Ribosomal Protein mRNAs Research Articles

METTL3 alters capping enzyme expression and its activity on ribosomal proteins

The 5’ cap, catalyzed by RNA guanylyltransferase and 5’-phosphatase (RNGTT), is a vital mRNA modification for the functionality of mRNAs. mRNA capping occurs in the nucleus for the maturation of the functional mRNA and in the cytoplasm for fine-tuning gene expression. Given the fundamental importance of RNGTT in mRNA maturation and expression there is a need to further investigate the regulation of RNGTT. N6-methyladenosine (m6A) is one of the most abundant RNA modifications involved in the regulation of protein translation, mRNA stability, splicing, and export. We sought to investigate whether m6A could regulate the expression and activity of RNGTT. In this short report, we demonstrated that the 3’UTR of RNGTT mRNA is methylated with m6a by the m6A writer methyltransferase 3 (METTL3). Knockdown of METTL3 resulted in reduced protein expression of RNGTT. Sequencing of capped mRNAs identified an underrepresentation of ribosomal protein mRNA overlapping with 5’ terminal oligopyrimidine (TOP) mRNAs, and genes are dysregulated when cytoplasmic capping is inhibited. Pathway analysis identified disruptions in the mTOR and p70S6K pathways. A reduction in RPS6 mRNA capping, protein expression, and phosphorylation was detected with METTL3 knockdown

Ccr4-not ubiquitin ligase signaling regulates ribosomal protein homeostasis and inhibits 40S ribosomal autophagy

The Ccr4-Not complex contains the poorly understood Not4 ubiquitin ligase that functions in transcription, mRNA decay, translation, proteostasis, and endolysosomal nutrient signaling. To gain further insight into the in vivo functions of the ligase, we performed quantitative proteomics in Saccharomyces cerevisiae using yeast cells lacking Not4, or cells overexpressing wild-type Not4 or an inactive Not4 mutant. Herein, we provide evidence that balanced Not4 activity maintains ribosomal protein (RP) homeostasis independent of changes to RP mRNA or known Not4 ribosomal substrates. Intriguingly, we also find that Not4 loss activates 40S ribosomal autophagy independently of canonical Atg7-dependent macroautophagy, indicating that microautophagy is responsible. We previously demonstrated that Ccr4-Not stimulates target of rapamycin complex 1 (TORC1) signaling, which activates RP expression and inhibits autophagy, by maintaining vacuole V-ATPase H+ pump activity. Importantly, combining Not4 deficient cells with a mutant that blocks vacuole H+ export fully restores RP expression and increases 40S RP autophagy efficiency. In contrast, restoring TORC1 activity alone fails to rescue either process, indicating that Not4 loss disrupts additional endolysosomal functions that regulate RP expression and 40S autophagy. Analysis of the Not4 regulated proteome reveals increases in endolysosomal and autophagy-related factors that functionally interact with Not4 to control RP expression and affect 40S autophagy. Collectively, our data indicate that balanced Ccr4-Not ubiquitin ligase signaling maintains RP homeostasis and inhibits 40S autophagy via the ligase’s emerging role as an endolysosomal regulator.

Distinct roles of LARP1 and 4EBP1/2 in regulating translation and stability of 5'TOP mRNAs.

A central mechanism of mTOR complex 1 (mTORC1) signaling is the coordinated translation of ribosomal protein and translation factor mRNAs mediated by the 5'-terminal oligopyrimidine motif (5'TOP). Recently, La-related protein 1 (LARP1) was proposed to be the specific regulator of 5'TOP mRNA translation downstream of mTORC1, while eIF4E-binding proteins (4EBP1/2) were suggested to have a general role in translational repression of all transcripts. Here, we use single-molecule translation site imaging of 5'TOP and canonical mRNAs to study the translation of single mRNAs in living cells. Our data reveal that 4EBP1/2 has a dominant role in repression of translation of both 5'TOP and canonical mRNAs during pharmacological inhibition of mTOR. In contrast, we find that LARP1 selectively protects 5'TOP mRNAs from degradation in a transcriptome-wide analysis of mRNA half-lives. Our results clarify the roles of 4EBP1/2 and LARP1 in regulating 5'TOP mRNAs and provide a framework to further study how these factors control cell growth during development and disease.

