Transcription Translation Research Articles

THE NEWLY DISCOVERED MONUMENTS OF THE OLD PERMIAN LANGUAGE AND SCRIPT

The paper for the first time publishes monuments of the Old Permian language written with Abur, or the script of St. Stephen of Perm; these sources are previously unknown or have not been introduced into academic circulation. They are published here as fac-similes, with transliteration, transcription, and Russian translation. Perhaps the oldest of these inscriptions (from the 1460s — the early 1470s?) is the postscript written in a mixture of Old Permian and Russian at the end of the Church Slavonic Homilae by St. Gregory the Great: it was copied in the Ferapontov Monastery, in the White Lake area, perhaps by the hand of St. Martinianus of White Lake (Belozersky). The next earliest of the Old Permian documents — and the earliest to be dated precisely — is scribal mar-ginalia on a manuscript book with the spiritual homilies of St. Isaac the Syrian in a Church Slavonic translation; it was copied in Ust-Vym (the Komi area) in 1486 by Gabriel (Gavrila) the Deacon (Ki̮ldaś). Other Old Permian postscripts were made at the court of the archbishop of Novgorod the Great in the early 1490s in two volumes with the new Church Slavonic translations from the Vulgate; they were prepared in the circle of Archbishop Gennady of Novgorod and Pskov. Finally, the last word of the late 15th — early 16th century inscription in the Church Slavonic Corpus Areopagiticum has been re-attributed as Old Permian rather than Slavic cryptog-raphy in Abur; this book was donated to the Annunciation Church of Ust-Vym by St. Pitirim, bishop of Perm. The total number of new texts is 37 word-forms, including lexemes that were not previously recorded for this period — this is significant for the Old Permian corpus of the 15th — early 16th centuries. Although from the graphic, phonetic, grammatical, and lexical points of view, these texts basically represent the same linguistic system found in previously known Old Permian monu-ments, they demonstrate, on the one hand, the inclusion of Old Permian scribes into the activities of professional Old Russian scrip-toria and, on the other, they testify to the emergence of interest on the part of East Slavic bookmen in “indigenous” languages. Knowing these languages could be a sign of belonging to a special intellectual stratum that included both the creators of the first Church Slavonic complete biblical collection (the Gennady Bible) and members of the so-called heresy of the Judaizers.

Yeast stress granules at a glance.

The formation of stress granules (SGs), membrane-less organelles that are composed of mainly messenger ribonucleoprotein assemblies, is the result of a conserved evolutionary strategy to cellular stress. During their formation, which is triggered by robust environmental stress, SGs sequester translationally inactive mRNA molecules, which are either forwarded for further processing elsewhere or stored during a period of stress within SGs. Removal of mRNA molecules from active translation and their sequestration in SGs allows preferential translation of stress response transcripts. By affecting the specificity of mRNA translation, mRNA localization and stability, SGs are involved in the overall cellular reprogramming during periods of environmental stress and viral infection. Over the past two decades, we have learned which processes drive SGs assembly, how their composition varies under stress, and how they co-exist with other subcellular organelles. Yeast as a model has been instrumental in our understanding of SG biology. Despite the specific differences between the SGs of yeast and mammals, yeast have been shown to be a valuable tool to the study of SGs in translation-related stress response. This review summarizes the data surrounding SGs that are formed under different stress conditions in Saccharomyces cerevisiae and other yeast species. It offers a comprehensive and up-to-date view on these still somewhat mysterious entities.

Transfer Specifics of Spanish Realities into Russian

Abstract: The article deals with the problem of the transfer of Spanish realities in translation. It was found out that the difficulties in translating realities, on the one hand, are due to the lack of an equivalent or analogue in the translation language, and on the other hand, the need to transfer the subject (semantic) meaning, taking into account the connotation (nationalhistorical coloring). As a result of the analysis of the translation text of the novel, it was found that translators mainly resort to such methods of translating realities as transcription, descriptive and approximate translation. Keywords: realities; transcription; transliteration; semantics; descriptive translation; approximate translation

Quantitative model suggests both intrinsic and contextual features contribute to the transcript coding ability determination in cells.

