assembled with chaperones in the cytoplasm and forms transcription-dependent protein clusters upon transport into the nucleus. The largest subunit (RPC1) depletion through an auxin-inducible degron leads to rapid degradation and disassembly of Pol III complex in the nucleus and cytoplasm, respectively. This generates a pool of partially assembled Pol III intermediates, which can be rapidly mobilized into the nucleus upon the restoration of RPC1. Our study highlights the critical role of subcellular localization in determining Pol III's fate and provides insight into the dynamic regulation of nuclear Pol III levels and the origin of cytoplasmic Pol III complexes involved in mediating viral immunity.

Rtr1 is required for Rpb1-Rpb2 assembly of RNAPII and prevents their cytoplasmic clump formation

RNA polymerase II (RNAPII) is an essential machinery for catalyzing mRNA synthesis and controlling cell fate in eukaryotes. Although the structure and function of RNAPII have been relatively defined, the molecular mechanism of its assembly process is not clear. The identification and functional analysis of assembly factors will provide new understanding to transcription regulation. In this study, we identify that RTR1, a known transcription regulator, is a new multicopy genetic suppressor of mutants of assembly factors Gpn3, Gpn2, and Rba50. We demonstrate that Rtr1 is directly required to assemble the two largest subunits of RNAPII by coordinating with Gpn3 and Npa3. Deletion of RTR1 leads to cytoplasmic clumping of RNAPII subunit and multiple copies of RTR1 can inhibit the formation of cytoplasmic clump of RNAPII subunit in gpn3-9 mutant, indicating a new layer function of Rtr1 in checking proper assembly of RNAPII. In addition, we find that disrupted activity of Rtr1 phosphatase does not trigger the formation of cytoplasmic clump of RNAPII subunit in a catalytically inactive mutant of RTR1. Based on these results, we conclude that Rtr1 cooperates with Gpn3 and Npa3 to assemble RNAPII core.

A remodeled RNA polymerase II complex catalyzing viroid RNA-templated transcription

Viroids, a fascinating group of plant pathogens, are subviral agents composed of single-stranded circular noncoding RNAs. It is well-known that nuclear-replicating viroids exploit host DNA-dependent RNA polymerase II (Pol II) activity for transcription from circular RNA genome to minus-strand intermediates, a classic example illustrating the intrinsic RNA-dependent RNA polymerase activity of Pol II. The mechanism for Pol II to accept single-stranded RNAs as templates remains poorly understood. Here, we reconstituted a robust in vitro transcription system and demonstrated that Pol II also accepts minus-strand viroid RNA template to generate plus-strand RNAs. Further, we purified the Pol II complex on RNA templates for nano-liquid chromatography-tandem mass spectrometry analysis and identified a remodeled Pol II missing Rpb4, Rpb5, Rpb6, Rpb7, and Rpb9, contrasting to the canonical 12-subunit Pol II or the 10-subunit Pol II core on DNA templates. Interestingly, the absence of Rpb9, which is responsible for Pol II fidelity, explains the higher mutation rate of viroids in comparison to cellular transcripts. This remodeled Pol II is active for transcription with the aid of TFIIIA-7ZF and appears not to require other canonical general transcription factors (such as TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, and TFIIS), suggesting a distinct mechanism/machinery for viroid RNA-templated transcription. Transcription elongation factors, such as FACT complex, PAF1 complex, and SPT6, were also absent in the reconstituted transcription complex. Further analyses of the critical zinc finger domains in TFIIIA-7ZF revealed the first three zinc finger domains pivotal for RNA template binding. Collectively, our data illustrated a distinct organization of Pol II complex on viroid RNA templates, providing new insights into viroid replication, the evolution of transcription machinery, as well as the mechanism of RNA-templated transcription.