Discovery of novel microRNA mimic repressors of ribosome biogenesis.

While microRNAs and other non-coding RNAs are the next frontier of novel regulators of mammalian ribosome biogenesis (RB), a systematic exploration of microRNA-mediated RB regulation has not yet been undertaken. We carried out a high-content screen in MCF10A cells for changes in nucleolar number using a library of 2603 mature human microRNA mimics. Following a secondary screen for nucleolar rRNA biogenesis inhibition, we identified 72 novel microRNA negative regulators of RB after stringent hit calling. Hits included 27 well-conserved microRNAs present in MirGeneDB, and were enriched for mRNA targets encoding proteins with nucleolar localization or functions in cell cycle regulation. Rigorous selection and validation of a subset of 15 microRNA hits unexpectedly revealed that most of them caused dysregulated pre-rRNA processing, elucidating a novel role for microRNAs in RB regulation. Almost all hits impaired global protein synthesis and upregulated CDKN1A (p21) levels, while causing diverse effects on RNA Polymerase 1 (RNAP1) transcription and TP53 protein levels. We provide evidence that the MIR-28 siblings, hsa-miR-28-5p and hsa-miR-708-5p, potently target the ribosomal protein mRNA RPS28 via tandem primate-specific 3' UTR binding sites, causing a severe pre-18S pre-rRNA processing defect. Our work illuminates novel microRNA attenuators of RB, forging a promising new path for microRNA mimic chemotherapeutics.

σ28-dependent small RNA regulation of flagella biosynthesis.

Flagella are important for bacterial motility as well as for pathogenesis. Synthesis of these structures is energy intensive and, while extensive transcriptional regulation has been described, little is known about the posttranscriptional regulation. Small RNAs (sRNAs) are widespread posttranscriptional regulators, most base pairing with mRNAs to affect their stability and/or translation. Here, we describe four UTR-derived sRNAs (UhpU, MotR, FliX and FlgO) whose expression is controlled by the flagella sigma factor σ28 (fliA) in Escherichia coli. Interestingly, the four sRNAs have varied effects on flagellin protein levels, flagella number and cell motility. UhpU, corresponding to the 3´ UTR of a metabolic gene, likely has hundreds of targets including a transcriptional regulator at the top flagella regulatory cascade connecting metabolism and flagella synthesis. Unlike most sRNAs, MotR and FliX base pair within the coding sequences of target mRNAs and act on ribosomal protein mRNAs connecting ribosome production and flagella synthesis. The study shows how sRNA-mediated regulation can overlay a complex network enabling nuanced control of flagella synthesis.

Role of the RNA-binding protein ZC3H41 in the regulation of ribosomal protein messenger RNAs in trypanosomes

BackgroundTrypanosomes are single-celled eukaryotes that rely heavily on post-transcriptional mechanisms to regulate gene expression. RNA-binding proteins play essential roles in regulating the fate, abundance and translation of messenger RNAs (mRNAs). Among these, zinc finger proteins of the cysteine3histidine (CCCH) class have been shown to be key players in cellular processes as diverse as differentiation, regulation of the cell cycle and translation. ZC3H41 is an essential zinc finger protein that has been described as a component of spliced leader RNA granules and nutritional stress granules, but its role in RNA metabolism is unknown.MethodsCell cycle analysis in ZC3H41- and Z41AP-depleted cells was carried out using 4′,6-diamidino-2-phenylindole staining, microscopic examination and flow cytometry. The identification of ZC3H41 protein partners was done using tandem affinity purification and mass spectrometry. Next-generation sequencing was used to evaluate the effect of ZC3H41 depletion on the transcriptome of procyclic Trypanosoma brucei cells, and also to identify the cohort of mRNAs associated with the ZC3H41/Z41AP complex. Levels of 5S ribosomal RNA (rRNA) species in ZC3H41- and Z41AP-depleted cells were assessed by quantitative reverse transcription-polymerase chain reaction. Surface sensing of translation assays were used to monitor global translation.ResultsWe showed that depletion of the zinc finger protein ZC3H41 resulted in marked cell cycle defects and abnormal cell morphologies. ZC3H41 was found associated with an essential protein, which we named Z41AP, forming a stable heterodimer, and also with proteins of the poly(A)-binding protein 1 complex. The identification of mRNAs associated with the ZC3H41/Z41AP complex revealed that it is primarily composed of ribosomal protein mRNAs, and that binding to target transcripts is diminished upon nutritional stress. In addition, we observed that mRNAs encoding several proteins involved in the maturation of 5S rRNA are also associated with the ZC3H41/Z41AP complex. Finally, we showed that depletion of either ZC3H41 or Z41AP led to the accumulation of 5S rRNA precursors and a decrease of protein translation.ConclusionsWe propose that ZC3H41 and Z41AP play important roles in controlling the fate of ribosomal components in response to environmental cues.Graphical