Gene transcription and protein translation are two key steps of the 'central dogma.' It is still a major challenge to quantitatively deconvolute factors contributing to the coding ability of transcripts in mammals. Here, we propose ribosome calculator (RiboCalc) for quantitatively modeling the coding ability of RNAs in human genome. In addition to effectively predicting the experimentally confirmed coding abundance via sequence and transcription features with high accuracy, RiboCalc provides interpretable parameters with biological information. Large-scale analysis further revealed a number of transcripts with a variety of coding ability for distinct types of cells (i.e. context-dependent coding transcripts), suggesting that, contrary to conventional wisdom, a transcript's coding ability should be modeled as a continuous spectrum with a context-dependent nature.

Global Analysis of Transcriptome and Translatome Revealed That Coordinated WNT and FGF Regulate the Carapacial Ridge Development of Chinese Soft-Shell Turtle.

The turtle carapace is composed of severely deformed fused dorsal vertebrae, ribs, and bone plates. In particular, the lateral growth in the superficial layer of turtle ribs in the dorsal trunk causes an encapsulation of the scapula and pelvis. The recent study suggested that the carapacial ridge (CR) is a new model of epithelial–mesenchymal transition which is essential for the arrangement of the ribs. Therefore, it is necessary to explore the regulatory mechanism of carapacial ridge development to analyze the formation of the turtle shell. However, the current understanding of the regulatory network underlying turtle carapacial ridge development is poor due to the lack of both systematic gene screening at different carapacial ridge development stages and gene function verification studies. In this study, we obtained genome-wide gene transcription and gene translation profiles using RNA sequencing and ribosome nascent-chain complex mRNA sequencing from carapacial ridge tissues of Chinese soft-shell turtle at different development stages. A correlation analysis of the transcriptome and translatome revealed that there were 129, 670, and 135 codifferentially expressed genes, including homodirection and opposite-direction differentially expressed genes, among three comparison groups, respectively. The pathway enrichment analysis of codifferentially expressed genes from the Kyoto Encyclopedia of Genes and Genomes showed dynamic changes in signaling pathways involved in carapacial ridge development. Especially, the results revealed that the Wnt signaling pathway and MAPK signaling pathway may play important roles in turtle carapacial ridge development. In addition, Wnt and Fgf were expressed during the carapacial ridge development. Furthermore, we discovered that Wnt5a regulated carapacial ridge development through the Wnt5a/JNK pathway. Therefore, our studies uncover that the morphogenesis of the turtle carapace might function through the co-operation between conserved WNT and FGF signaling pathways. Consequently, our findings revealed the dynamic signaling pathways acting on the carapacial ridge development of Chinese soft-shell turtle and provided new insights into uncover the molecular mechanism underlying turtle shell morphogenesis.

Abstract PO-028: Pancreatic ductal adenocarcinoma is dependent on an unconventional pathway for polyamine synthesis