Development of a Methodology to Adapt an Equilibrium Buffer/Wash Applied to the Purification of hGPN2 Protein Expressed in Escherichia coli Using an IMAC Immobilized Metal Affinity Chromatography System

Protein purification is a complex and non-standardized process; the fact that proteins have different structural types making it difficult to create a standard methodology to obtain them in a pure, soluble, and homogeneous form. The present study shows the selective development of a buffer suitable for proteins of interest that allows high concentrations of hGPN2 protein to be obtained with low polydispersion and high homogeneity and purity. By taking the different reagents used in the construction of different buffers as a basis and performing purifications using different additives in different concentrations to determine the optimal amounts, the developed process helps to minimize the bonds, maintain solubility, release the proteins present in inclusion bodies, and provide an adequate environment for obtaining high concentrations of pure protein. GPN proteins are of unknown function, have not been purified in high concentrations, and have been found as part of the RNA polymerase assembly; if they are not expressed, the cell dies, and overexpression of certain GPN proteins has been linked to decreased survival in patients with invasive ductal carcinoma breast cancer types ER+ and HER2+. The results of the present study show that the use of the buffer developed for recombinant hGPN2 protein expressed in Escherichia coli could be manipulated in order to isolate the protein in a totally pure form and without the use of protease inhibitor tablets. The resulting homogeneity and low polydispersion was corroborated by studies carried out using dynamic dispersion analysis. Thanks to these properties, it can be used for crystallography or structural genomics studies.

Synthetic negative genome screen of the GPN-loop GTPase NPA3 in Saccharomyces cerevisiae

The GPN-loop GTPase Npa3 is encoded by an essential gene in the yeast Saccharomyces cerevisiae. Npa3 plays a critical role in the assembly and nuclear accumulation of RNA polymerase II (RNAPII), a function that may explain its essentiality. Genetic interactions describe the extent to which a mutation in a particular gene affects a specific phenotype when co-occurring with an alteration in a second gene. Discovering synthetic negative genetic interactions has long been used as a tool to delineate the functional relatedness between pairs of genes participating in common or compensatory biological pathways. Previously, our group showed that nuclear targeting and transcriptional activity of RNAPII were unaffected in cells expressing exclusively a C-terminal truncated mutant version of Npa3 (npa3∆C) lacking the last 106 residues naturally absent from the single GPN protein in Archaea, but universally conserved in all Npa3 orthologs of eukaryotes. To gain insight into novel cellular functions for Npa3, we performed here a genome-wide Synthetic Genetic Array (SGA) study coupled to bulk fluorescence monitoring to identify negative genetic interactions of NPA3 by crossing an npa3∆C strain with a 4,389 nonessential gene-deletion collection. This genetic screen revealed previously unknown synthetic negative interactions between NPA3 and 15 genes. Our results revealed that the Npa3 C-terminal tail extension regulates the participation of this essential GTPase in previously unknown biological processes related to mitochondrial homeostasis and ribosome biogenesis.

Npa3-Gpn3 cooperate to assemble RNA polymerase II and prevent clump of its subunits in the cytoplasm

RNA polymerase II (RNAPII) is an essential machinery in eukaryotes that catalyzes mRNA synthesis and controls cell fate. Although the structure and function of RNAPII are relatively well defined, the molecular mechanism of its assembly process is poorly understood. Three members of GPN-loop GTPase family Npa3/Gpn1, Gpn2, and Gpn3 participate in the biogenesis of RNAPII with non-redundant roles. In this study, we demonstrate that Gpn3 and Npa3 directly participate in the assembly of the two largest subunits during biogenesis of RNAPII. When Gpn3 is defective, assembly of RNAPII is disrupted, leading to cytoplasmic foci of RNAPII subunits. Long-term assembly factor defects will lead to the accumulation of different kind of newly synthesized RNAPII subunits in the cytoplasm to form foci, and this can be prevented by recovery of the defective assembly factor. Cytoplasmic foci of RNAPII subunits in mutants of these assembly factors reveals a new cellular rescue response named the 'RNAPII assembly stress response'.