Inhibition of Ribosome Assembly and Ribosome Translation Has Distinctly Different Effects on Abundance and Paralogue Composition of Ribosomal Protein mRNAs in Saccharomyces cerevisiae.

Many mutations in genes for ribosomal proteins (r-proteins) and assembly factors cause cell stress and altered cell fate, resulting in congenital diseases collectively called ribosomopathies. Even though all such mutations depress the cell's protein synthesis capacity, they generate many different phenotypes, suggesting that the diseases are not due simply to insufficient protein synthesis capacity. To learn more, we investigated how the global transcriptome in Saccharomyces cerevisiae responds to reduced protein synthesis generated in two different ways: abolishing the assembly of new ribosomes and inhibiting ribosomal function. Our results showed that the mechanism by which protein synthesis is obstructed affects the ribosomal protein transcriptome differentially: ribosomal protein mRNA abundance increases during the abolition of ribosome formation but decreases during the inhibition of ribosome function. Interestingly, the ratio between mRNAs from some, but not all, pairs of paralogous ribosomal protein genes encoding slightly different versions of a given r-protein changed differently during the two types of stress, suggesting that expression of specific ribosomal protein paralogous mRNAs may contribute to the stress response. Unexpectedly, the abundance of transcripts for ribosome assembly factors and translation factors remained relatively unaffected by the stresses. On the other hand, the state of the translation apparatus did affect cell physiology: mRNA levels for some other proteins not directly related to the translation apparatus also changed differentially, though not coordinately with the r-protein genes, in response to the stresses. IMPORTANCE Mutations in genes for ribosomal proteins or assembly factors cause a variety of diseases called ribosomopathies. These diseases are typically ascribed to a reduction in the cell's capacity for protein synthesis. Paradoxically, ribosomal mutations result in a wide variety of disease phenotypes, even though they all reduce protein synthesis. Here, we show that the transcriptome changes differently depending on how the protein synthesis capacity is reduced. Most strikingly, inhibiting ribosome formation and ribosome function had opposite effects on the abundance of mRNA for ribosomal proteins, while genes for ribosome translation and assembly factors showed no systematic responses. Thus, the process by which the protein synthesis capacity is reduced contributes decisively to global mRNA composition. This emphasis on process is a new concept in understanding ribosomopathies and other stress responses.

Effects of L-arginine and arginine-arginine dipeptide on amino acids uptake and αS1-casein synthesis in bovine mammary epithelial cells.

