Mechanisms coordinating ribosomal protein gene transcription in response to stress

Stm1 regulates Ifh1 activity revealing crosstalk between ribosome biogenesis and ribosome dormancy

Nutrient abundance boosts ribosome biogenesis, whereas ribosome dormancy factors limit ribosome degradation upon starvation. The equilibrium between the two pathways governs cell growth. In this study, we identified suppressor of Tom1 (Stm1) as a molecular link between ribosome protection and biogenesis in Saccharomyces cerevisiae. While Stm1 was previously described as a dormancy factor, we show that it activates Ifh1, a transcriptional activator of ribosomal protein genes. Stm1 transiently localizes to the nucleolus, where it interacts with pre-ribosomes and directly binds RNA and Ifh1 through its C-terminal intrinsically disordered region (IDR). Although the IDR is dispensable for ribosome protection, its loss compromises cell growth. The IDR is phosphorylated upon nutrient starvation, which disrupts its interaction with Ifh1. Our findings reveal a molecular pathway sensing and adjusting ribosome abundance in response to nutrient availability, reinforcing the relevance of regulated ribosome homeostasis in physiology and disease.

How the concentric organization of the nucleolus and chromatin ensures accuracy of ribosome biogenesis and drives transport

The biogenetic transport of ribosomal subunit precursors must be conducted with precision to ensure production of functional ribosomes. With a focus on ribosome biogenesis in higher eukaryotic cells, we here discuss the following: (1) the concentric organization of the phases/subcompartments of the nucleus-including chromatin, (2) why the nucleolus reorganizes when ribosomal RNA synthesis is inhibited, and (3) the mechanism responsible for vectorial transport of particulate subunit intermediates between subcompartments. We call attention to evidence that (1) nucleolar proteins can access the entire volume of the nucleus, (2) that the packaging of rDNA is a key determinant of topology, (3) the constancy of contacts between subcompartments, and the likely importance of a Brownian ratchet for imparting both directionality and quality control upon transport. Transport appears to depend on "self-immersion," whereby the surfaces of particulate intermediates successively interact with components of the surrounding milieux, each of which may be thought of as a distinct solvent. The result is a vectorial and ordered process.

A two-step regulatory mechanism dynamically controls histone H3 acetylation by SAGA complex at growth-related promoters

Acetylation of histone H3 at residue K9 (H3K9ac) is a dynamically regulated mark associated with transcriptionally active promoters in eukaryotes. However, our understanding of the relationship between H3K9ac and gene expression remains mostly correlative. In this study, we identify a large suite of growth-related (GR) genes in yeast that undergo a particularly strong down-regulation of both transcription and promoter-associated H3K9ac upon stress, and delineate the roles of transcriptional activators (TAs), repressors, SAGA (Spt-Ada-Gcn5 acetyltransferase) histone acetyltransferase, and RNA-polymerase II in this response. We demonstrate that H3K9 acetylation states are orchestrated by a two-step mechanism driven by the dynamic binding of transcriptional repressors (TRs) and activators, that is independent of transcription. In response to stress, promoter release of TAs at GR genes is a prerequisite for rapid reduction of H3K9ac, whereas binding of TRs is required to establish a hypo-acetylated, strongly repressed state.

Suppressed Protein Translation Caused by MSP-8 Deficiency Determines Fungal Multidrug Resistance with Fitness Cost

Antifungal resistance, particularly the rise of multidrug-resistance strains, poses a significant public health threat. In this study, the study identifies a novel multidrug-resistance gene, msp-8, encoding a helicase, through experimental evolution with Neurospora crassa as a model. Deletion of msp-8 conferred multidrug resistance in N. crassa, Aspergillus fumigatus, and Fusarium verticillioides. However, the transcript levels of genes encoding known drug targets or efflux pumps remain unaltered with msp-8 deletion. Interestingly, MSP-8 interacted with ribosomal proteins, and this mutant displays compromised ribosomal function, causing translational disturbance. Notably, inhibition of protein translation enhances resistance to azoles, amphotericin B, and polyoxin B. Furthermore, MSP-8 deficiency or inhibition of translation reduces intracellular ketoconazole accumulation and membrane-bound amphotericin B content, directly causing antifungal resistance. Additionaly, MSP-8 deficiency induces cell wall remodeling, and decreases intracellular ROS levels, further contributing to resistance. The findings reveal a novel multidrug resistance mechanism independent of changes in drug target or efflux pump, while MSP-8 deficiency suppresses protein translation, thereby facilitating the development of resistance with fitness cost. This study provides the first evidence that MSP-8 participates in protein translation and that translation suppression can cause multidrug resistance in fungi, offering new insights into resistance mechanisms in clinical and environmental fungal strains.

Minimal Perturbation Analysis of mRNA Degradation Rates with Tet-Off and RT-qPCR

Messenger RNA stability is an important variable in gene expression and its dynamics. High stability ensures a constant level of synthesized protein, whereas mRNA instability can be critical for regulatory processes in which protein production needs to be stopped, such as development, inflammation, or adaptation to stress. Accurate measurements of RNA degradation rates are important for understanding how RNA features and RNA binding proteins affect the posttranscriptional life of an mRNA. As an alternative to global transcriptional inhibition methods, the use of a Tet-off repressible promoter has the advantage that cells are minimally perturbed by the addition of doxycyclin during the assay. We illustrate the use of a reporter mRNA expressed from a plasmid in Saccharomyces cerevisiae cells, but similar methods can be applied to other regulated promoters, on plasmids or by genome editing, and in other organisms. RNA levels are measured by reverse transcription followed by quantitative PCR. An exponential decay law is then used to estimate how well the measurements follow this expected trend for the simplest possible mechanism of RNA degradation, where the decay is proportional to the amount of RNA present at any given time.