Rba50 and Gpn2 recruit the second largest subunits for the assembly of RNA polymerase II and III

Although remarkable progress has been made toward understanding the structures of eukaryotic RNA polymerases, the pathways and factors that facilitate their assembly remain unresolved. Essential proteins Rba50 and Gpn2 are required for Rpb3 subcomplex assembly, but whether they participate in subsequent assembly steps is unknown. Herein, we performed comprehensive genetic screens to explore Rba50 function. We identified two unique extragenic rba50-3-suppressing mutations that map to genes encoding the Rba50-interacting protein Gpn2, and Rpb2, the second largest subunit of RNAPII. Both gpn2-R347S and rpb2-V1171G variants bypass Rpb1 cytoplasmic arrest and temperature-sensitive growth defects of the rba50-3 mutant. GPN2 and RPB2 were also identified as novel multicopy suppressors of the rba50-3 mutant. Rapid depletion of Rba50 affected Rpb3-Rpb2 association during RNAPII assembly. Importantly, we demonstrated that Gpn2 facilitates the association of Rba50 and Rpb2. Our results imply that Rba50-Gpn2 interaction is essential for Rpb2 recruitment during RNAPII assembly following Rpb3 subcomplex assembly. Furthermore, the Rba50-Gpn2 complex appears to play a similar role in the assembly of RNAPIII. We therefore propose a model in which Rba50 interacts with Gpn2 and thereby promotes loading of the second largest subunit of RNAP II and III onto the previously assembled subcomplex.

The Association of Rpb4 with RNA Polymerase II Depends on CTD Ser5P Phosphatase Rtr1 and Influences mRNA Decay in Saccharomyces cerevisiae

Rtr1 is an RNA polymerase II (RNA pol II) CTD-phosphatase that influences gene expression during the transition from transcription initiation to elongation and during transcription termination. Rtr1 interacts with the RNA pol II and this interaction depends on the phosphorylation state of the CTD of Rpb1, which may influence dissociation of the heterodimer Rpb4/7 during transcription. In addition, Rtr1 was proposed as an RNA pol II import factor in RNA pol II biogenesis and participates in mRNA decay by autoregulating the turnover of its own mRNA. Our work shows that Rtr1 acts in RNA pol II assembly by mediating the Rpb4/7 association with the rest of the enzyme. RTR1 deletion alters RNA pol II assembly and increases the amount of RNA pol II associated with the chromatin that lacks Rpb4, decreasing Rpb4-mRNA imprinting and, consequently, increasing mRNA stability. Thus, Rtr1 interplays RNA pol II biogenesis and mRNA decay regulation. Our data also indicate that Rtr1 mediates mRNA decay regulation more broadly than previously proposed by cooperating with Rpb4. Interestingly, our data include new layers in the mechanisms of gene regulation and in the crosstalk between mRNA synthesis and decay by demonstrating how the association of Rpb4/7 to the RNA pol II influences mRNA decay.

A nuclear proteome localization screen reveals the exquisite specificity of Gpn2 in RNA polymerase biogenesis

The GPN proteins are a conserved family of GTP-binding proteins that are involved in the assembly and subsequent import of RNA polymerase II and III. In this study, we sought to ascertain the specificity of yeast GPN2 for RNA polymerases by screening the localization of a collection of 1350 GFP-tagged nuclear proteins in WT or GPN2 mutant cells. We found that the strongest mislocalization occurred for RNA polymerase II and III subunits and only a handful of other RNAPII associated proteins were altered in GPN2 mutant cells. Our screen identified Ess1, an Rpb1 C-terminal domain (CTD) prolyl isomerase, as mislocalized in GPN2 mutants. Building on this observation we tested for effects of mutations in other factors which regulate Rpb1-CTD phosphorylation status. This uncovered significant changes in nuclear-cytoplasmic distribution of Rpb1-GFP in strains with disrupted RNA polymerase CTD kinases or phosphatases. Overall, this screen shows the exquisite specificity of GPN2 for RNA polymerase transport, and reveals a previously unappreciated role for CTD modification in RNAPII nuclear localization.