Arginine (Arg), as an important functional amino acids (AA), is essential for milk protein synthesis in lactating ruminants. Arg shares transporters with cationic and neutral AA in mammary epithelial cells. Therefore, competitive inhibition might exist among these AA in uptake by mammary epithelial cells. In this study, cultured bovine mammary epithelial cells (BMEC) were used as the model to investigate whether the availability of L-Arg (0.7, 1.4, 2.8, 5.6, and 11.2 mM) affects the uptake of other AA and if this related to αS1-casein synthesis, and whether Arginine-Arginine (Arg-Arg) substituting part of free L-Arg can alleviate competitive inhibition among Arg and other AA, so as to promote αS1-casein synthesis. Our results showed that 2.8 mM L-Arg generated the greatest positive effects on αS1-casein synthesis and the activation of mammalian target of rapamycin (mTOR) signaling pathway (P < 0.01). With L-Arg supply increasing from 0.7 to 11.2 mM, the net-uptake of other AA (except Glu and Ala) decreased linearly and quadratically (Plinear < 0.01; Pquadratic < 0.01). Compared with 2.8 mM, the net-uptake of essential amino acids (EAA) and total amino acids (TAA) were lower at 11.2 mM L-Arg group, while greater at 1.4 mM L-Arg group (P < 0.01). Arg-Arg dipeptide replacing 10% free L-Arg increased αS1-casein synthesis (P < 0.05), net-uptake of EAA and TAA, as well as phosphorylation level of mTOR and p70 ribosomal protein S6 kinase (P70S6K) and mRNA expression of oligopeptide transporter 2 (PepT2; P < 0.01). These observations suggested that the increased αS1-casein synthesis by 10% Arg-Arg dipeptide might be related to the increase of AA availability and the activation of mTOR signaling pathway in BMEC.

Development of transcriptomics-based growth rate indices in two model eukaryotes and relevance to metatranscriptomics datasets.

Growth rate estimation is important to understand the flow of energy and nutrient elements in an ecosystem, but it has remained challenging, especially on microscopic organisms. In this study, we propose four growth rate indices that use mRNA abundance ratios between nuclear and mitochondrial genes: (1) total nuclear and mitochondrial mRNA ratio (Nuc:Mito‐TmRNA); (2) nuclear and mitochondrial ribosomal protein mRNA ratio (Nuc:Mito‐RPmRNA); (3) gene ontology (GO) terms and total mitochondrial mRNA ratios; and (4) nuclear and mitochondrial specific gene mRNA ratio. We examine these proposed ratios using RNA‐Seq datasets of Daphnia magna, and Saccharomyces cerevisiae retrieved from the NCBI Short Read Archive. The results showed that both Nuc:Mito‐TmRNA and Nuc:Mito‐RPmRNA ratio indices showed significant correlations with the growth rate for both species. A large number of GO terms mRNA ratios showed significant correlations with the growth rate of S. cerevisiae. Lastly, we identified mRNA ratios of several specific nuclear and mitochondrial gene pairs that showed significant correlations. We foresee future implications for the proposed mRNA ratios used in metatranscriptome analyses to estimate the growth rate of communities and species.

RNA G-quadruplex structures control ribosomal protein production

Four-stranded G-quadruplex (G4) structures form from guanine-rich tracts, but the extent of their formation in cellular RNA and details of their role in RNA biology remain poorly defined. Herein, we first delineate the presence of endogenous RNA G4s in the human cytoplasmic transcriptome via the binding sites of G4-interacting proteins, DDX3X (previously published), DHX36 and GRSF1. We demonstrate that a sub-population of these RNA G4s are reliably detected as folded structures in cross-linked cellular lysates using the G4 structure-specific antibody BG4. The 5′ UTRs of protein coding mRNAs show significant enrichment in folded RNA G4s, particularly those for ribosomal proteins. Mutational disruption of G4s in ribosomal protein UTRs alleviates translation in vitro, whereas in cells, depletion of G4-resolving helicases or treatment with G4-stabilising small molecules inhibit the translation of ribosomal protein mRNAs. Our findings point to a common mode for translational co-regulation mediated by G4 structures. The results reveal a potential avenue for therapeutic intervention in diseases with dysregulated translation, such as cancer.

Identification of novel proteins and mRNAs differentially bound to the Leishmania Poly(A) Binding Proteins reveals a direct association between PABP1, the RNA-binding protein RBP23 and mRNAs encoding ribosomal proteins.