Abstract Targeting altered metabolism in pancreatic ductal adenocarcinoma (PDAC) has been an area of extensive investigation for over a decade now. A major hurdle however, for most anti-tumor metabolic strategies, is the high risk for toxicity, given the essential roles of metabolic pathways in the maintenance of normal tissue homeostasis. Indeed, this has been the case for targeting polyamines in cancers. Polyamines are small, highly positively charged molecules involved in multiple fundamental processes of cell growth and survival, including the synthesis of nucleic acids, modifications of chromatin structure, gene transcription and mRNA translation. Polyamine levels are significantly increased in many cancers, including PDAC. Prior anti-tumor strategies focused on pharmacological inhibition of the rate-limiting enzyme of polyamine synthesis, ornithine decarboxylase (ODC1) with little success, partially due to risk of harming normal tissues at higher drug doses. In this project, using both in vitro and in vivo mouse models of PDAC, we identified a dependency of PDAC on an unconventional way for the synthesis of the polyamine precursor ornithine, specifically from glutamine via ornithine aminotransferase (OAT); this is in contrast to its synthesis in most adult normal tissues from arginine via arginase (ARG) activity. We also identified potential key players mediating the induction of this metabolic pathway via KRAS, the main oncogenic driver in PDAC and are currently characterizing the downstream effects of polyamines on pancreatic tumor cells. The high dependency of PDAC, compared to normal tissue, on de novo ornithine synthesis via OAT provides an attractive therapeutic window for treating pancreatic cancer patients with minimal toxicity. Citation Format: Min-Sik Lee, Insia Naqvi, Courtney Dennis, Lucas Dailey, Alireza Lorzadeh, Tamara Zaytouni, Ashley Adler, Daniel S. Hitchcock, Lin Lin, Unmesh Jadhav, Clary B. Clish, Nada Y. Kalaany. Pancreatic ductal adenocarcinoma is dependent on an unconventional pathway for polyamine synthesis [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2021 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2021;81(22 Suppl):Abstract nr PO-028.

Rapid Analysis and Prediction of Drug Resistance in Leukemia By Novel Nascent RNA-Driven Flow Imaging Technologies and Biomarkers

Background:Drug selectivity and resistance is a major obstacle to successful cancer therapy, including traditional chemotherapies (Vasan, N. et al. Nature 2019), immunotherapy (Hu-Lieskovan, S. et al. Future Oncol, 2021), and epigenetic therapy (Saliba, A.N. et al. Cancer Drug Resist,2021). However, no reliable technologies and biomarkers have been developed to analyze and predict drug resistance in clinical settings. Nascent RNAs composed of mostly non-coding RNAs undergo extensive modifications at co- and post-transcriptional levels. Nascent RNAs, and their associated modifications and modifying proteins (RMPs), such as RNA 5-methylcytosine (RNA:m 5C) and RNA cytosine methyltransferases (RCMTs), regulate almost all essential bioprocesses, including chromatin remodeling, DNA transcription, RNA processing/splicing and protein translation. Largely due to technology limitation, the role of nascent RNAs and RNA epigenetics remain largely unknown. Our previous publication first demonstrated distinct cell lineage-associated, RCMTs/BRD4-mediated, drug (azacitidine)-resistant transcriptionally active chromatin structures (TAC) at nascent (newly synthesized) RNAs in leukemia cells (Cheng, J.X. et al. Nat Commun. 2018). The goal of this study is to develop novel nascent RNA/TAC-driven technologies and biomarkers that enable us to rapidly analyze and predict drug resistance in clinical settings.Results: 1.Our experimental data demonstrated that TAC and RNA epigenetics regulate the resistance to venetoclax, a selective inhibitor of the anti-apoptotic protein BCL2, in leukemia cells. There is a significant, lineage-associated, increase in specific RCMTs, such as NSUN2 and NSUN1/NOP2, in venetoclax-resistant leukemia cells. Knockdown of NSUN2 and/or NSUN1 overcome venetoclax resistance in these leukemia cells.2.Our data also demonstrated distinct patterns of drug- and lineage-specific RNA synthesis dynamics in drug-sensitive vs. -resistant leukemia cells. In drug-sensitive leukemia cells, dinaciclib, a potent a potent, selective small molecule inhibitor of CDKs inhibiting CDK1, CDK2, CDK5 and CDK9 at nano-molar concentrations (Parry, D. et al. Mol.Cancer Ther, 2010), completely inhibit nascent RNA synthesis within 3-5 min, while venetoclax and azacitidine partially inhibit nascent RNA synthesis within 15 min and 240 min, respectively. Such drug-induced inhibition of nascent RNA synthesis is completely independent of apoptosis and program cell death. In contrast, no drug-induced inhibition of nascent RNA synthesis is observed in drug-resistant leukemia cells.3.Based on our data, we have developed a novel multifactorial system that targets the unique drug- and lineage-specific features of nascent RNA synthesis, TAC and RNA epigenetics for rapid analysis and prediction of drug resistance in clinical settings.Conclusion:Our data demonstrated distinct drug- and lineage-specific patterns of RNA synthesis in drug-sensitive vs. -resistant leukemia cells, which enabled us to develop novel nascent RNA/TAC-drive technologies and biomarkers for rapid analysis and prediction of anticancer drug resistance. DisclosuresNo relevant conflicts of interest to declare.