Integrating genetics, physiology and morphology to study desert adaptation in a lizard species

Integration of multiple approaches is key to understand the evolutionary processes of local adaptation and speciation. Reptiles have successfully colonized desert environments, that is, extreme and arid conditions that constitute a strong selective pressure on organisms. Here, we studied genomic, physiological and morphological variations of the lizard Liolaemus fuscus to detect adaptations to the Atacama Desert. By comparing populations of L. fuscus inhabiting the Atacama Desert with populations from the Mediterranean forests from central Chile, we aimed at characterizing features related to desert adaptation. We combined ddRAD sequencing with physiological (evaporative water loss, metabolic rate and selected temperature) and morphological (linear and geometric morphometrics) measurements. We integrated the genomic and phenotypic data using redundancy analyses. Results showed strong genetic divergence, along with a high number of fixed loci between desert and forest populations. Analyses detected 110 fixed and 30 outlier loci located within genes, from which 43 were in coding regions, and 12 presented non-synonymous mutations. The candidate genes were associated with cellular membrane and development. Desert lizards presented lower evaporative water loss than those from the forest. Morphological data showed that desert lizards had smaller body size, different allometry, larger eyeballs and more dorsoventrally compressed heads. Our results suggest incipient speciation between desert and forest populations. The adaptive signal must be cautiously interpreted since genetic drift could also contribute to the divergence pattern. Nonetheless, we propose water and resource availability, and changes in habitat structure, as the most relevant challenges for desert reptiles. This study provides insights of the mechanisms that allow speciation as well as desert adaptation in reptiles at multiple levels, and highlights the benefit of integrating independent evidence.

Biogenesis of RNA Polymerases in Yeast

Eukaryotic RNA polymerases (RNA pols) transcriptional processes have been extensively investigated, and the structural analysis of eukaryotic RNA pols has been explored. However, the global assembly and biogenesis of these heteromultimeric complexes have been narrowly studied. Despite nuclear transcription being carried out by three RNA polymerases in eukaryotes (five in plants) with specificity in the synthesis of different RNA types, the biogenesis process has been proposed to be similar, at least for RNA pol II, to that of bacteria, which contains only one RNA pol. The formation of three different interacting subassembly complexes to conform the complete enzyme in the cytoplasm, prior to its nuclear import, has been assumed. In Saccharomyces cerevisiae, recent studies have examined in depth the biogenesis of RNA polymerases by characterizing some elements involved in the assembly of these multisubunit complexes, some of which are conserved in humans. This study reviews the latest studies governing the mechanisms and proteins described as being involved in the biogenesis of RNA polymerases in yeast.

RNA polymerase II associated proteins regulate stomatal development through direct interaction with stomatal transcription factors in Arabidopsis thaliana

RNA polymerase II (Pol II) associated proteins (RPAPs) have been ascribed diverse functions at the cellular level; however, their roles in developmental processes in yeasts, animals and plants are very poorly understood. Through screening for interactors of NRPB3, which encodes the third largest subunit of Pol II, we identified RIMA, the orthologue of mammalian RPAP2. A combination of genetic and biochemical assays revealed the role of RIMA and other RPAPs in stomatal development in Arabidopsis thaliana. We show that RIMA is involved in nuclear import of NRPB3 and other Pol II subunits, and is essential for restraining division and for establishing cell identity in the stomatal cell lineage. Moreover, plant RPAPs IYO/RPAP1 and QQT1/RPAP4, which interact with RIMA, are also crucial for stomatal development. Importantly, RIMA and QQT1 bind physically to stomatal transcription factors SPEECHLESS, MUTE, FAMA and SCREAMs. The RIMA-QQT1-IYO complex could work together with key stomatal transcription factors and Pol II to drive cell fate transitions in the stomatal cell lineage. Direct interactions with stomatal transcription factors provide a novel mechanism by which RPAP proteins may control differentiation of cell types and tissues in eukaryotes.