Poly(A) Binding Proteins (PABPs) are major eukaryotic RNA-binding proteins (RBPs) with multiple roles associated with mRNA stability and translation and characterized mainly from multicellular organisms and yeasts. A variable number of PABP homologues are seen in different organisms however the biological reasons for multiple PABPs are generally not well understood. In the unicellular Leishmania, dependent on post-transcriptional mechanisms for the control of its gene expression, three distinct PABPs are found, with yet undefined functional distinctions. Here, using RNA-immunoprecipitation sequencing analysis we show that the Leishmania PABP1 preferentially associates with mRNAs encoding ribosomal proteins, while PABP2 and PABP3 bind to an overlapping set of mRNAs distinct to those enriched in PABP1. Immunoprecipitation studies combined to mass-spectrometry analysis identified RBPs differentially associated with PABP1 or PABP2, including RBP23 and DRBD2, respectively, that were investigated further. Both RBP23 and DRBD2 bind directly to the three PABPs in vitro, but reciprocal experiments confirmed preferential co-immunoprecipitation of PABP1, as well as the EIF4E4/EIF4G3 based translation initiation complex, with RBP23. Other RBP23 binding partners also imply a direct role in translation. DRBD2, in contrast, co-immunoprecipitated with PABP2, PABP3 and with RBPs unrelated to translation. Over 90% of the RBP23-bound mRNAs code for ribosomal proteins, mainly absent from the transcripts co-precipitated with DRBD2. These experiments suggest a novel and specific route for translation of the ribosomal protein mRNAs, mediated by RBP23, PABP1 and the associated EIF4E4/EIF4G3 complex. They also highlight the unique roles that different PABP homologues may have in eukaryotic cells associated with mRNA translation.

Neuronal ribosomes exhibit dynamic and context-dependent exchange of ribosomal proteins

Owing to their morphological complexity and dense network connections, neurons modify their proteomes locally, using mRNAs and ribosomes present in the neuropil (tissue enriched for dendrites and axons). Although ribosome biogenesis largely takes place in the nucleus and perinuclear region, neuronal ribosomal protein (RP) mRNAs have been frequently detected remotely, in dendrites and axons. Here, using imaging and ribosome profiling, we directly detected the RP mRNAs and their translation in the neuropil. Combining brief metabolic labeling with mass spectrometry, we found that a group of RPs rapidly associated with translating ribosomes in the cytoplasm and that this incorporation was independent of canonical ribosome biogenesis. Moreover, the incorporation probability of some RPs was regulated by location (neurites vs. cell bodies) and changes in the cellular environment (following oxidative stress). Our results suggest new mechanisms for the local activation, repair and/or specialization of the translational machinery within neuronal processes, potentially allowing neuronal synapses a rapid means to regulate local protein synthesis.

Genome profiles of pathologist-defined cell clusters by multiregional LCM and G&T-seq in one triple-negative breast cancer patient

SummaryPathological examination is the gold standard for cancer diagnosis, and breast tumor cells are often found in clusters. We report a case study on one triple-negative breast cancer (TNBC) patient, analyzing tumor development, metastasis, and prognosis with simultaneous DNA and RNA sequencing of pathologist-defined cell clusters from multiregional frozen sections. The cell clusters are isolated by laser capture microdissection (LCM) from primary tumor tissue, lymphatic vessels, and axillary lymph nodes. Data are reported for a total of 97 cell clusters. A combination of tumor cell-cluster clonality and phylogeny reveals 3 evolutionarily distinct pathways for this patient, each associated with a unique mRNA signature, and each correlated with disparate survival outcomes. Hub gene analysis indicates that extensive downregulation of ribosomal protein mRNA is a potential marker of poor prognosis in breast cancer.

111 Single cell RNA seq revealed altered cytoskeletal dynamics and the formation of cytoplasmic RNA-Lamin A bodies during keratinocyte terminal differentiation