Surviving the heat: the role of macromolecular assemblies in promoting cellular shutdown

During heat shock (HS), cells orchestrate a gene expression program that promotes the synthesis of HS proteins (HSPs) while simultaneously repressing the synthesis of other proteins, including growth-promoting housekeeping proteins. Recent studies show that mRNAs encoding housekeeping proteins, along with associated processing factors, form macromolecular assemblies during HS. These assemblies inhibit transcription, nuclear export, and translation of housekeeping mRNAs, and coincide with structural rearrangements in proteins. These findings reveal a mechanism linking temperature sensitivity through structural rearrangements and macromolecular assembly to the 'shut down' of housekeeping protein synthesis. This review delves into recent findings in yeast, with a focus on macromolecular assembly, offering perspectives into mechanisms that regulate gene expression during HS and how these processes may be conserved.

Anchor-Away: Efficient, Conditional Depletion of Nuclear Proteins in Saccharomyces cerevisiae

For functional studies of proteins in cells, effective tools that trigger rapid and efficient inactivation of the proteins are indispensable. The anchor-away (AA) system is designed to deplete nuclear-localized proteins through cellular relocation. The target protein is sequestered by an anchor receptor protein from the nucleus to the cytoplasm. The depletion is achieved through the formation of a stable complex that is solely driven by the addition of rapamycin, between the FRB domain of human mTOR and the FKBP12-binding domain of the FRP protein. The target protein and the receptor protein are fused through genetic recombination with the FRB and FKBP12 domains, respectively, to mediate the interaction. The export of the nuclear protein of interest is executed by the receptor protein, i.e., ribosomal protein RPL13A, which is transiently imported into the nucleus and then exported to the cytoplasm within the pre-ribosome. The proteins of interest can be depleted within minutes although the depleting conditions need to be optimized. AA is a valuable tool to help dissect the biological functions of nuclear proteins, especially ones that are essential for cell viability. In this chapter, we describe the steps to construct the necessary strains and several biochemical and functional experiments to confirm the functional abrogation of target proteins by AA.

The transcription factor FgSfp1 orchestrates mycotoxin deoxynivalenol biosynthesis in Fusarium graminearum

Fusarium graminearum (F. graminearum) and its derivative mycotoxin deoxynivalenol (DON) are highly concerned with food safety and sustainability worldwide. Although several transcription factors (TFs) had been elucidated, molecular mechanism participates in DON biosynthesis regulation remains largely unrevealed. Here, we first characterized a zinc finger-contained TF in F. graminearum, FgSfp1, which is indispensable for DON production since its depletion resulting in a 95.4% DON yielding reduction. Interestingly, contrast to previous knowledge, all TRI-cluster genes were abnormally upregulated in ΔFgSfp1 while Tri proteins abundance rationally decreased simultaneously. Further evidence show FgSfp1 could coordinate genetic translation pace by manipulating ribosomal biogenesis process. Specifically, FgSfp1-depletion leads to ribosome biogenesis assembly factor (RiBi) expression attenuation along with DON precursor acetyl-CoA synthase reduction since FgSfp1 actively interacts with RNA 2'-O-methylation enzyme FgNop1 revealed by Bi-FC. It subsequently influences mRNA translation pace. In conclusion, we elucidated that the FgSfp1 orchestrates DON biosynthesis via participating RNA posttranscriptional modification for ribosomal RNA maturation, offering insights into the DON biosynthesis regulation. Ultimately, this TF might be a key regulator for DON contamination control in the whole food chain.

Ribosome Structural Changes Dynamically Affect Ribosome Function

Ribosomes were known to be multicomponent complexes as early as the 1960s. Nonetheless, the prevailing view for decades considered active ribosomes to be a monolithic population, in which all ribosomes are identical in composition and function. This implied that ribosomes themselves did not actively contribute to the regulation of protein synthesis. In this perspective, I review evidence for a different model, based on results showing that ribosomes can harbor different types of ribosomal RNA (rRNA) and ribosomal proteins (r-proteins) and, furthermore, need not contain a complete set of r-proteins. I also summarize recent results favoring the notion that such distinct types of ribosomes have different affinities for specific messenger RNAs and may execute the translation process differently. Thus, ribosomes should be considered active contributors to the regulation of protein synthesis.

