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Biology subjects

Knop, M.

Publications and source records attributed to Knop, M..

At least 19 recordsLinked to original sources

A Modular Chromosomally Integrated Yeast Surface Display Platform for Quantitative Serology and Immune Profiling

Precise quantification of antigen-specific antibodies is essential for assessing immune status and fundamental to both clinical and research settings. However, current serological platforms remain limited in their ability to combine quantitative performance, flexibility, and scalability. Here, we present a chromosomally integrated yeast surface display (YSD) system engineered for stable, quantitative, and scalable antibody profiling. Genomic integration of the YSD cassette supports uniform antigen presentation without continuous selective pressure, reducing variability associated with plasmid-based systems. Two distinct cell-wall anchoring strategies are implemented within a modular synthetic framework that enables rapid, cloning-free strain construction. Coupled with flow-cytometric readout, the system provides sensitive detection of antigen-specific antibodies with single-cell normalization for antigen expression. In addition, the combination of barcoded YSD strain libraries with fluorescence-activated cell sorting and next-generation sequencing enables multiplexed serological profiling across multiple samples and antigens. As a proof of concept, we demonstrate quantitative antibody detection against SARS-CoV-2 and extend the approach to hepatitis virus antigens, highlighting the utility of this platform as a flexible framework for serological assay development and immune profiling.

bioengineering↗

Cell organization and disturbance-mapping using image activated cell-profiling (CODIAC)

Protein localization and abundance are tightly regulated to maintain cellular homeostasis, and their dysregulation is a hallmark of disease. However, methods that monitor the spatial localization changes of many proteins at once, and at scale, remain limited. Here we introduce CODIAC (Cell Organization and Disturbance-mapping using Image-Activated Cell-profiling), which couples image-enabled cell sorting (ICS) with improved Cas12a-assisted endogenous PCR tagging and machine-learning-guided gating to profile pools of fluorescently tagged proteins. Rather than isolating discrete cell populations, CODIAC reads the "phenotypic fingerprint" of each fluorescently tagged protein, defined by its distribution across a fixed set of image-defined sort bins. The method resolves localization-associated phenotypes, reproducibly profiles complex pools, generalizes to proteins absent from the training set, and detects shifts in protein localization and abundance following chemical perturbation. CODIAC thus extends ICS from outlier screening toward systematic profiling of the spatial proteome and its remodeling under perturbation.

cell biology↗

Improved cloning-free one-step CRISPR-Cas12a-assisted tagging of mammalian genes using PCR generated reagents (PCR tagging)

Precise DNA integration in mammalian genomes using CRISPR/Cas based strategies remains challenging due to competing DNA repair pathways. We present an update for our CRISPR/Cas12a-assisted PCR-tagging method using linear donor cassettes and self-targeting gRNAs for gene tagging. By incorporating 2A-linked selection markers and chemically modifying PCR cassettes with phosphorothioate and biotin, along with the inhibition of NHEJ, we improve precise insertions while reducing unwanted integration products and we devise a variant of the method for seamless gene tagging. To profile integration outcomes, we further developed our integration site sequencing protocol (Tn5-Anchor-Seq, Meurer et al., 2018) to obtain a protocol using long-read (ONT) sequencing coupled with a custom computational pipeline. This enables high-resolution quantification of all integration events with respect to integration by HDR or NHEJ, as well as the presence of concatemers and off-target integrations. Our data reveal gene-specific editing profiles and demonstrate that combining cassette design with DNA repair modulation yields up to 5-fold increases in HDR and suppression of concatemers and indels. Together, our improvements outline an robust strategy for efficient and high-fidelity gene tagging in mammalian cells, facilitating functional genomics and cell engineering applications.

molecular biology↗

The hepatitis E virus capsid protein ORF2 counteracts cell-intrinsic antiviral responses to enable persistence in hepatocytes