Keratinocyte cornification and epidermal barrier formation are tightly controlled processes, requiring degradation of organelles, including the nucleus. However, the underlying molecular mechanisms are not well defined. Post-confluent cultures of rat epidermal keratinocytes (REKs) undergo spontaneous and complete differentiation, allowing visualisation and perturbation of the differentiation process in vitro. Using this model, we have shown that the actomyosin network and the non-muscle Myosin IIa - Myh9 are required for key processes involved in nuclear degradation, comprising Akt1-mediated phosphorylation of Lamin A and the dispersal of phosphorylated Lamin A into the cytoplasmic bodies followed by rapid nuclear shrinkage. Based on these finding, we hypothesised that specific changes in actomyosin dynamics and the actin cytoskeleton are required for Lamin dispersal and nuclear shrinkage during epidermal terminal differentiation. We have designed a single-cell transcriptomics pipeline to better analyse these ’sub-optimal’, dying/cornifying cells, and high-throughput confocal imaging to analyse the actin cytoskeleton and related markers during nuclear degradation. We identified changes in expression of actin remodelling genes that coincided with nuclear degradation processes and altered distribution of the actin cytoskeleton in terminally differentiating keratinocytes. We also identified widespread up-regulation of ribosomal protein mRNAs, that correlated with the formation cytoplasmic RNA bodies associating with phosphorylated lamin A. Therefore, actin dynamics, increased translation, and increased cytoplasmic RNA are all potentially involved, and may serve as signposts for key stages in nuclear degradation and end-stage terminal differentiation in keratinocytes.

The 3'tsRNAs are aminoacylated: Implications for their biogenesis.

Emerging evidence indicates that tRNA-derived small RNAs (tsRNAs) are involved in fine-tuning gene expression and become dysregulated in various cancers. We recently showed that the 22nt LeuCAG3´tsRNA from the 3´ end of tRNALeu is required for efficient translation of a ribosomal protein mRNA and ribosome biogenesis. Inactivation of this 3´tsRNA induced apoptosis in rapidly dividing cells and suppressed the growth of a patient-derived orthotopic hepatocellular carcinoma in mice. The mechanism involved in the generation of the 3´tsRNAs remains elusive and it is unclear if the 3´-ends of 3´tsRNAs are aminoacylated. Here we report an enzymatic method utilizing exonuclease T to determine the 3´charging status of tRNAs and tsRNAs. Our results showed that the LeuCAG3´tsRNA, and two other 3´tsRNAs are fully aminoacylated. When the leucyl-tRNA synthetase (LARS1) was inhibited, there was no change in the total tRNALeu concentration but a reduction in both the charged tRNALeu and LeuCAG3´tsRNA, suggesting the 3´tsRNAs are fully charged and originated solely from the charged mature tRNA. Altering LARS1 expression or the expression of various tRNALeu mutants were also shown to affect the generation of the LeuCAG3´tsRNA further suggesting they are created in a highly regulated process. The fact that the 3´tsRNAs are aminoacylated and their production is regulated provides additional insights into their importance in post-transcriptional gene regulation that includes coordinating the production of the protein synthetic machinery.

Abstract 2443: APOBEC3G is a sex-specific determinant of post-transcriptional RNA processing and survival in diffuse large B-cell lymphoma

Abstract APOBEC3G is a cytidine deaminase with a well-characterized anti-viral role against HIV and other retroviruses. Its deaminase activity yields G to A edits in ssDNA to disrupt viral coding sequences and inhibits cDNA production during reverse transcription. However, APOBEC3G is also highly expressed in cells and tumors of B-lymphocyte lineage. In this study we aimed to evaluate the biological and clinical relevance of APOBEC3G in Diffuse Large B Cell Lymphomas (DLBCL), where it is expressed in absence of viral infection. We first confirmed the high expression of APOBEC3G in a panel of DLBCL cell lines. Interestingly, immunofluorescence of APOBEC3G in DLBCL cells demonstrated localization to p-bodies. SILAC mass-spectrometry of Flag-APOBEC3G further revealed its association with several RNA binding proteins (RBPs) involved in RNA metabolism. Using the enhanced crosslinking and immunoprecipitation (eCLIP) assay for identification of bound RNA species, we demonstrated that APOBEC3G binds to 3' UTR and exonic RNA sequences, mostly of genes encoding ribosomal components. To study the functional effects of APOBEC3G in DLBCL, we generated multiple DLBCL knockout (KO) lines for APOBEC3G loss using CRISPR-Cas9. Whole transcriptome sequencing in SC1 cells revealed that knockout of APOBEC3G led to a global reduction in the RNA transcripts for ribosomal proteins. Together, these results suggest a role for APOBEC3G in binding/regulating cellular RNA species and RNA processing in DLBCL, in the absence of viral infection. We then evaluated the clinical relevance of APOBEC3G expression in DLBCL using publicly available gene expression datasets. We noted a correlation between APOBEC3G and ribosomal protein mRNAs in DLBCL. Interestingly however the expression of APOBEC3G was linked to survival only in male patients of germinal center subtype DLBCL. On further study of our cell line knockout models (n=2 each of M/F) we noted a sex specific role of APOBEC3G in modulating cellular stress. In male cells, the loss of APOBEC3G led to decreased protein synthesis, differential expression of Y-chromosomal genes, endogenous retroviruses and interferon stimulated genes. These effects were not noted in female KO cells KO. As APOBEC3G loss did not affect viability following exposure to chemotherapeutics in-vitro, we postulate that the sex-specific association of APOBEC3G with survival is a function of possible immunomodulatory effects of its binding/processing complex RNA species. The biological significance of this sex-specific role of APOBEC3G in normal B-cell development and maturation is as yet unclear, and represents an important area for future research. Citation Format: Joanna D. Wardyn, Michal M. Hoppe, Allison S. Chan, Jia Li, Omer An, Shruthi Venguidessane, Dominic P. Sheng, Henry Yang, Gene W. Yeo, Daniel J. Hodson, Reuben S. Harris, Anand D. Jeyasekharan. APOBEC3G is a sex-specific determinant of post-transcriptional RNA processing and survival in diffuse large B-cell lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2443.