B Cell Transcriptional Coactivator POU2AF1 (BOB-1) Is an Early Transcription Factor Modulating the Protein Synthesis and Ribosomal Biogenesis in Multiple Myeloma: With Therapeutic Implication

Multiple Myeloma (MM) is a malignancy driven by numerous genetic and epigenetic alterations. Recurrent IgH translocations, somatic mutations and copy number abnormalities all contribute to myelomagenesis, however true drivers of the disease have not been well defined.To identify new targetable dependencies in MM, we generated high-quality active enhancer landscape using large cohort of primary patient myeloma cells (n=70), MM cell lines, and normal plasma cells. We integrated this data with an in-house curated atlas of 600+ active enhancer profile across a wide range of tumor types and normal tissues. Combining these data with gene expression and genetic dependency (CRISPR KO) enabled a multidimensional integration of how transcriptional regulation intersects with tumor specific dependencies. We identified that many of the specific and potent dependencies in MM are transcription factors, especially those establishing plasma cell identity. Among these, the POU2AF1 gene, which encodes the OCA-B/BOB-1, a B cell transcriptional coactivator protein, represented the most striking dependency in MM. Although BOB-1 is expressed throughout B-cell development, we found it to be highly expressed in CD138+ plasma cells from patients with precursor conditions (MGUS and SMM) as well as symptomatic MM compared to normal plasma cells.To functionally validate the role of BOB-1 in MM, we performed loss-of-function studies using shRNA, siRNAs and antisense GapMers specific for BOB-1 and observed a significant impact on MM cell viability and cell cycle arrest. Transcriptomic analysis upon BOB-1 depletion by RNA-sequencing revealed a small set of genes commonly modulated in all 3 MM cell lines tested including the plasma cell differentiation related transcription factor XBP1 and heme oxygenase (HMOX1). Importantly, we observed ribosome biogenesis, RNA polymerase 1A transcription and mRNA translation and elongation processes to be significantly enriched among genes modulated by BOB-1 depletion in MM cells. Bob1 KD resulted in a rapid and robust decrease in the level of transcription of rDNA by RNA polymerase I as determined by qRT-PCR quantification of pre-rRNA (47S). In addition, ChiP assay revealed decreased binding of RNA polymerase 1A to the 18S ribosomal DNA promoter region in BOB-1 depleted cells compared to control. These data indicate that BOB1 downregulation results in the suppression of RNA-polymerase I activity in MM cells.RNA Pol I-dependent transcription governs abundance of rRNA and directly regulates cellular translational and proliferative capacity. Since high protein load is a feature of MM, we evaluated the role of BOB-1 in the translational efficiency of MM cells. We observed that in MM cells compared to control cells, BOB-1 KD decreased, while its overexpression significantly enhanced de novo protein synthesis. As MM is characterized by excess production of monoclonal immunoglobulins, we evaluated impact of BOB-1 perturbation on intracellular light chains (kappa or lambda) production. We observed changes in the intracellular abundance of the light chains with BOB-1 modulation in all MM cell lines tested. As a result of decreased protein production, BOB-1 depletion was associated with induction of resistance to proteasome inhibition suggesting that high expression of BOB-1 may be one the factors driving the exquisite sensitivity of MM cells to proteasome inhibitor. Interestingly, mass spectrometry analysis revealed BOB1 in a protein complex with mTOR, Raptor and mLST8 proteins which are members of mTORC1 complex which is also involved in ribosomal function and may suggest the mechanism of action of Bob-1 at molecular level.In conclusion, here we report BOB1 as a specific proximal dependency in MM cells with potential role in modulating the protein load/capacity balance and ribosomal biogenesis essential for MM cell protein production function and therefore their sensitivity to proteasome inhibition. DisclosuresShirasaki: FIMECS: Consultancy. Mitsiades: BMS: Research Funding; Nurix: Research Funding; H3 Biomedicine: Research Funding; Novartis: Research Funding; Abbvie: Research Funding; Arch Oncology: Research Funding; Janssen/Johnson & Johnson: Research Funding; Fate Therapeutics: Consultancy, Honoraria; Karyopharm: Research Funding; Sanofi: Research Funding; TEVA: Research Funding; EMD Serono: Research Funding; Adicet Bio: Membership on an entity's Board of Directors or advisory committees; FIMECS: Consultancy, Honoraria; Ionis Pharmaceuticals: Consultancy, Honoraria. Hajek: BMS: Consultancy, Honoraria, Research Funding; AbbVie: Consultancy, Honoraria; Celgene: Consultancy, Honoraria, Research Funding; Novartis: Consultancy, Research Funding; Janssen: Consultancy, Honoraria, Research Funding; Takeda: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Amgen: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Pharma MAR: Consultancy, Honoraria. Munshi: Abbvie: Consultancy; Oncopep: Consultancy, Current equity holder in publicly-traded company, Other: scientific founder, Patents & Royalties; Pfizer: Consultancy; Legend: Consultancy; Bristol-Myers Squibb: Consultancy; Janssen: Consultancy; Karyopharm: Consultancy; Celgene: Consultancy; Adaptive Biotechnology: Consultancy; Takeda: Consultancy; Amgen: Consultancy; Novartis: Consultancy.