Hepatitis E virus (HEV) is a significant human pathogen causing both acute and chronic infections worldwide. The cell-intrinsic antiviral response serves as the initial defense against viruses and has been shown to be activated upon HEV infection. HEV can replicate in the presence of this response, but the underlying mechanisms remain poorly understood. Here, we investigated the role of the HEV structural proteins ORF2 and ORF3 in immunocompetent cells. Mechanistically, we validated that ectopic ORF2, but not ORF3, interfered with antiviral and inflammatory signaling downstream of pattern recognition receptors, in part through interaction with the central adaptor protein TANK binding kinase 1. In the full-length viral context, ORF2 contributed to a reduced antiviral response and consequently, more efficient viral replication. In addition, we discovered a protective mechanism mediated by ORF2 that shielded viral replication from antiviral effectors. Using single-cell RNA-sequencing, we confirmed that the presence of ORF2 in infected cells dampened antiviral responses in both actively infected cells and bystanders. As a consequence, we found that early in the infection process, the progression of authentic HEV infection relied on the presence of ORF2, facilitating a balance between viral replication and the antiviral response within immunocompetent cells. Altogether, our findings shed new light on the multifaceted role of ORF2 in the HEV life cycle and improve our understanding of the determinants that may contribute to HEV persistence. Significance statementHepatitis E virus (HEV) is an important yet often underestimated pathogen. Depending on the genotype, HEV infections can progress to chronicity, but the underlying mechanisms remain poorly understood. To gain insight into potential determinants, we investigated how HEV evades the bodys first line of defense, the cell-intrinsic antiviral response. We discovered that the HEV capsid protein ORF2 is crucial in limiting this response by interfering with antiviral signaling pathways and shielding viral replication from immune effectors. This balance between viral replication and the antiviral response contributes to persistent HEV infection in immunocompetent cells. Our findings reveal a new role for the HEV capsid protein in the viral life cycle and highlight it as an important target for novel therapeutic approaches.

microbiology↗

A marsh samphire (Salicornia europaea) extract induces a strictly sex-specific, Tor-signaling-dependent extension of lifespan and exhibits anti-obesogenic properties

We have studied the health-promoting properties of the marsh samphire Salicornia europaea by employing the fruit fly Drosophila melanogaster. Supplementing a standard diet with 0.2% of an aqueous extract of this halophilic plant (SEE), which grows in sandy and muddy habitats in intertidal zones, extended the lifespan of two different Drosophila strains by up to a third. This effect was strictly sex-specific and only affected females. When analyzing the body composition, we found that the body fat content of SEE-treated female flies was lower compared to controls. The extract also positively impacted the lifespan of flies fed a high-fat diet but not a high-sugar diet. It is of note in this context that SEE exhibited a lipase-inhibitory activity in vitro. Moreover, SEE counteracted ageing-associated loss of intestinal barrier integrity. The sex-specific lifespan extensions induced by the SEE were entirely dependent on functional Tor signaling in the flies. Tissue-specific silencing of the Tor signalling pathway in different cellular compartments of the intestine reduced, but did not completely abolish, the lifespan-prolonging effect in females. This suggests that other organs also contribute to this effect. In contrast to the observation that Tor signalling is necessary for the life-prolonging effect, Foxo deficiency led to a reduction in the effect, but not to its complete absence. In conclusion, the SEE is a promising candidate for a health-promoting intervention, and we laid the current groundwork for identifying the compounds that mediate this effect in future studies.

physiology↗

FoxO factors are essential for maintaining organ homeostasis by acting as stress sensors in airway epithelial cells

Airway epithelia must maintain functional and structural homeostasis despite exposure to diverse environmental stressors. FoxO transcription factors are well suited to this task, acting as integration hubs that translate extrinsic and intrinsic signals into appropriate physiological responses. We show that FoxO factors in Drosophila, mouse, and human airway epithelial cells (AECs) undergo nuclear translocation in response to stressors including hypoxia, temperature, and oxidative stress. In human airway epithelial cell lines, individual hFOXO factors show distinct, cell-type-specific activation patterns. In Drosophila, hypoxia was the only stressor among those tested that triggered a dfoxo-dependent innate immune response. Because Drosophila possesses a single FoxO ortholog, loss-of-function analysis directly demonstrated that dfoxo is required for stress resistance in the airway epithelium. Reduced FoxO expression was similarly observed in mouse models of asthma and in airway samples from asthma patients, paralleling the increased stress sensitivity seen upon FoxO loss in flies. While our data do not establish that reduced FOXO levels cause asthma, they indicate that FoxO-dependent stress pathways are altered in diseased airways across species. Together, these findings support a model in which FoxO coordinates adaptive epithelial stress responses that maintain airway homeostasis under environmental challenge.

