Suppressor of clathrin deficiency (Scd6)-An emerging RGG-motif translation repressor

Tdh3 and Rom2 are functional modulators of a conserved condensate-resident RNA-binding protein, Scd6, in Saccharomyces cerevisiae

Arginine-glycine-glycine motif proteins play a crucial role in determining mRNA fate. Suppressor of clathrin deficiency 6 (Scd6) is a conserved arginine-glycine-glycine motif containing ribonucleoprotein (RNP) condensate-resident, translation repressor, and decapping activator protein in Saccharomyces cerevisiae. Identifying protein factors that can modulate Scd6 function is critical to understanding the regulation of mRNA fate by Scd6. In this study, using an approach that combined mRNA tethering assay with flow cytometry, we screened 50 genes for their role in modulating the translation repression activity of Scd6. We identified 8 conserved modulators with human homologs. Of these, we further characterized in detail guanine nucleotide exchange factor Rho1 multicopy suppressor 2 (Rom2) and glycolytic enzyme triose phosphate dehydrogenase 3 (Tdh3), which, respectively, impede and promote translation repression activity of Scd6. Our study reveals that Rom2 negatively regulates the arginine methylation of Scd6 and antagonizes its localization to P-bodies. Tdh3, on the other hand, promotes Scd6 interaction with Hmt1, thereby promoting the arginine methylation of Scd6 and enhanced eIF4G1 interaction, which is known to promote its repression activity. Identifying these novel modulators provides exciting new insights into the role of a metabolic enzyme of the glycolytic pathway and guanine nucleotide exchange factor implicated in the cell wall integrity pathway in regulating Scd6 function and, thereby, cytoplasmic mRNA fate.

Dual Input-Controlled Synthetic mRNA Circuit for Bidirectional Protein Expression Regulation

Synthetic mRNA circuits manipulate cell fate by controlling output protein expression via cell-specific input molecule detection. Most current circuits either repress or enhance output production upon input binding. Such binary input-output mechanisms restrict the fine-tuning of protein expression to control complex cellular events. Here we designed mRNA circuits using enhancer/repressor modules that were independently controlled by different input molecules, resulting in bidirectional output regulation; the maximal enhancement over maximal repression was 57 fold. The circuit either enhances or represses protein production in different cells based on the difference in the expression of two microRNAs. This study examined novel bidirectional circuit designs capable of fine-tuning protein production by sensing multiple input molecules. It also broadened the scope of cell manipulation by synthetic mRNA circuits, facilitating the development of mRNA circuits for precise cell manipulation and providing cell-based solutions to biomedical problems.

Condensation properties of stress granules and processing bodies are compromised in Myotonic Dystrophy Type 1

RNA regulation in mammalian cells requires complex physical compartmentalisation, using structures thought to be formed by liquid-liquid phase separation. Disruption of these structures is implicated in numerous degenerative diseases. Myotonic dystrophy type 1 (DM1) is a multi-systemic trinucleotide repeat disorder resulting from an expansion of nucleotides CTG (CTGexp) in the DNA encoding DM1 protein kinase (DMPK). The cellular hallmark of DM1 is the formation of nuclear foci that contain expanded DMPK RNA (CUGexp) (with thymine instead of uracil). We report here the deregulation of stress granules (SGs) and processing bodies (P-bodies), two cytoplasmic structures key for mRNA regulation, in cell culture models of DM1. Alterations to the rates of formation and dispersal of SGs suggest an altered ability of cells to respond to stress associated with DM1, while changes to the structure and dynamics of SGs and P-bodies suggest that a widespread alteration to the biophysical properties of cellular structures is a consequence of the presence of CUGexp RNA.

Summary: Validation of an inducible model of myotonic dystrophy type 1 that shows altered cellular stress responses. These involve phase-separated cellular structures also implicated in other degenerative conditions.