High-Copy Yeast Library Construction and High-Copy Rescue Genetic Screen in Saccharomyces cerevisiae

High-copy rescue genetic screening is a powerful strategy for the identification of suppression genetic interactions in the model eukaryotic organism Saccharomyces cerevisiae (budding yeast). The strain carrying the mutant allele of interest is transformed with a genomic library cloned in a high-copy plasmid. Each clone carries a genomic fragment insertion of around 10 kb, typically containing one to three complete genes under their own promoters. The high-copy vector favors the accumulation of high levels of the corresponding protein, aimed at suppressing the mutant phenotype. Typically, high-copy genetic screens select for viable clones under conditions restrictive or lethal for the query mutant strain. Here, we describe in detail the procedure to generate a high-copy genomic library and a protocol for rescue genetic screening and identification of the suppressor clones.

Dual Repressive Function by Cip1, a Budding Yeast Analog of p21, in Cell-Cycle START Regulation

Cip1, a newly identified yeast analog of p21, is a Cln3-CDK inhibitor that negatively regulates cell-cycle START. However, its function remains poorly understood. In this study, we found that deletion of CLN3 did not result in bypass of G1-phase arrest caused by Cip1 overexpression. Cip1 depletion in cln3-null mutants significantly advanced the timing of Cln2 expression, supporting the idea that Cip1 represses START in a Cln3-independent manner. We set to search for novel Cip1 interacting proteins and found that Ccr4, a known START regulator, and its associated factor Caf120, interact with Cip1. Ccr4-Caf120 acts redundantly with Cdk1-Cln3 to inhibit Whi5-mediated regulation of START. This interaction was conserved between human Ccr4 and p21. In addition, deletion of WHI5 robustly suppressed G1-phase arrest caused by Cip1 overexpression. We conclude that Cip1 negatively regulates START by acting as a dual repressor of Ccr4 in parallel with Cln3.

Setosphaeria turcica ATR turns off appressorium-mediated maize infection and triggers melanin-involved self-protection in response to genotoxic stress

Eukaryotic organisms activate conserved signalling networks to maintain genomic stability in response to DNA genotoxic stresses. However, the coordination of this response pathway in fungal pathogens remains largely unknown. In the present study, we investigated the mechanism by which the northern corn leaf blight pathogen Setosphaeria turcica controls maize infection and activates self-protection pathways in response to DNA genotoxic insults. Appressorium-mediated maize infection by S. turcica was blocked by the S-phase checkpoint. This repression was dependent on the checkpoint central kinase Ataxia Telangiectasia and Rad3 related (ATR), as inhibition of ATR activity or knockdown of the ATR gene recovered appressorium formation in the presence of genotoxic reagents. ATR promoted melanin biosynthesis in S. turcica as a defence response to stress. The melanin biosynthesis genes StPKS and StLac2 were induced by the ATR-mediated S-phase checkpoint. The responses to DNA genotoxic stress were conserved in a wide range of phytopathogenic fungi, including Cochliobolus heterostrophus, Cochliobolus carbonum, Alternaria solani, and Alternaria kikuchiana, which are known causal agents for plant diseases. We propose that in response to genotoxic stress, phytopathogenic fungi including S. turcica activate an ATR-dependent pathway to suppress appressorium-mediated infection and induce melanin-related self-protection in addition to conserved responses in eukaryotes.

Gpn3 Is Essential for Cell Proliferation of Breast Cancer Cells Independent of Their Malignancy Degree