physiology↗

A mitochondrial sirtuin shapes the intestinal microbiota by controlling lysozyme expression

Sirtuins act as cellular sensors in the gut that control a substantial change in gut properties in response to environmental changes. Here we show that the only mitochondrial sirtuin of Drosophila, dSirt4, is strongly up-regulated by a protein-reduced diet. Flies with a dSirt4 defect show strong changes in the protein pattern and physiological properties of their intestine. One of the most notable effects was the strong induction of lysozyme gene expression in the intestine, which also translates into enhanced lysozyme activity. This effect was cell autonomous, as it was also observed in flies with dsirt4 was exclusively silenced in enterocytes of the intestine. Although this strongly increased lysozyme expression, it did not reduce total bacterial load in the intestine, but rather changed the composition of the microbiota by reducing the number of gram-positive bacteria. This effect on microbiota composition can be attributed to the dSirt4-dependent lysozyme expression, as it was absent in a lysozyme-deficient background. dSirt4 deficiency in enterocytes reduced lifespan of flies, which was also observed in those flies experiencing ectopic lysozyme overexpression in enterocytes. This implies that strong lysozyme expression leads to a dysbiotic state associated with reduced lifespan.

cell biology↗

Components of TOR and MAP kinase signaling control chemotropism and pathogenicity in a fungal pathogen

Filamentous fungi can sense useful resources and hazards in their environment and direct growth of their hyphae accordingly. Chemotropism ensures access to nutrients, contact with other individuals (e.g., for mating), and interaction with hosts in the case of pathogens. Previous studies have revealed a complex chemotropic sensing landscape during host-pathogen interactions, but the underlying molecular machinery remains poorly characterized. Here we studied mechanisms controlling directed hyphal growth of the important plant-pathogenic fungus Verticillium dahliae towards different chemoattractants. We found that the homologs of the Rag GTPase Gtr1 and the GTPase-activating protein Tsc2, an activator and a repressor of the TOR kinase respectively, play important roles in hyphal chemotropism towards nutrients, plant-derived signals, and heterologous -pheromone of Fusarium oxysporum. Furthermore, important roles of these regulators were identified in fungal development and pathogenicity. We also found that the mitogen-activated protein kinase (MAPK) Fus3 is required for chemotropism towards nutrients, while the G protein-coupled receptor (GPCR) Ste2 and the MAPK Slt2 control chemosensing of plant-derived signals and -pheromone. Our study establishes V. dahliae as a suitable model for the analysis of fungal chemotropism and discovers new components of chemotropic signaling, during growth and host-pathogen interactions of V. dahliae.

microbiology↗

The NADPH Oxidase A of Verticillium dahliae is Essential for Pathogenicity, Normal Development, and Stress Tolerance, and it Interacts with Yap1 to Regulate Redox Homeostasis

Maintenance of redox homeostasis is vital for aerobic organisms and particularly relevant to plant pathogens. These need to balance between endogenous ROS production that is required for their development and pathogenicity, and host-derived oxidative stress. Endogenous ROS in fungi are generated by the membrane-bound NADPH oxidase (NOX) complexes and the mitochondrial respiratory chain, while the transcription factor Yap1 is a major regulator of the antioxidant response. Here we investigated the roles of NoxA and Yap1 in fundamental biological processes of the important plant pathogen Verticillium dahliae. Deletion of noxA impaired growth and morphogenesis, compromised formation of hyphopodia, diminished penetration ability and pathogenicity, increased sensitivity against antifungal agents, and dysregulated expression of antioxidant genes. On the other hand, deletion of yap1 resulted in defects in conidial and microsclerotia formation, increased sensitivity against oxidative stress, and down-regulated antioxidant genes. Localized accumulation of ROS was observed before conidial fusion and during the heterokaryon incompatibility reaction upon nonself fusion. The frequency of inviable fusions was not affected by deletion of Yap1. Analysis of a double knockout mutant revealed an epistatic relationship between noxA and yap1. Our results collectively reveal instrumental roles of NoxA and ROS homeostasis in the biology of V. dahliae.

genetics↗

Starvation-induced cell fusion and heterokaryosis frequently escape imperfect allorecognition systems to enable parasexual interactions in an asexual fungal pathogen