Decoding ribosome complexity: role of ribosomal proteins in cancer and disease

The ribosome is a remarkably complex machinery, at the interface with diverse cellular functions and processes. Evolutionarily conserved, yet intricately regulated, ribosomes play pivotal roles in decoding genetic information into the synthesis of proteins and in the generation of biomass critical for cellular physiological functions. Recent insights have revealed the existence of ribosome heterogeneity at multiple levels. Such heterogeneity extends to cancer, where aberrant ribosome biogenesis and function contribute to oncogenesis. This led to the emergence of the concept of 'onco-ribosomes', specific ribosomal variants with altered structural dynamics, contributing to cancer initiation and progression. Ribosomal proteins (RPs) are involved in many of these alterations, acting as critical factors for the translational reprogramming of cancer cells. In this review article, we highlight the roles of RPs in ribosome biogenesis, how mutations in RPs and their paralogues reshape the translational landscape, driving clonal evolution and therapeutic resistance. Furthermore, we present recent evidence providing new insights into post-translational modifications of RPs, such as ubiquitylation, UFMylation and phosphorylation, and how they regulate ribosome recycling, translational fidelity and cellular stress responses. Understanding the intricate interplay between ribosome complexity, heterogeneity and RP-mediated regulatory mechanisms in pathology offers profound insights into cancer biology and unveils novel therapeutic avenues targeting the translational machinery in cancer.

Hmo1: A versatile member of the high mobility group box family of chromosomal architecture proteins

Eukaryotic chromatin consisting of nucleosomes connected by linker DNA is organized into higher order structures, which is facilitated by linker histone H1. Formation of chromatin compacts and protects the genome, but also hinders DNA transactions. Cells have evolved mechanisms to modify/remodel chromatin resulting in chromatin states suitable for genome functions. The high mobility group box (HMGB) proteins are non-histone chromatin architectural factors characterized by one or more HMGB motifs that bind DNA in a sequence nonspecific fashion. They play a major role in chromatin dynamics. The Saccharomyces cerevisiae (yeast hereafter) HMGB protein Hmo1 contains two HMGB motifs. However, unlike a canonical HMGB protein that has an acidic C-terminus, Hmo1 ends with a lysine rich, basic, C-terminus, resembling linker histone H1. Hmo1 exhibits characteristics of both HMGB proteins and linker histones in its multiple functions. For instance, Hmo1 promotes transcription by RNA polymerases I and II like canonical HMGB proteins but makes chromatin more compact/stable like linker histones. Recent studies have demonstrated that Hmo1 destabilizes/disrupts nucleosome similarly as other HMGB proteins in vitro and acts to maintain a common topological architecture of genes in yeast genome. This minireview reviews the functions of Hmo1 and the underlying mechanisms, highlighting recent discoveries.

Integrated organismal responses induced by projected levels of CO2 and temperature exposures in the early life stages of lake sturgeon

Atmospheric CO2 and temperature are rising concurrently, and may have profound impacts on the transcriptional, physiological and behavioural responses of aquatic organisms. Further, spring snowmelt may cause transient increases of pCO2 in many freshwater systems. We examined the behavioural, physiological and transcriptomic responses of an ancient fish, the lake sturgeon (Acipenser fulvescens) to projected levels of warming and pCO2 during its most vulnerable period of life, the first year. Specifically, larval fish were raised in either low (16°C) or high (22°C) temperature, and/or low (1000 μatm) or high (2500 μatm) pCO2 in a crossed experimental design over approximately 8 months. Following overwintering, lake sturgeon were exposed to a transient increase in pCO2 of 10,000 μatm, simulating a spring melt based on data in freshwater systems. Transcriptional analyses revealed potential connections to otolith formation and reduced growth in fish exposed to high pCO2 and temperature in combination. Network analyses of differential gene expression revealed different biological processes among the different treatments on the edges of transcriptional networks. Na+/K+-ATPase activity increased in fish not exposed to elevated pCO2 during development, and mRNA abundance of the β subunit was most strongly predictive of enzyme activity. Behavioural assays revealed a decrease in total activity following an acute CO2 exposure. These results demonstrate compensatory and compounding mechanisms of pCO2 and warming dependent on developmental conditions in lake sturgeon. Conserved elements of the cellular stress response across all organisms provide key information for how other freshwater organisms may respond to future climate change.

Yeast Crf1p is an activator with different roles in regulation of target genes

Under stress conditions, ribosome biogenesis is downregulated. This process requires that expression of ribosomal RNA, ribosomal protein, and ribosome biogenesis genes be controlled in a coordinated fashion. The mechanistic Target of Rapamycin Complex 1 (mTORC1) participates in sensing unfavorable conditions to effect the requisite change in gene expression. In Saccharomyces cerevisiae, downregulation of ribosomal protein genes involves dissociation of the activator Ifh1p in a process that depends on Utp22p, a protein that also functions in pre-rRNA processing. Ifh1p has a paralog, Crf1p, which was implicated in communicating mTORC1 inhibition and hence was perceived as a repressor. We focus here on two ribosomal biogenesis genes, encoding Utp22p and the high mobility group protein Hmo1p, both of which are required for communication of mTORC1 inhibition to target genes. Crf1p functions as an activator on these genes as evidenced by reduced mRNA abundance and RNA polymerase II occupancy in a crf1Δ strain. Inhibition of mTORC1 has distinct effects on expression of HMO1 and UTP22; for example, on UTP22, but not on HMO1, the presence of Crf1p promotes the stable depletion of Ifh1p. Our data suggest that Crf1p functions as a weak activator, and that it may be required to prevent re-binding of Ifh1p to some gene promoters after mTORC1 inhibition in situations when Ifh1p is available. We propose that the inclusion of genes encoding proteins required for mTORC1-mediated downregulation of ribosomal protein genes in the same regulatory circuit as the ribosomal protein genes serves to optimize transcriptional responses during mTORC1 inhibition.