Controlling tissue patterning by translational regulation of signaling transcripts through the core translation factor eIF3c.

Although gene expression is tightly regulated during embryonic development, the impact of translational control has received less experimental attention. Here, we find that eukaryotic translation initiation factor-3 (eIF3) is required for Shh-mediated tissue patterning. Analysis of loss-of-function eIF3 subunit c (Eif3c) mice reveal a unique sensitivity to the Shh receptor patched 1 (Ptch1) dosage. Genome-wide invivo enhanced cross-linking immunoprecipitation sequence (eCLIP-seq) shows unexpected specificity for eIF3 binding to a pyrimidine-rich motif present in subsets of 5'-UTRs and a corresponding change in the translation of these transcripts by ribosome profiling in Eif3c loss-of-function embryos. We further find a transcript specific effect in Eif3c loss-of-function embryos whereby translation of Ptch1 through this pyrimidine-rich motif is specifically sensitive to eIF3 amount. Altogether, this work uncovers hidden specificity of housekeeping translation initiation machinery for the translation of key developmental signaling transcripts.

RNA regulation in immunity.

RNA regulation in immunity.

John Philpot – Archdeacon of Winchester and Martyr (1515–1555)

This is the most comprehensive account yet of the life of John Philpot, archdeacon of Winchester cathedral and martyr, burned at the stake in 1555. Included is an outline of his trial from which it is shown that he was promised the position of archdeacon by the ultra conservative bishop of Winchester, Stephen Gardiner. Evidence is also provided from the trial and from his family, contrary to the opinion of Muriel St. Clare Byrne, that he was not related to Clement Philpot who was executed in 1540. A transcript translation of his father's will is provided giving a good indication of his family circumstances. This will was drawn up in 1540 at a pivotal point in English law when, in order to overcome the default position of inheritance through primogeniture, the rules of will writing were altered. This will was written to abide by the rules that existed before the new Statute of Wills was passed by Parliament, and, also, to abide by the new rules set out in the Statute. From this will and other evidence a new genealogy of the Philpot family down to the 1650s is provided. The authenticity of the so-called portrait of John Philpot held at Winchester cathedral is also discussed.

MiRNA-Based Regulation of Alternative RNA Splicing in Metazoans.