Insights into the functions and RNA binding of Trypanosoma brucei ZC3H22, RBP9 and DRBD7.

Trypanosoma brucei is unusually reliant on mRNA-binding proteins to control mRNA fate, because its protein-coding genes lack individual promoters. We here focus on three trypanosome RNA-binding proteins. ZC3H22 is specific to Tsetse fly forms, RBP9 is preferentially expressed in bloodstream forms; and DRBD7 is constitutively expressed. Depletion of RBP9 or DRBD7 did not affect bloodstream-form trypanosome growth. ZC3H22 depletion from procyclic forms caused cell clumping, decreased expression of genes required for cell growth and proliferation, and increased expression of some epimastigote markers. Apart from decreases in mRNAs encoding enzymes of glucose metabolism, levels of most ZC3H22-bound transcripts were unaffected by ZC3H22 depletion. We compared ZC3H22, RBP9 and DRBD7 RNA binding with that of 16 other RNA-binding proteins. ZC3H22, PUF3 and ERBP1 show a preference for ribosomal protein mRNAs. RBP9 preferentially binds mRNAs that are more abundant in bloodstream forms than in procyclic forms. RBP9, ZC3H5, ZC3H30 and DRBD7 prefer mRNAs with long coding regions; UBP1-associated mRNAs have long 3'-untranslated regions; and RRM1 prefers mRNAs with long 3'or 5'-untranslated regions. We suggest that proteins that prefer long mRNAs may have relatively short or degenerate binding sites, and that preferences for A or U increase binding in untranslated regions.

Parallel global profiling of plant TOR dynamics reveals a conserved role for LARP1 in translation.

Target of rapamycin (TOR) is a protein kinase that coordinates eukaryotic metabolism. In mammals, TOR specifically promotes translation of ribosomal protein (RP) mRNAs when amino acids are available to support protein synthesis. The mechanisms controlling translation downstream from TOR remain contested, however, and are largely unexplored in plants. To define these mechanisms in plants, we globally profiled the plant TOR-regulated transcriptome, translatome, proteome, and phosphoproteome. We found that TOR regulates ribosome biogenesis in plants at multiple levels, but through mechanisms that do not directly depend on 5' oligopyrimidine tract motifs (5'TOPs) found in mammalian RP mRNAs. We then show that the TOR-LARP1-5'TOP signaling axis is conserved in plants and regulates expression of a core set of eukaryotic 5'TOP mRNAs, as well as new, plant-specific 5'TOP mRNAs. Our study illuminates ancestral roles of the TOR-LARP1-5'TOP metabolic regulatory network and provides evolutionary context for ongoing debates about the molecular function of LARP1.