Fission Yeast TORC1 Promotes Cell Proliferation through Sfp1, a Transcription Factor Involved in Ribosome Biogenesis

Target of rapamycin complex 1 (TORC1) is activated in response to nutrient availability and growth factors, promoting cellular anabolism and proliferation. To explore the mechanism of TORC1-mediated proliferation control, we performed a genetic screen in fission yeast and identified Sfp1, a zinc-finger transcription factor, as a multicopy suppressor of temperature-sensitive TORC1 mutants. Our observations suggest that TORC1 phosphorylates Sfp1 and protects Sfp1 from proteasomal degradation. Transcription analysis revealed that Sfp1 positively regulates genes involved in ribosome production together with two additional transcription factors, Ifh1/Crf1 and Fhl1. Ifh1 physically interacts with Fhl1, and the nuclear localization of Ifh1 is regulated in response to nutrient levels in a manner dependent on TORC1 and Sfp1. Taken together, our data suggest that the transcriptional regulation of the genes involved in ribosome biosynthesis by Sfp1, Ifh1, and Fhl1 is one of the key pathways through which nutrient-activated TORC1 promotes cell proliferation.

Single-cell RNA sequencing reveals sexual diversity in the human bladder and its prospective impacts on bladder cancer and urinary tract infection

BACKGROUND

Some bladder-related diseases, such as bladder urinary tract infection (UTI) and bladder cancer (BCa), have significant six differences in incidence and prognosis. However, the molecular mechanisms underlying these sex differences are still not fully understood. Understanding the sex-biased differences in gene expression in normal bladder cells can help resolve these problems.

METHODS

We first collected published single-cell RNA sequencing (scRNA-seq) data of normal human bladders from females and males to map the bladder transcriptomic landscape. Then, Gene Ontology (GO) analysis and gene set enrichment analysis (GSEA) were used to determine the significant pathways that changed in the specific cell populations. The Monocle2 package was performed to reconstruct the differentiation trajectories of fibroblasts. In addition, the scMetabolism package was used to analyze the metabolic activity at the single-cell level, and the SCENIC package was used to analyze the regulatory network.

RESULTS

In total, 27,437 cells passed stringent quality control, and eight main cell types in human bladder were identified according to classical markers. Sex-based differential gene expression profiles were mainly observed in human bladder urothelial cells, fibroblasts, B cells, and T cells. We found that urothelial cells in males demonstrated a higher growth rate. Moreover, female fibroblasts produced more extracellular matrix, including seven collagen genes that may mediate BCa progression. Furthermore, the results showed that B cells in female bladders exhibited more B-cell activated signals and a higher expression of immunoglobulin genes. We also found that T cells in female bladders exhibited more T-cell activated signals. These different biological functions and properties of these cell populations may correlate with sex differences in UTI and BCa, and result in different disease processes and outcomes.

CONCLUSIONS

Our study provides reasonable insights for further studies of sex-based physiological and pathological disparities in the human bladder, which will contribute to the understanding of epidemiological differences in UTI and BCa.

Transcription by the Three RNA Polymerases under the Control of the TOR Signaling Pathway in Saccharomyces cerevisiae

Ribosomes are the basis for protein production, whose biogenesis is essential for cells to drive growth and proliferation. Ribosome biogenesis is highly regulated in accordance with cellular energy status and stress signals. In eukaryotic cells, response to stress signals and the production of newly-synthesized ribosomes require elements to be transcribed by the three RNA polymerases (RNA pols). Thus, cells need the tight coordination of RNA pols to adjust adequate components production for ribosome biogenesis which depends on environmental cues. This complex coordination probably occurs through a signaling pathway that links nutrient availability with transcription. Several pieces of evidence strongly support that the Target of Rapamycin (TOR) pathway, conserved among eukaryotes, influences the transcription of RNA pols through different mechanisms to ensure proper ribosome components production. This review summarizes the connection between TOR and regulatory elements for the transcription of each RNA pol in the budding yeast Saccharomyces cerevisiae. It also focuses on how TOR regulates transcription depending on external cues. Finally, it discusses the simultaneous coordination of the three RNA pols through common factors regulated by TOR and summarizes the most important similarities and differences between S. cerevisiae and mammals.

Yeast Ribonucleotide Reductase Is a Direct Target of the Proteasome and Provides Hyper Resistance to the Carcinogen 4-NQO

Various external and internal factors damaging DNA constantly disrupt the stability of the genome. Cells use numerous dedicated DNA repair systems to detect damage and restore genomic integrity in a timely manner. Ribonucleotide reductase (RNR) is a key enzyme providing dNTPs for DNA repair. Molecular mechanisms of indirect regulation of yeast RNR activity are well understood, whereas little is known about its direct regulation. The study was aimed at elucidation of the proteasome-dependent mechanism of direct regulation of RNR subunits in Saccharomyces cerevisiae. Proteome analysis followed by Western blot, RT-PCR, and yeast plating analysis showed that upregulation of RNR by proteasome deregulation is associated with yeast hyper resistance to 4-nitroquinoline-1-oxide (4-NQO), a UV-mimetic DNA-damaging drug used in animal models to study oncogenesis. Inhibition of RNR or deletion of RNR regulatory proteins reverses the phenotype of yeast hyper resistance to 4-NQO. We have shown for the first time that the yeast Rnr1 subunit is a substrate of the proteasome, which suggests a common mechanism of RNR regulation in yeast and mammals.