Alternative RNA splicing is an important regulatory process used by genes to increase their diversity. This process is mainly executed by specific classes of RNA binding proteins that act in a dosage-dependent manner to include or exclude selected exons in the final transcripts. While these processes are tightly regulated in cells and tissues, little is known on how the dosage of these factors is achieved and maintained. Several recent studies have suggested that alternative RNA splicing may be in part modulated by microRNAs (miRNAs), which are short, non-coding RNAs (~22 nt in length) that inhibit translation of specific mRNA transcripts. As evidenced in tissues and in diseases, such as cancer and neurological disorders, the dysregulation of miRNA pathways disrupts downstream alternative RNA splicing events by altering the dosage of splicing factors involved in RNA splicing. This attractive model suggests that miRNAs can not only influence the dosage of gene expression at the post-transcriptional level but also indirectly interfere in pre-mRNA splicing at the co-transcriptional level. The purpose of this review is to compile and analyze recent studies on miRNAs modulating alternative RNA splicing factors, and how these events contribute to transcript rearrangements in tissue development and disease.

Synchrony between daily rhythms of malaria parasites and hosts is driven by an essential amino acid.

Background: Rapid asexual replication of blood stage malaria parasites is responsible for the severity of disease symptoms and fuels the production of transmission forms. Here, we demonstrate that a Plasmodium chabaudi's schedule for asexual replication can be orchestrated by isoleucine, a metabolite provided to the parasite in a periodic manner due to the host's rhythmic intake of food. Methods: We infect female C57BL/6 and Per1/2-null mice which have a disrupted canonical (transcription translation feedback loop, TTFL) clock with 1×10 5 red blood cells containing P. chabaudi (DK genotype). We perturb the timing of rhythms in asexual replication and host feeding-fasting cycles to identify nutrients with rhythms that match all combinations of host and parasite rhythms. We then test whether perturbing the availability of the best candidate nutrient in vitrochanges the schedule for asexual development. Results: Our large-scale metabolomics experiment and follow up experiments reveal that only one metabolite - the amino acid isoleucine - fits criteria for a time-of-day cue used by parasites to set the schedule for replication. The response to isoleucine is a parasite strategy rather than solely the consequences of a constraint imposed by host rhythms, because unlike when parasites are deprived of other essential nutrients, they suffer no apparent costs from isoleucine withdrawal. Conclusions: Overall, our data suggest parasites can use the daily rhythmicity of blood-isoleucine concentration to synchronise asexual development with the availability of isoleucine, and potentially other resources, that arrive in the blood in a periodic manner due to the host's daily feeding-fasting cycle. Identifying both how and why parasites keep time opens avenues for interventions; interfering with the parasite's time-keeping mechanism may stall replication, increasing the efficacy of drugs and immune responses, and could also prevent parasites from entering dormancy to tolerate drugs.

The 1804 examination for the chair of Elementary Mathematics at the University of Prague

In 1804 the chair of Elementary Mathematics at Prague University became vacant and a selection procedure, which consisted of a written and an oral examination, was announced. Only Bernard Bolzano and Ladislav Jandera took part in it. Jandera was appointed to the chair, whereas Bolzano became Professor of “Religious Doctrine.” In this paper we examine the context of this Concursprüfung, the performance of both candidates and the outcome, based on a number of related papers preserved at the Czech National Archives. In addition to this, we publish for the first time, albeit only in the online version of this paper, the transcription and English translation of Bolzano's written examination.

Transcriptomic Changes in Hot Spring Frog Tadpoles (Buergeria otai) in Response to Heat Stress

Buergeria frog tadpoles exhibit high thermal tolerance and are occasionally found in water pools that temporarily exceed 40°C. With the aim of understanding how they can cope with the severe heat stress, we performed RNA-seq of three heat-treated (38°C) and three control (25°C) tadpoles and compared their transcriptomic profiles. We identified 382 differentially expressed transcripts. A protein-protein interaction (PPI) network analysis of these transcripts further identified hub proteins involved in protein degradation, stress granule assembly, and global suppression of DNA transcription and mRNA translation. Along with the avoidance behavior against high water temperature, these endurance mechanisms potentially support tadpoles to survive in high temperatures for short periods of time. Similar mechanisms may exist in many other amphibian species whose habitats are prone to high temperatures.