TDP-43 transports ribosomal protein mRNA to regulate axonal local translation in neuronal axons

Mislocalization and abnormal deposition of TDP-43 into the cytoplasm (TDP-43 proteinopathy) is a hallmark in neurons of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). However, the pathogenic mechanism of the diseases linked to TDP-43 is largely unknown. We hypothesized that the failure of mRNA transport to neuronal axons by TDP-43 may contribute to neurodegeneration in ALS and FTLD, and sought to examine the function of TDP-43 by identifying its target mRNA for axonal transport. We found that mRNAs related to translational function including ribosomal proteins (RPs) were decreased by shRNA-based TDP-43 knock-down in neurites of cortical neurons. TDP-43 binds to and transports the RP mRNAs through their 5' untranslated region, which contains a common 5' terminal oligopyrimidine tract motif and a downstream GC-rich region. We showed by employing in vitro and in vivo models that the RP mRNAs were translated and incorporated into native ribosomes locally in axons to maintain functionality of axonal ribosomes, which is required for local protein synthesis in response to stimulation and stress to axons. We also found that RP mRNAs were reduced in the pyramidal tract of sporadic ALS cases harboring TDP-43 pathology. Our results elucidated a novel function of TDP-43 to control transport of RP mRNAs and local translation by ribosomes to maintain morphological integrity of neuronal axons, and proved the influence of this function of TDP-43 on neurodegeneration in ALS and FTLD associated with TDP-43 proteinopathy.

Abstract 5865: The composition of the human ribosome varies significantly in different normal and malignant tissues

Abstract Background: In all organisms, the ribosome performs the unique and essential function of translating mRNA into protein. Since deletion of any ribosomal protein (RP) is embryonic lethal in complex eukaryotes, the ribosome is believed to be structurally uniform throughout the organism, with all RPs essential for cell viability. Results: We tested the structural homogeneity of RP use in ribosomes for normal and cancer tissues and cell lines using RP mRNA, ribosome profiling, and protein data. Analysis of RP mRNA data from 11,688 normal samples for 53 human tissues from 714 subjects and 10,363 tumor samples for 33 human cancers, normalized by total RP mRNA level per sample, showed that both normal (non-diseased) and tumor samples cluster by tissue type in humans. Matrix factorization showed that at least 3 RP mRNA signatures are necessary to describe normal blood and brain tissues, and a minimum of 16 RP mRNA signatures are necessary to describe data from 53 different normal tissues. A pan-cancer analysis of copy number variation (CNV) in 10,845 tumor samples for 33 human cancers showed that loss of one or both copies of RP genes was prevalent in every cancer type. Furthermore, there was no association between the number of double-deleted RP genes in tumors and patient survival, showing that RP loss does not reduce tumor fitness. CRISPR-Cas9 deletion of RP genes shows that many RPs are not essential in many cell lines. In several cancers, multiple RP-subtypes exist, with significant survival and genomic differences among them. These RP-subtypes often map to known molecular subtypes, and various RP genes are often deleted in one or both subtypes. This suggests that when genomic landscapes are modified in tumors, genes coding RPs are often lost, but these losses do not affect tumor viability. Analysis of mRNA data and ribosome profiling data of RP genes for cells and tissues from human, mouse and rat showed that these are highly correlated, showing that transcripts encoding ribosomal proteins are being translated into ribosomal proteins at rates proportional to their mRNA levels. Consistently, both mRNA data and ribosome profiling data of RP genes, normalized by total level per sample, showed tissue specific and development-stage specific clusters. Finally, analysis of RP protein levels in human adult and fetal tissues, standardized per sample, showed both development-stage and tissue specificity, showing that there is both tissue and development-stage specific heterogeneity of RP protein usage. Conclusions: These results suggest that there are multiple ribosome types in complex eukaryotes, with different RP composition which are regulated in a tissue and development-stage specific manner by some novel, yet unknown mechanism. Citation Format: Anshuman Panda, Anupama Yadav, Huwate Yeerna, Amartya Singh, Michael Biehl, Markus Lux, Alexander Schulz, Tyler Klecha, Sebastian Doniach, Hossein Khiabanian, Shridar Ganesan, Pablo Tamayo, Gyan Bhanot. The composition of the human ribosome varies significantly in different normal and malignant tissues [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5865.