Identification of reliable reference genes for gene expression studies in mouse models under microplastics stress

Microplastics (MPs) and nanoplastics (NPs) have been deemed to be newly emerged contaminants interfering with various physiological processes closely related with gene expression alteration. Reverse transcriptase quantitative real-time polymerase chain reaction (RT-qPCR) serves as a powerful tool to assess gene expression, however highly dependent on a reliable reference gene. Therefore, it is necessary to identify stable reference genes for gene expression study under MP or NP stress. We constructed a mouse model postexposure to polypropylene microplastics (PP-MPs) to assess PP-MPs bioaccumulation in kidney, evaluate the kidney pathological changes, and then explore potential reference genes via RT-qPCR. Although the hematoxylin-eosin staining showed no obvious damage in kidney tissues, we observed significant PP-MPs accumulation in kidney using Raman spectra analysis supported by spectral multivariate analysis. The expression of 19 candidate reference genes were examined, including the commonly used ones of β-actin, glyceraldehyde 3-phosphate dehydrogenase (Gapdh), Cytochrome c oxidase subunit 4I1 (Cox4i), Histocompatibility 13 (H13) and ribosomal protein. Their expression stability and reliability were assessed by the combination of four algorithms including geNorm, NormFinder, BestKeeper and Delta Cq. The geNorm analysis revealed that the top three genes with the lowest variability were Cox4il, Rps9 and Gapdh, whereas NormFinder results ranked Rps3, Cox4il and Rps18 as the top three ones. Rpl15, Cox4i1 and Rps3 were the most reliable reference genes in BestKeeper results, and Delta Cq proposed Rps3 and Cox4il as the stable genes. The overall ranking indicated by GMR value gave the five most stable reference genes (Cox4i1, Rps3, Rps9, Rps18 and Gapdh). Three genes associated with different biochemical processes (Atp5f1, Crebbp and Dele1) were chosen to verify the characterized reference genes using the least stable gene as a control, exhibiting different expression profiles and implying the essentiality to select the reliable reference genes. Our results documented the expression fluctuations of acknowledged reference gene (Ubc) and proposed a set of reliable reference genes for future studies of gene expression profiles in MP treated mouse models.

Targeting of Hmo1 to subcompartments of the budding yeast nucleolus

The nucleolus is a multilayered, membraneless organelle made up of liquidlike biogenesis compartments surrounding an array of ribosomal RNA genes (rDNA). Biogenesis factors accumulate in the outer compartments through RNA binding and phase separation promoted by intrinsically disordered protein regions. In contrast, the nucleolar localization of rDNA-binding proteins, which reside in the central chromatin compartment, is less well characterized. To gain mechanistic insight, we analyzed the localization, mitotic segregation, nucleic acid binding, and nuclear dynamics of the budding yeast rDNA-binding protein Hmo1. Deletion of the main DNA-binding domain, the HMG boxB, compromised Hmo1 transfer to daughter cells in mitosis and transcription-independent rDNA association but still allowed nucleolar localization. The C-terminal lysine-rich region turned out to be a combined nuclear and nucleolar localization sequence (NLS-NoLS). Its integrity was required for maximal enrichment and efficient retention of Hmo1 in the nucleolus and nucleolar localization of the ΔboxB construct. Moreover, the NLS-NoLS region was sufficient to promote nucleolar accumulation and bound nucleic acids in vitro with some preference for RNA. Bleaching experiments indicated mobility of Hmo1 inside the nucleolus but little exchange with the nucleoplasm. Thus, a bilayered targeting mechanism secures proper localization of Hmo1 to the nucleolus.

JAZF1: A metabolic actor subunit of the NuA4/TIP60 chromatin modifying complex

The multisubunit NuA4/TIP60 complex is a lysine acetyltransferase, chromatin modifying factor and gene co-activator involved in diverse biological processes. The past decade has seen a growing appreciation for its role as a metabolic effector and modulator. However, molecular insights are scarce and often contradictory, underscoring the need for further mechanistic investigation. A particularly exciting route emerged with the recent identification of a novel subunit, JAZF1, which has been extensively linked to metabolic homeostasis. This review summarizes the major findings implicating NuA4/TIP60 in metabolism, especially in light of JAZF1 as part of the complex.

Performing in spite of starvation: How Saccharomyces cerevisiae maintains robust growth when facing famine zones in industrial bioreactors

In fed-batch operated industrial bioreactors, glucose-limited feeding is commonly applied for optimal control of cell growth and product formation. Still, microbial cells such as yeasts and bacteria are frequently exposed to glucose starvation conditions in poorly mixed zones or far away from the feedstock inlet point. Despite its commonness, studies mimicking related stimuli are still underrepresented in scale-up/scale-down considerations. This may surprise as the transition from glucose limitation to starvation has the potential to provoke regulatory responses with negative consequences for production performance. In order to shed more light, we performed gene-expression analysis of Saccharomyces cerevisiae grown in intermittently fed chemostat cultures to study the effect of limitation-starvation transitions. The resulting glucose concentration gradient was representative for the commercial scale and compelled cells to tolerate about 76 s with sub-optimal substrate supply. Special attention was paid to the adaptation status of the population by discriminating between first time and repeated entry into the starvation regime. Unprepared cells reacted with a transiently reduced growth rate governed by the general stress response. Yeasts adapted to the dynamic environment by increasing internal growth capacities at the cost of rising maintenance demands by 2.7%. Evidence was found that multiple protein kinase A (PKA) and Snf1-mediated regulatory circuits were initiated and ramped down still keeping the cells in an adapted trade-off between growth optimization and down-regulation of stress response. From this finding, primary engineering guidelines are deduced to optimize both the production host's genetic background and the design of scale-down experiments.