Synchrony between daily rhythms of malaria parasites and hosts is driven by an essential amino acid

Background: Rapid asexual replication of blood stage malaria parasites is responsible for the severity of disease symptoms and fuels the production of transmission forms. Here, we demonstrate that a Plasmodium chabaudi’s schedule for asexual replication can be orchestrated by isoleucine, a metabolite provided to the parasite in a periodic manner due to the host’s rhythmic intake of food. Methods: We infect female C57BL/6 and Per1/2-null mice which have a disrupted canonical (transcription translation feedback loop, TTFL) clock with 1×10 5 red blood cells containing P. chabaudi (DK genotype). We perturb the timing of rhythms in asexual replication and host feeding-fasting cycles to identify nutrients with rhythms that match all combinations of host and parasite rhythms. We then test whether perturbing the availability of the best candidate nutrient in vitro changes the schedule for asexual development. Results: Our large-scale metabolomics experiment and follow up experiments reveal that only one metabolite - the amino acid isoleucine – fits criteria for a time-of-day cue used by parasites to set the schedule for replication. The response to isoleucine is a parasite strategy rather than solely the consequences of a constraint imposed by host rhythms, because unlike when parasites are deprived of other essential nutrients, they suffer no apparent costs from isoleucine withdrawal. Conclusions: Overall, our data suggest parasites can use the daily rhythmicity of blood-isoleucine concentration to synchronise asexual development with the availability of isoleucine, and potentially other resources, that arrive in the blood in a periodic manner due to the host’s daily feeding-fasting cycle. Identifying both how and why parasites keep time opens avenues for interventions; interfering with the parasite’s time-keeping mechanism may stall replication, increasing the efficacy of drugs and immune responses, and could also prevent parasites from entering dormancy to tolerate drugs.

ZNF545 loss promotes ribosome biogenesis and protein translation to initiate colorectal tumorigenesis in mice

Ribosome biogenesis plays a pivotal role in tumorigenesis by supporting robust protein translation. We investigate the functional and molecular mechanism of Zinc finger protein 545 (ZNF545), a transcriptional repressor for ribosomal RNA (rRNA), in colorectal cancer (CRC). ZNF545 was silenced in CRC compared to adjacent normal tissues (P < 0.0001), implying a tumor-suppressive role. Colon-specific Znf545 knockout in mice accelerated CRC in ApcMin/+ and azoxymethane/dextran sulfate sodium-induced CRC. Mechanistically, we demonstrated that ZNF545 uses its two zinc finger clusters to bind to minimal rDNA promoter, where it assembled transcriptional repressor complex by interacting with KAP1. Znf545 deletion in mouse embryonic fibroblasts not only increased rRNA transcription rate and the nucleolar size and number but also altered the nucleolar composition and architecture with an increased number of fibrillar centers surrounded by net-like dense fibrillar components. Consequently, Znf545 deletion promoted the gene expression of translation machinery, protein translation, and cell growth. Consistent with its tumor-suppressive role, ZNF545 overexpression in CRC cells induced growth arrest and apoptosis. Finally, administration of rRNA synthesis inhibitor, CX-5461, inhibited CRC development in Znf545Δ/ΔApcMin/+ mice. In conclusion, ZNF545 suppresses CRC through repressing rRNA transcription and protein translation. Targeting rRNA biosynthesis in ZNF545-silenced tumors is a potential therapeutic strategy for CRC.