O_LIAsexual fungi include important pathogens of plants and other organisms, and their effective management requires understanding of their evolutionary dynamics. Genetic recombination is critical for species adaptability and could be achieved via heterokaryosis and the parasexual cycle in asexual fungi. Here, we investigate the extent and mechanisms of heterokaryosis in the asexual plant pathogen Verticillium dahliae. C_LIO_LIWe used live-cell imaging and genetic complementation assays of tagged V. dahliae strains to analyze the extent of nonself vegetative fusion, heterokaryotic cell fate and nuclear behavior. An efficient CRISPR/Cas9-mediated system was developed to investigate the involvement of autophagy in heterokaryosis. C_LIO_LIUnder starvation, nonself fusion of germinating spores occurs frequently regardless of the previously assessed vegetative compatibility of the partners. Supposedly "incompatible" fusions often establish viable heterokaryotic cells and mosaic mycelia, where nuclei can engage in fusion or transfer of genetic material. The molecular machinery of autophagy has a protective function against destruction of "incompatible" heterokaryons. C_LIO_LIOur results suggest an autophagy-mediated trade-off between parasexual interactions for genetic exchange and allorecognition systems possibly for mycelial protection from parasitic elements. Our study reveals unexpected capacity for heterokaryosis in V. dahliae and suggests, therefore, important roles of parasexuality in the evolution of asexual fungi. C_LI

genetics↗

Sex without crossing over in the yeast Saccharomycodes ludwigii

Meiotic recombination is a ubiquitous function of sexual reproduction throughout eukaryotes. Here we report that recombination is extremely suppressed during meiosis in the yeast species Saccharomycodes ludwigii. DNA double-strand break formation, processing and repair are required for normal meiosis but do not lead to crossing over. Although the species has retained an intact meiotic gene repertoire, genetic and population analyses suggest the exceptionally rare occurrence of meiotic crossovers. We propose that Sd. ludwigii has followed a unique evolutionary trajectory that possibly derives fitness benefits from the combination of frequent fertilization within the meiotic tetrad with the absence of meiotic recombination.

genetics↗

Conidial fusion in the asexual fungus Verticillium dahliae

Cell-to-cell fusion is a fundamental biological process across the tree of life. In filamentous fungi, somatic fusion (or anastomosis) is required for the normal development of their syncytial hyphal networks, and it can initiate non-sexual genetic exchange processes, such as horizontal genetic transfer and the parasexual cycle. Although these could be important drivers of the evolution of asexual fungi, this remains a largely unexplored possibility due to the lack of suitable resources for their study in these puzzling organisms. In this study, we report that the spores of the important asexual plant-pathogenic fungus Verticillium dahliae often engage in cell fusion via Conidial Anastomosis Tubes (CATs). We optimized appropriate procedures for their highly reproducible quantification and live-cell imaging, which were used to characterize their physiology and cell biology, and to start elucidating their underlying genetic machinery. Formation of CATs was shown to depend on growth conditions and require functional Fus3 and Slt2 MAP kinases, as well as the NADPH oxidase NoxA, whereas the GPCR Ste2 and the mating-type protein MAT1-2-1 were dispensable. We show that nuclei and other organelles can migrate through CATs, which often leads to the formation of transient dikaryons. Their nuclei have possible windows of opportunity for genetic interaction before degradation of one by a presumably homeostatic mechanism. We establish here CAT-mediated fusion in V. dahliae as an experimentally convenient system for the cytological analysis of fungal non-sexual genetic interactions. We expect that it will facilitate the dissection of sexual alternatives in asexual fungi.

microbiology↗

Hex1, the Major Component of Woronin Bodies, is Required for Normal Development, Pathogenicity and Stress Response in the Plant Pathogenic Fungus Verticillium dahliae