Sen1 is a key regulator of transcription-driven conflicts

Cellular homeostasis requires the coordination of several machineries concurrently engaged in the DNA. Wide-spread transcription can interfere with other processes, and transcription-replication conflicts (TRCs) threaten genome stability. The conserved Sen1 helicase not only terminates non-coding transcription but also interacts with the replisome and reportedly resolves genotoxic R-loops. Sen1 prevents genomic instability, but how this relates to its molecular functions remains unclear. We generated high-resolution, genome-wide maps of transcription-dependent conflicts and R-loops using a Sen1 mutant that has lost interaction with the replisome but is termination proficient. We show that, under physiological conditions, Sen1 removes RNA polymerase II at TRCs within genes and the rDNA and at sites of transcription-transcription conflicts, thus qualifying as a "key regulator of conflicts." We demonstrate that genomic stability is affected by Sen1 mutation only when in addition to its role at the replisome, the termination of non-coding transcription or R-loop removal are additionally compromised.

Ribosome biogenesis and the cellular energy economy

Cell growth relies upon the ability to produce new proteins, which requires energy and chemical precursors, and an adequate supply of the molecular machines for protein synthesis - ribosomes. Although not widely appreciated, ribosomes are remarkably abundant in all cells. For example, in a rapidly growing yeast cell there are ∼2-4 x 10⁵ ribosomes, produced and exported to the cytoplasm at a rate of ∼2,000-4,000 per minute, with ribosomal proteins making up ∼50% of total cellular protein number and ∼30% of cellular protein mass. Even in a typical human cell ribosomal proteins constitute ∼4-6% of total protein mass, and ribosomes are present at ∼10⁷ per cell. We begin this primer by exploring the tight relationship between ribosome production and cell growth, which has important implications not just for the cell's global protein expression profile and maximum growth rate, but also for the molecular composition of the ribosome itself. We then discuss how and to what extent the expression of the RNA and protein components of ribosomes is fine-tuned to match the cell's needs and minimise waste. Finally, we highlight the importance of coordinated ribosomal RNA (rRNA) and ribosomal protein expression in eukaryotes and explore how defects in this process are associated with proteotoxicity and disease. A central underlying question addressed throughout is whether regulation of ribosome biogenesis has evolved to optimise energy efficiency or is instead (or in addition) driven by other goals, such as maximising cell growth rate, promoting adaptation to changing environmental conditions, or maintaining the stability of the cellular proteome.

Dedicated chaperones coordinate co-translational regulation of ribosomal protein production with ribosome assembly to preserve proteostasis

The biogenesis of eukaryotic ribosomes involves the ordered assembly of around 80 ribosomal proteins. Supplying equimolar amounts of assembly-competent ribosomal proteins is complicated by their aggregation propensity and the spatial separation of their location of synthesis and pre-ribosome incorporation. Recent evidence has highlighted that dedicated chaperones protect individual, unassembled ribosomal proteins on their path to the pre-ribosomal assembly site. Here, we show that the co-translational recognition of Rpl3 and Rpl4 by their respective dedicated chaperone, Rrb1 or Acl4, reduces the degradation of the encoding RPL3 and RPL4 mRNAs in the yeast Saccharomyces cerevisiae. In both cases, negative regulation of mRNA levels occurs when the availability of the dedicated chaperone is limited and the nascent ribosomal protein is instead accessible to a regulatory machinery consisting of the nascent-polypeptide-associated complex and the Caf130-associated Ccr4-Not complex. Notably, deregulated expression of Rpl3 and Rpl4 leads to their massive aggregation and a perturbation of overall proteostasis in cells lacking the E3 ubiquitin ligase Tom1. Taken together, we have uncovered an unprecedented regulatory mechanism that adjusts the de novo synthesis of Rpl3 and Rpl4 to their actual consumption during ribosome assembly and, thereby, protects cells from the potentially detrimental effects of their surplus production.

Living cells are packed full of molecules known as proteins, which perform many vital tasks the cells need to survive and grow. Machines called ribosomes inside the cells use template molecules called messenger RNAs (or mRNAs for short) to produce proteins. The newly-made proteins then have to travel to a specific location in the cell to perform their tasks. Some newly-made proteins are prone to forming clumps, so cells have other proteins known as chaperones that ensure these clumps do not form.

The ribosomes themselves are made up of several proteins, some of which are also prone to clumping as they are being produced. To prevent this from happening, cells control how many ribosomal proteins they make, so there are just enough to form the ribosomes the cell needs at any given time. Previous studies found that, in yeast, two ribosomal proteins called Rpl3 and Rpl4 each have their own dedicated chaperone to prevent them from clumping. However, it remained unclear whether these chaperones are also involved in regulating the levels of Rpl3 and Rpl4.