Exploring the role of RRM domains and conserved aromatic residues in RGG motif of eIF4G-binding translation repressor protein Sbp1

Background: RNA binding proteins play crucial role in determining if a given mRNA will be translated, stored, or degraded. Sbp1 is an RGG-motif containing protein that is implicated in affecting mRNA decapping and translation. Sbp1 represses translation by binding eIF4G1 through its RGG-motif and activates decapping when overexpressed. In this report, we have assessed the genetic interaction of Sbp1 with decapping activators such as Dhh1, Pat1, and Scd6. We have further analyzed the importance of different domains and specific conserved residues of Sbp1 in its ability to cause over-expression mediated growth defect. Method: Sequence alignment was performed to identify conserved aromatic residues to be mutated. Using site-directed mutagenesis several point mutations and domain deletions were created in Sbp1 expressed under a galactose-inducible promoter. The mutants were tested for their ability to cause growth defect upon over-expression. The ability of Sbp1 to affect over-expression mediated growth defect of other decapping activators was tested using growth assay. Live cell imaging was done to study localization of Sbp1 and its RRM-deletion mutants to RNA granules upon glucose starvation. Results: Mutation of several aromatic residues in the RGG-motif and that of the phosphorylation sites in the RRM domain of Sbp1 did not affect the growth defect phenotype. Deletion of another eIF4G1-binding RGG-motif protein Scd6 does not affect the ability of Sbp1 to cause growth defect. Moreover, absence of Sbp1 did not affect the growth defect phenotypes observed upon overexpression of decapping activators Dhh1 and Pat1. Strikingly deletion of both the RRM domains (RRM1 and RRM2) and not the RNP motifs within them compromised the growth defect phenotype. Sbp1 mutant lacking both RRM1 and RRM2 was highly defective in localizing to RNA granules.   Conclusion: This study identifies an important role of RRM domains independent of the RNP motif in Sbp1 function.

Involvement of RNA granule proteins in meiotic silencing by unpaired DNA

In Neurospora crassa, expression from an unpaired gene is suppressed by a mechanism known as meiotic silencing by unpaired DNA (MSUD). MSUD utilizes common RNA interference (RNAi) factors to silence target mRNAs. Here, we report that Neurospora CAR-1 and CGH-1, homologs of two Caenorhabditis elegans RNA granule components, are involved in MSUD. These fungal proteins are found in the perinuclear region and P-bodies, much like their worm counterparts. They interact with components of the meiotic silencing complex (MSC), including the SMS-2 Argonaute. This is the first time MSUD has been linked to RNA granule proteins.

Elucidation of the RNA-granule inducing sodium azide stress response through transcriptome analysis

Sodium azide is a commonly used cytochrome oxidase inhibitor that leads to translation repression and RNA granule assembly. The global changes in mRNA abundance in response to this stressor are unknown. RGG-motif proteins Scd6 and Sbp1 are translation-repressors and decapping-activators that localize to and affect the assembly of RNA granules in response to sodium azide stress. Transcriptome-wide effects of these proteins remain unknown. To address this, we have sequenced transcriptome of the: a) wild type strain under unstressed and sodium azide stress, b) Δscd6 and Δsbp1 strains under unstressed and sodium azide stress. Transcriptome analysis identified altered abundance of many transcripts belonging to stress-responsive pathways which were further validated by qRT-PCR results. Abundance of several transcripts was altered in Δscd6/Δsbp1 under normal conditions and upon stress. Overall, this study provides critical insights into transcriptome changes in response to sodium azide stress and the role of RGG-motif proteins in these changes.