Woronin bodies are membrane-bound organelles of filamentous ascomycetes that mediate hyphal compartmentalization by plugging septal pores upon hyphal damage. Their major component is the peroxisomal protein Hex1, which has also been implicated in additional cellular processes in fungi. Here, we analyzed the Hex1 homolog of Verticillium dahliae, an important asexual plant pathogen, and we report its pleiotropic involvement in fungal growth, physiology, stress response and pathogenicity. Alternative splicing of the Vdhex1 gene can lead to the production of two Hex1 isoforms, which are structurally similar to their Neurospora crassa homolog. We show that VdHex1 is targeted to the septum, consistently with its demonstrated function in sealing hyphal compartments to prevent excessive cytoplasmic bleeding upon injury. Furthermore, our investigation provides direct evidence for significant contributions of Hex1 in growth and morphogenesis, as well as in asexual reproduction capacity. We discovered that Hex1 is required both for normal responses to osmotic stress and factors that affect the cell wall and plasma membrane integrity, and for normal resistance to oxidative stress and ROS homeostasis. The Vdhex1 mutant exhibited diminished ability to colonize and cause disease on eggplant. Overall, we show that Hex1 has fundamentally important multifaceted roles in the biology of V. dahliae.

microbiology↗

Extensive 5'-Surveillance Guards Against Non-Canonical NAD-Caps of Nuclear mRNAs in Yeast

The ubiquitous redox coenzyme nicotinamide adenine dinucleotide (NAD) acts as a non-canonical cap structure on prokaryotic and eukaryotic ribonucleic acids. Here we find that in budding yeast, NAD-RNAs are abundant (>1400 species), short (<170 nt), and mostly correspond to mRNA 5-ends. The modification percentage is low (<5%). NAD is incorporated during the initiation step by RNA polymerase II, which uses distinct promoters with a YAAG core motif for this purpose. Most NAD-RNAs are 3-truncated. At least three decapping enzymes, Rai1, Dxo1, and Npy1, guard against NAD-RNA at different cellular locations, targeting overlapping transcript populations. NAD-mRNAs do not support translation in vitro. Our work indicates that in budding yeast, most of the NAD incorporation into RNA seems to be accidental and undesirable to the cell, which has evolved a diverse surveillance machinery to prematurely terminate, decap and reject NAD-RNAs. In BriefIn budding yeast, most of the NAD incorporation into RNA seems to be accidental and undesirable to the cell, which has evolved a diverse surveillance machinery to prematurely terminate, decap and reject NAD-RNAs. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=175 SRC="FIGDIR/small/065920v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@19b86f4org.highwire.dtl.DTLVardef@1b923f3org.highwire.dtl.DTLVardef@1e74f69org.highwire.dtl.DTLVardef@10e787f_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIYeast cells have thousands of short NAD-RNAs related to the 5-ends of mRNAs C_LIO_LIRNA polymerase II prefers a YAAG promoter motif for NAD incorporation into RNA C_LIO_LINAD-RNA is strongly guarded against by Rai1, Dxo1, and Npy1 decapping enzymes at different subcellular sites C_LIO_LIIn vitro, NAD-mRNAs are rejected from translation C_LI

cell biology↗

Mechanisms of up-regulation of Ubiquitin-Proteasome activity in the absence of NatA dependent N-terminal acetylation

N-terminal acetylation is a prominent protein modification and inactivation of N-terminal acetyltransferases (NATs) cause protein homeostasis stress. Using multiplexed protein stability (MPS) profiling with linear ubiquitin fusions as reporters for the activity of the ubiquitin proteasome system (UPS) we observed increased UPS activity in NatA, but not NatB or NatC mutants. We find several mechanisms contributing to this behavior. First, NatA-mediated acetylation of the N-terminal ubiquitin independent degron regulates the abundance of Rpn4, the master regulator of the expression of proteasomal genes. Second, the abundance of several E3 ligases involved in degradation of UFD substrates is increased in cells lacking NatA. Finally, we identify the E3 ligase Tom1 as a novel chain elongating enzyme (E4) involved in the degradation of linear ubiquitin fusions via the formation of branched K11 and K29 ubiquitin chains, independently of the known E4 ligases involved in UFD, leading to enhanced ubiquitination of the UFD substrates.