To address this question, Pillet et al. studied both of these dedicated chaperones in yeast cells. The experiments showed that the chaperones bound to their target proteins (either units of Rpl3 or Rpl4) as they were being produced on the ribosomes. This protected the template mRNAs the ribosomes were using to produce these proteins from being destroyed, thus allowing further units of Rpl3 and Rpl4 to be produced. When enough Rpl3 and Rpl4 units were made, there were not enough of the chaperones to bind them all, leaving the mRNA templates unprotected. This led to the destruction of the mRNA templates, which decreased the numbers of Rpl3 and Rpl4 units being produced.

The work of Pillet et al. reveals a feedback mechanism that allows yeast to tightly control the levels of Rpl3 and Rpl4. In the future, these findings may help us understand diseases caused by defects in ribosomal proteins, such as Diamond-Blackfan anemia, and possibly also neurodegenerative diseases caused by clumps of proteins forming in cells. The next step will be to find out whether the mechanism uncovered by Pillet et al. also exists in human and other mammalian cells.

Yeast Crf1p: An activator in need is an activator indeed

Ribosome biogenesis is an energetically costly process, and tight regulation is required for stoichiometric balance between components. This requires coordination of RNA polymerases I, II, and III. Lack of nutrients or the presence of stress leads to downregulation of ribosome biogenesis, a process for which mechanistic target of rapamycin complex I (mTORC1) is key. mTORC1 activity is communicated by means of specific transcription factors, and in yeast, which is a primary model system in which transcriptional coordination has been delineated, transcription factors involved in regulation of ribosomal protein genes include Fhl1p and its cofactors, Ifh1p and Crf1p. Ifh1p is an activator, whereas Crf1p has been implicated in maintaining the repressed state upon mTORC1 inhibition. Computational analyses of evolutionary relationships have indicated that Ifh1p and Crf1p descend from a common ancestor. Here, we discuss recent evidence, which suggests that Crf1p also functions as an activator. We propose a model that consolidates available experimental evidence, which posits that Crf1p functions as an alternate activator to prevent the stronger activator Ifh1p from re-binding gene promoters upon mTORC1 inhibition. The correlation between retention of Crf1p in related yeast strains and duplication of ribosomal protein genes suggests that this backup activation may be important to ensure gene expression when Ifh1p is limiting. With ribosome biogenesis as a hallmark of cell growth, failure to control assembly of ribosomal components leads to several human pathologies. A comprehensive understanding of mechanisms underlying this process is therefore of the essence.

Mediator dynamics during heat shock in budding yeast

The Mediator complex is central to transcription by RNA polymerase II (Pol II) in eukaryotes. In budding yeast (Saccharomyces cerevisiae), Mediator is recruited by activators and associates with core promoter regions, where it facilitates preinitiation complex (PIC) assembly, only transiently before Pol II escape. Interruption of the transcription cycle by inactivation or depletion of Kin28 inhibits Pol II escape and stabilizes this association. However, Mediator occupancy and dynamics have not been examined on a genome-wide scale in yeast grown in nonstandard conditions. Here we investigate Mediator occupancy following heat shock or CdCl₂ exposure, with and without depletion of Kin28. We find that Pol II occupancy shows similar dependence on Mediator under normal and heat shock conditions. However, although Mediator association increases at many genes upon Kin28 depletion under standard growth conditions, little or no increase is observed at most genes upon heat shock, indicating a more stable association of Mediator after heat shock. Unexpectedly, Mediator remains associated upstream of the core promoter at genes repressed by heat shock or CdCl₂ exposure whether or not Kin28 is depleted, suggesting that Mediator is recruited by activators but is unable to engage PIC components at these repressed targets. This persistent association is strongest at promoters that bind the HMGB family member Hmo1, and is reduced but not eliminated in hmo1Δ yeast. Finally, we show a reduced dependence on PIC components for Mediator occupancy at promoters after heat shock, further supporting altered dynamics or stronger engagement with activators under these conditions.

The ribosome assembly factor Nop53 has a structural role in the formation of nuclear pre-60S intermediates, affecting late maturation events

Eukaryotic ribosome biogenesis is an elaborate process during which ribosomal proteins assemble with the pre-rRNA while it is being processed and folded. Hundreds of assembly factors (AF) are required and transiently recruited to assist the sequential remodeling events. One of the most intricate ones is the stepwise removal of the internal transcribed spacer 2 (ITS2), between the 5.8S and 25S rRNAs, that constitutes together with five AFs the pre-60S ‘foot’. In the transition from nucleolus to nucleoplasm, Nop53 replaces Erb1 at the basis of the foot and recruits the RNA exosome for the ITS2 cleavage and foot disassembly. Here we comprehensively analyze the impact of Nop53 recruitment on the pre-60S compositional changes. We show that depletion of Nop53, different from nop53 mutants lacking the exosome-interacting motif, not only causes retention of the unprocessed foot in late pre-60S intermediates but also affects the transition from nucleolar state E particle to subsequent nuclear stages. Additionally, we reveal that Nop53 depletion causes the impairment of late maturation events such as Yvh1 recruitment. In light of recently described pre-60S cryo-EM structures, our results provide biochemical evidence for the structural role of Nop53 rearranging and stabilizing the foot interface to assist the Nog2 particle formation.