Exploring the role of RRM domains and conserved aromatic residues in RGG motif of eIF4G-binding translation repressor protein Sbp1

Background: Mechanisms of mRNA fate decisions play an important role in determining if a given mRNA will be translated, stored or degraded upon arrival to cytoplasm. Sbp1 is an important RGG-motif containing protein that is implicated in affecting mRNA decapping and translation. Sbp1 represses translation by binding eIF4G1 through its RGG-motif and activates decapping when overexpressed. In this report we have assessed the genetic interaction of Sbp1 with  decapping activators such as Dhh1, Pat1 and Scd6.  We have further analyzed the importance of different domains and specific conserved residues of Sbp1 in translation repression activity. Method: Sequence alignment was performed to identify conserved aromatic residues to be mutated. Using site-directed mutagenesis several point mutations and domain deletions was created in Sbp1 expressed under a galactose-inducible promoter. The mutants were tested for their ability to cause growth defect upon over-expression. The ability of Sbp1 to affect over expression mediated growth defect of other decapping activators was tested using growth assay. Live cell imaging was done to study localization of Sbp1 and its RRM-deletion mutants to RNA granules upon glucose starvation. Results: Mutation of several aromatic residues in the RGG-motif and that of the phosphorylation sites in the RRM domain of Sbp1 did not affect the growth defect phenotype. Deletion of another eIF4G1-binding RGG-motif protein Scd6 does not affect the ability of Sbp1 to cause growth defect. Moreover, absence of Sbp1 did not affect the growth defect phenotypes observed upon overexpression of decapping activators Dhh1 and Pat1. Strikingly deletion of both the RRM domains (RRM1 and RRM2) and not the RNP motifs within them compromised the growth defect phenotype. Sbp1 mutant lacking both RRM1 and RRM2 was highly defective in localizing to RNA granules.   Conclusion: This study identifies an important role of RRM domains independent of RNP motif in Sbp1 repression activity.

DEKTV and YVG motifs in the Lsm domain are important for the activity of Scd6, a conserved translation repressor protein

Scd6 is a conserved RGG-motif protein which represses translation by binding eIF4G through its RGG-motif. Lsm and FDF are two other conserved domains present in the protein, however the role of both these domains is unclear. We provide evidence in this report that the Lsm domain is important for the role of Scd6 in translation. Mutant of Scd6 lacking the Lsm domain does not cause overexpression growth defect in a manner comparable to the wild type. Similar results were observed with two distinct point mutants of Scd6 wherein putative RNA-binding motifs DxEKxTV and YVG were mutated. Upon overexpression, the three mutants were defective in inducing formation of P-bodies and stress granules which are conserved sites of translation repression. Importantly localization to granules in response to glucose deprivation and sodium azide stress was defective for Lsm domain mutants indicating that the inability to localize to granules could be a reason for their defective role in translation. Deletion of scd6 impairs Lsm1 foci formation upon glucose deprivation stress which could not be rescued by complementation with Lsm-domain deletion mutant of Scd6 when compared to the full-length protein. Put together, our results highlight the role of Lsm domain and its specific motifs in Scd6 activity and provide crucial insight into its function.

Arginine methylation augments Sbp1 function in translation repression and decapping

The fate of messenger RNA in cytoplasm plays a crucial role in various cellular processes. However, the mechanisms that decide whether mRNA will be translated, degraded or stored remain unclear. Single stranded nucleic acid binding protein (Sbp1), an Arginine‐Glycine‐Glycine (RGG‐motif) protein, is known to promote transition of mRNA into a repressed state by binding eukaryotic translation initiation factor 4G1 (eIF4G1) and to promote mRNA decapping, perhaps by modulation of Dcp1/2 activity. Sbp1 is known to be methylated on arginine residues in RGG‐motif; however, the functional relevance of this modification in vivo remains unknown. Here, we report that Sbp1 is arginine‐methylated in an hnRNP methyl transferase (Hmt1)‐dependent manner and that methylation is enhanced upon glucose deprivation. Characterization of an arginine‐methylation‐defective (AMD) mutant provided evidence that methylation affects Sbp1 function in vivo. The AMD mutant is compromised in causing growth defect upon overexpression, and the mutant is defective in both localizing to and inducing granule formation. Importantly, the Sbp1‐eIF4G1 interaction is compromised both for the AMD mutant and in the absence of Hmt1. Upon overexpression, wild‐type Sbp1 increases localization of another RGG motif containing protein, Scd6 (suppressor of clathrin deficiency) to granules; however, this property of Sbp1 is compromised in the AMD mutant and in the absence of Hmt1, indicating that Sbp1 repression activity could involve other RGG‐motif translation repressors. Additionally, the AMD mutant fails to increase localization of the decapping activator DEAD box helicase homolog to foci and fails to rescue the decapping defect of a dcp1‐2Δski8 strain, highlighting the role of Sbp1 methylation in decapping. Taken together, these results suggest that arginine methylation modulates Sbp1 role in mRNA fate determination.