cell biology↗

Single-color Fluorescence Lifetime Cross-Correlation Spectroscopy in vivo

The ability to quantify protein concentrations and to measure protein interactions in vivo is key information needed for the understanding of complex processes inside cells, but the acquisition of such information from living cells is still demanding. Fluorescence based methods like two-color fluorescence cross-correlation spectroscopy can provide this information but measurement precision is hampered by various sources of errors caused by instrumental or optical limitations such as imperfect overlap of detection volumes or detector cross-talk. Furthermore, the nature and properties of used fluorescent proteins or fluorescent dyes, such as labeling efficiency, fluorescent protein maturation, photo-stability, bleaching and fluorescence brightness can have an impact. Here we take advantage of lifetime differences as a mean to discriminate fluorescent proteins with similar spectral properties and to use them for single-color fluorescence lifetime cross-correlation spectroscopy (sc-FLCCS). By using only one excitation and one detection wavelength, this setup avoids all sources of errors resulting from chromatic aberrations and detector cross-talk. To establish sc-FLCCS we first engineered and tested multiple GFP-like fluorescent proteins for their suitability. This identified a novel GFP variant termed slmGFP (short lifetime monomeric GFP) with the so-far shortest lifetime. Monte-Carlo simulations were employed to explore the suitability of different combinations of GFP variants. Two GFPs, Envy and slmGFP were predicted to constitute the best performing couple for sc-FLCCS measurements. We demonstrated application of this GFP pair for measuring protein interactions between the proteasome and interacting proteins and for measuring protein interactions between three partners when combined with a red florescent protein. Together, our findings establish sc-FLCCS as a valid alternative for conventional dual-color(dc)-FCCS measurements. STATEMENT OF SIGNIFICANCEThe quantification of protein concentrations and protein-protein interactions in vivo is a crucial information needed for the understanding of complex processes inside cells. Determination of such information is unfortunately still challenging. Fluorescence-based method like fluorescence cross-correlation spectroscopy (FCCS) is the only method which provides this information in vivo and almost in the real time, however it suffers from limitations caused by experimental setup and biological origin of fluorescent proteins. We present single-color fluorescence lifetime cross-correlation spectroscopy as an alternative to FCCS, which uses the information of fluorescence lifetime to overcome some of these limitations. We challenged the method and determined its advantages and limitations and demonstrated the applicability of the method on the proteins of yeast proteasome.

cell biology↗

Nα-terminal acetylation of proteins by NatA and NatB serves distinct physiological roles in Saccharomyces cerevisiae

SO_SCPLOWUMMARYC_SCPLOWN-terminal (Nt)-acetylation is a highly prevalent co-translational protein modification in eukaryotes, catalyzed by at least five Nt-acetyltransferases (Nat) with differing specificities. Nt-acetylation has been implicated in protein quality control but its broad biological significance remains elusive. We investigated the roles of the two major Nats of S. cerevisiae, NatA and NatB, by performing transcriptome, translatome and proteome profiling of natA{Delta} and natB{Delta} mutants. Our results do not support a general role of Nt-acetylation in protein degradation but reveal an unexpected range of Nat-specific phenotypes. NatA is implicated in systemic adaptation control, as natA{Delta} mutants display altered expression of transposons, sub-telomeric genes, pheromone response genes and nuclear genes encoding mitochondrial ribosomal proteins. NatB predominantly affects protein folding, as natB{Delta} mutants accumulate protein aggregates, induce stress responses and display reduced fitness in absence of the ribosome-associated chaperone Ssb. These phenotypic differences indicate that controlling Nat activities may serve to elicit distinct cellular responses.

molecular biology↗

CDK1 couples proliferation with protein synthesis

Cell proliferation exerts a high demand on protein synthesis, yet the mechanisms coupling the two processes are not fully understood. A kinase and phosphatase screen for activators of translation, based on the formation of stress granules in human cells, revealed cell cycle-associated kinases as major candidates. CDK1 was identified as a positive regulator of global translation, and cell synchronization experiments showed that this is an extra-mitotic function of CDK1. Dephosphorylation of eIF2 and S6K1 signaling were found to act downstream of CDK1. Moreover, Ribo-Seq analysis uncovered that CDK1 exerts a particularly strong effect on the translation of 5TOP mRNAs, which includes mRNAs encoding for ribosomal proteins and several translation factors. This effect requires the 5TOP mRNA-binding protein LARP1, concurrent to our finding that LARP1 phosphorylation is strongly dependent on CDK1. Taken together, our results show that CDK1 provides a direct means to couple cell proliferation with biosynthesis of the translation machinery and the rate of protein synthesis.

biochemistry↗