Successful therapies for patients with breast cancer often lose their initial effectiveness. Thus, identifying new molecular targets is a constant goal in the fight against breast cancer. Gpn3 is a protein required for RNA polymerase II nuclear targeting in both yeast and human cells. We investigated here the effect of suppressing Gpn3 expression on cell proliferation in a progression series of isogenic cell lines derived from the nontumorigenic MCF-10A breast cells that recapitulate different stages of breast carcinogenesis. Gpn3 protein levels were comparable in all malignant derivatives of the nontumorigenic MCF-10A cells. shRNA-mediated inhibition of Gpn3 expression markedly decreased cell proliferation in all MCF-10A sublines. A fraction of the largest RNA polymerase II subunit Rpb1 was retained in the cytoplasm, but most Rpb1 remained nuclear after suppressing Gpn3 in all cell lines studied. Long-term proliferation experiments in cells with suppressed Gpn3 expression resulted in the eventual loss of all isogenic cell lines but MCF-10CA1d.cl1. In MCF-10CA1d.cl1 cells, Gpn3 knockdown reduced the proliferation of breast cancer stem cells as evaluated by mammosphere assays. After the identification that Gpn3 plays a key role in cell proliferation in mammary epithelial cells independent of the degree of transformation, we also analyzed the importance of Gpn3 in other human breast cancer cell lines from different subtypes. Gpn3 was also required for cell proliferation and nuclear translocation of RNA polymerase II in such cellular models. Altogether, our results show that Gpn3 is essential for breast cancer cell proliferation regardless of the transformation level, indicating that Gpn3 could be considered a molecular target for the development of new antiproliferative therapies. Importantly, our analysis of public data revealed that Gpn3 overexpression was associated with a significant decrease in overall survival in patients with estrogen receptor-positive and Human epidermal growth factor receptor 2 (HER2+) breast cancer, supporting our proposal that targeting Gpn3 could potentially benefit patients with breast cancer.

Identification of Domains and Factors Involved in MINIYO Nuclear Import

The transition of stem cells from self-renewal into differentiation is tightly regulated to assure proper development of the organism. Arabidopsis MINIYO (IYO) and its mammalian orthologue RNA polymerase II associated protein 1 (RPAP1) are essential factors for initiating stem cell differentiation in plants and animals. Moreover, there is evidence suggesting that the translocation of IYO and RPAP1 from the cytosol into the nucleus functions as a molecular switch to initiate this cell fate transition. Identifying the determinants of IYO subcellular localization would allow testing if, indeed, nuclear IYO migration triggers cell differentiation and could provide tools to control this crucial developmental transition. Through transient and stable expression assays in Nicotiana benthamiana and Arabidopsis thaliana, we demonstrate that IYO contains two nuclear localization signals (NLSs), located at the N- and C-terminus of the protein, which mediate the interaction with the NLS-receptor IMPA4 and the import of the protein into the nucleus. Interestingly, IYO also interacts with GPN GTPases, which are involved in selective nuclear import of RNA polymerase II. This interaction is prevented when the G1 motif in GPN1 is mutated, suggesting that IYO binds specifically to the nucleotide-bound form of GPN1. In contrast, deleting the NLSs in IYO does not prevent the interaction with GPN1, but it interferes with import of GPN1 into the nucleus, indicating that IYO and GPN1 are co-transported as a complex that requires the IYO NLSs for import. This work unveils key domains and factors involved in IYO nuclear import, which may prove instrumental to determine how IYO and RPAP1 control stem cell differentiation.

An optimized yeast display strategy for efficient scFv antibody selection using ribosomal skipping system and thermo resistant yeast

OBJECTIVES

Establish a method to restrict unexpected fragments including stop codons in scFv library and generate a thermo resistant strain for screening of thermal stable scFv sequences.

RESULTS

Here, we have constructed a T2A-Leu2 system for selection of yeast surface display libraries that blocks amplification of "stop codon" plasmids within the library, thereby increasing the quality of the library and efficiency of the selection screen. Also, we generated a temperature-resistant yeast strain, TR1, and validated its combined use with T2A-Leu2 for efficient screening. Thus, we developed a general approach for a fast and efficient screening of scFv libraries using a ribosomal skipping system and thermo-resistant yeast.

CONCLUSIONS

The method highlights the utility of the T2A-Leu2-based ribosomal skipping strategy for increasing the quality of the input library for selection, along with an optimized selection protocol based on thermo-resistant yeast cells.