Discovery of a novel role of tumor suppressor PDCD4 in stimulation of translation termination

Programmed cell death 4 protein (PDCD4) regulates many vital cell processes, although is classified as a tumor suppressor because it inhibits neoplastic transformation and tumor growth. For example, PCDC4 has been implicated in the regulation of transcription and mRNA translation. PDCD4 is known to inhibit translation initiation by binding to eukaryotic initiation factor 4A and elongation of oncogenic c- and A-myb mRNAs. Additionally, PDCD4 has been shown to interact with poly(A)-binding protein (PABP), which affects translation termination, although the significance of this interaction is not fully understood. Considering the interaction between PABP and PDCD4, we hypothesized that PDCD4 may also be involved in translation termination. Using in vitro translation systems, we revealed that PDCD4 directly activates translation termination. PDCD4 stimulates peptidyl-tRNA hydrolysis induced by a complex of eukaryotic release factors, eRF1-eRF3. Moreover, in combination with the PABP, which also stimulates peptide release, PDCD4 activity in translation termination increases. PDCD4 regulates translation termination by facilitating the binding of release factors to the ribosome, increasing the GTPase activity of eRF3, and dissociating eRF3 from the posttermination complex. Using a toe-printing assay, we determined the first stage at which PDCD4 functions—binding of release factors to the A-site of the ribosome. However, preventing binding of eRF3 with PABP, PDCD4 suppresses subsequent rounds of translation termination. Based on these data, we assumed that human PDCD4 controls protein synthesis during translation termination. The described mechanism of the activity of PDCD4 in translation termination provides a new insight into its functioning during suppression of protein biosynthesis.

The bacterial protein Hfq: Stable modifications and growth phase-dependent changes in SPAM profiles

In bacteria transcription is coupled to translation, and while it is broadly accepted that transcription–translation complexes (TTCs) are formed in growing bacterial cells, the exact spatial organization of these macromolecular assemblies is not known with certainty. Recent studies indicated the formation of orderly cytosolic superstructures in growing E. coli cells. The bacterial nucleic acid (NA)-binding protein Hfq has been shown to function at the interface of RNA synthesis–degradation machinery; multiple, independent studies link Hfq to orderly cytosolic assemblies. In this work, using fast cell lysis/2D-PAGE and in vitro reconstitution analyses we studied the Hfq modifications and small protein-associated molecules (SPAM). We demonstrate that native Hfq carries stable modifications and simulate 2D patterns of native Hfq–SPAM complexes in reconstitution experiments with purified Hfq and synthetic NA probes. We also demonstrate that genetically engineered Hfq lacking the conserved arginine residues positioned near the rim of the disc formed by the subunits’ N-terminal domains binds DNA with a reduced affinity in comparison with wild-type Hfq. These results are consistent with the proposed Hfq-mediated DNA remodeling and point to the involvement of this patch of conserved arginines in interactions with DNA.

MiR775 integrates light, sucrose and auxin associated pathways to regulate root growth in Arabidopsis thaliana

MicroRNAs (miRNAs), a class of single-stranded non-coding RNA of 20–24 nucleotides, regulate gene expression by target gene transcript cleavage or translation inhibition. The phytohormone auxin is a crucial regulator of almost every process involved in plant growth and development. Several studies have demonstrated the involvement of miRNA(s) in the regulation of the auxin signaling pathway and plant development. However, very few studies have identified the auxin-mediated regulation of miRNA(s). In this study, we reveal the detailed mechanism of auxin-mediated regulation of the cell wall-related miR775- Galactosyl transferase (GalT) module, which plays an important role in root growth in Arabidopsis thaliana. We also showed two interdependent mechanisms by which miR775 regulates root growth: miR775-GalT and light-mediated sucrose-dependent pathways. Treatment of GUS reporter lines with Indole Acetic Acid (IAA), sucrose, and light apparently enhanced the abundance of miR775 in root tissue. miR775 overexpressing (miR775OX) lines showed changes in root architecture, including increased primary root growth and root hair, by targeting GalT. miR775OX lines also showed tolerance toward low Pi. These results provide new insights into the auxin regulation of cell wall-related miR775 and suggest its significant role in plant root growth and development by modifying the cell wall.