Transcriptional control of ribosome biogenesis in yeast: links to growth and stress signals

Ribosome biogenesis requires prodigious transcriptional output in rapidly growing yeast cells and is highly regulated in response to both growth and stress signals. This minireview focuses on recent developments in our understanding of this regulatory process, with an emphasis on the 138 ribosomal protein genes (RPGs) themselves and a group of >200 ribosome biogenesis (RiBi) genes whose products contribute to assembly but are not part of the ribosome. Expression of most RPGs depends upon Rap1, a pioneer transcription factor (TF) required for the binding of a pair of RPG-specific TFs called Fhl1 and Ifh1. RPG expression is correlated with Ifh1 promoter binding, whereas Rap1 and Fhl1 remain promoter-associated upon stress-induced down regulation. A TF called Sfp1 has also been implicated in RPG regulation, though recent work reveals that its primary function is in activation of RiBi and other growth-related genes. Sfp1 plays an important regulatory role at a small number of RPGs where Rap1–Fhl1–Ifh1 action is subsidiary or non-existent. In addition, nearly half of all RPGs are bound by Hmo1, which either stabilizes or re-configures Fhl1–Ifh1 binding. Recent studies identified the proline rotamase Fpr1, known primarily for its role in rapamycin-mediated inhibition of the TORC1 kinase, as an additional TF at RPG promoters. Fpr1 also affects Fhl1–Ifh1 binding, either independently or in cooperation with Hmo1. Finally, a major recent development was the discovery of a protein homeostasis mechanism driven by unassembled ribosomal proteins, referred to as the Ribosome Assembly Stress Response (RASTR), that controls RPG transcription through the reversible condensation of Ifh1.

BET family members Bdf1/2 modulate global transcription initiation and elongation in Saccharomyces cerevisiae

Human bromodomain and extra-terminal domain (BET) family members are promising targets for therapy of cancer and immunoinflammatory diseases, but their mechanisms of action and functional redundancies are poorly understood. Bdf1/2, yeast homologues of the human BET factors, were previously proposed to target transcription factor TFIID to acetylated histone H4, analogous to bromodomains that are present within the largest subunit of metazoan TFIID. We investigated the genome-wide roles of Bdf1/2 and found that their important contributions to transcription extend beyond TFIID function as transcription of many genes is more sensitive to Bdf1/2 than to TFIID depletion. Bdf1/2 co-occupy the majority of yeast promoters and affect preinitiation complex formation through recruitment of TFIID, Mediator, and basal transcription factors to chromatin. Surprisingly, we discovered that hypersensitivity of genes to Bdf1/2 depletion results from combined defects in transcription initiation and early elongation, a striking functional similarity to human BET proteins, most notably Brd4. Our results establish Bdf1/2 as critical for yeast transcription and provide important mechanistic insights into the function of BET proteins in all eukaryotes.

Entamoeba histolytica-Gut Microbiota Interaction: More Than Meets the Eye

Amebiasis is a disease caused by the unicellular parasite Entamoeba histolytica. In most cases, the infection is asymptomatic but when symptomatic, the infection can cause dysentery and invasive extraintestinal complications. In the gut, E. histolytica feeds on bacteria. Increasing evidences support the role of the gut microbiota in the development of the disease. In this review we will discuss the consequences of E. histolytica infection on the gut microbiota. We will also discuss new evidences about the role of gut microbiota in regulating the resistance of the parasite to oxidative stress and its virulence.

Physiological function of FKBP12, a primary target of rapamycin/FK506: a newly identified role in transcription of ribosomal protein genes in yeast

In this review, we have summarized the information from a study on FKBP12 (FK506 binding protein 12 kDa) with a view to understand its drug-free, physiological roles in transcription of ribosomal protein gene in Saccharomyces cerevisiae. FKBP12 with peptidyl-prolylisomerase (PPIase) activity is widely conserved among many eukaryotes. FKBP12 is a primary target for the two structurally related drugs, FK506 and rapamycin. FKBP12 bound with FK506 or rapamycin inhibits calcineurin and target of rapamycin complex 1 (TORC1), respectively. The molecular mechanisms of the effect of FKBP12 in the presence of these drugs have been elucidated. Conversely, the physiological role of FKBP12 has been unclear, especially in yeast. Our study revealed that the deletion of FPR1 (FK506-sensitive prolinerotamase 1 gene), which encodes yeast FKBP12, induced severe growth defect synthetically with deletion of HMO1 (high mobility group family 1). HMO1 encodes an HMGB family protein involved in transcription of ribosomal component genes. Fpr1 was shown to bind specifically to the promoters of ribosomal protein genes (RPGs) dependent on Rap1 (repressor/activator binding protein 1). Importantly, Fpr1 and Hmo1 promote the binding of Fhl1/Ifh1 (forkhead-like 1/interacts with forkhead 1), key regulators of RPG transcription, to certain RPG promoters independently and/or cooperatively with each other. Taken together, we conclude that Fpr1 physiologically functions as transcription factor of RPGs in S. cerevisiae. To our knowledge, this is the first study to demonstrate that FKBP12 participates in ribosome synthesis independently of drugs, and it may also provide a clue to the unidentified function of other PPIase proteins.