The regulation, functions and clinical relevance of arginine methylation

Methylation of arginine residues by protein arginine methyltransferases (PRMTs) is involved in the regulation of fundamental cellular processes, including transcription, RNA processing, signal transduction cascades, the DNA damage response and liquid-liquid phase separation. Recent studies have provided considerable advances in the development of experimental tools and the identification of clinically relevant PRMT inhibitors. In this review, we discuss the regulation of PRMTs, their various cellular roles and the clinical relevance of PRMT inhibitors for the therapy of neurodegenerative diseases and cancer.

RGG-motif self-association regulates eIF4G-binding translation repressor protein Scd6

Regulation of mRNA translation plays a key role in the control of gene expression. Scd6, a conserved RGG-motif containing protein represses translation by binding to translation initiation factor eIF4G1. Here we report that Scd6 binds itself in RGG-motif dependent manner and self-association regulates its repression activity. Scd6 self-interaction competes with eIF4G1 binding and methylation of Scd6 RGG-motif by Hmt1 negatively affects self-association. Results pertaining to Sbp1 indicate that self-association could be a general feature of RGG-motif containing translation repressor proteins. Taken together, our study reveals a mechanism of regulation of eIF4G-binding RGG-motif translation repressors.

Characterizing mutations in and genetic interactions of RGG-motif translation repressor Sbp1

Background: Mechanisms of mRNA fate decisions play an important role in determining if a given mRNA will be translated, stored or degraded upon arrival to cytoplasm. Sbp1 is an important RGG-motif containing protein that is implicated in mRNA fate decisions since it can affect mRNA decapping and translation. Sbp1 represses translation by binding eIF4G1 through its RGG-motif and activates decapping when overexpressed. In order to understand the amino acids important for translation repression activity of Sbp1 we performed mutational analysis of Sbp1 combined with assessing its genetic interaction with another RGG-motif protein Scd6. We created two classes of point mutations a) in aromatic residues of the RGG-motif and b) in residues reported to be phosphorylated. Method: Sequence alignment was performed to identify aromatic residues to be mutated based on conservation. Site-directed mutagenesis approach was used to create several point mutations in Sbp1 expressed under galactose-inducible promoter. The mutants were tested for their ability to cause growth defect upon overexpression. The ability of Sbp1 to affect repression activity of other decapping activators was tested using the same growth assay. Results: Mutation of several aromatic residues in the RGG-motif of Sbp1 led to a weak rescue phenotype. However the phospho-mimetic mutants of Sbp1 did not lead to any kind of growth defect rescue. Deletion of another eIF4G1-binding RGG-motif protein Scd6 does not affect ability of Sbp1 to cause growth defect. On the other hand absence of Sbp1 does not affect ability of Dhh1 and Pat1 to repress translation. Conclusion: Based on our growth assay analysis we conclude that mutated aromatic residues contribute marginally to repression activity of Sbp1 whereas phospho-mimetic mutants do not alter ability of Sbp1 to cause growth defect. Interestingly Scd6 does not affect ability of Sbp1 to repress translation, which in turn does not affect Dhh1 and Pat1.