Cited by Respiratory Syncytial Virus (RSV) optimizes the translational landscape during infection

Optimizing Protein Production in the One-Pot PURE System: Insights into Reaction Composition and Expression Efficiency DOI

Yan Zhang, Matas Deveikis, Yanping Qiu

et al.

ACS Synthetic Biology, Journal Year: 2025, Volume and Issue: unknown

Published: April 10, 2025

The One-Pot PURE (Protein synthesis Using Recombinant Elements) system simplifies the preparation of traditional systems by coculturing and purifying 36 essential proteins for gene expression in a single step, enhancing accessibility affordability widespread laboratory adoption customization. However, replicating this protocol to match productivity can take considerable time effort due uncharacterized variability. In work, we observed unstable protein original strains, E. coli M15/pREP4 BL21(DE3), addressed issue using glucose-mediated catabolite repression minimize burdensome background expression. We also identified several limitations making strain unsuitable expression, including coculture incompatibility with BL21(DE3) proteolytic activity. showed that consolidating all vectors into protease-deficient minimized proteolysis, led more uniform cell growth at induction, improved stoichiometry critical translation initiation factors final mixture efficient cell-free production. addition optimizing composition, found variations commercial energy solution formulations could compensate suboptimal stoichiometry. Notably, altering source tRNAs alone significant differences capacity reactions, highlighting importance tRNA codon usage influencing yield. Taken together, work systematically investigates proteome biochemical productivity, offering insights enhance its robustness adaptability across laboratories.

Language: Английский

Citations

mRNA-based vaccines and therapies - a revolutionary approach for conquering fast-spreading infections and other clinical applications: a review DOI

Mingyue Pan,

Weiling Cao, Jingbo Zhai

et al.

International Journal of Biological Macromolecules, Journal Year: 2025, Volume and Issue: unknown, P. 143134 - 143134

Published: April 1, 2025

Language: Английский

Citations

Codon-dependent regulation of mRNA translation and stability by ZC3H7A and ZC3H7B RNA-binding proteins DOI

Patric Harris Snell,

Parisa Naeli,

Aitor Garzia

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 23, 2025

Summary Decelerated translation elongation caused by non-optimal codons can reduce mRNA stability through codon optimality-mediated degradation . A key element of this process is the coupling sensing usage with regulation efficiency and stability. We report that two paralog RNA-binding proteins (ZC3H7A ZC3H7B), which are only found in Chordates, preferentially bind to mRNAs enriched A/U at their wobble sites (A/U3 codons). ZC3H7A/B engage ribosomes lack factors induce or block initiation interactions CCR4-NOT GIGYF2/4EHP repressor complex, respectively. Depletion 4EHP impairs repression A/U3-rich mRNAs. This study provides insights into a unique mechanism higher eukaryotes couples

Language: Английский

Citations

Considerations for mRNA Product Development, Regulation and Deployment Across the Lifecycle DOI

John Howard Skerritt

Vaccines, Journal Year: 2025, Volume and Issue: 13(5), P. 473 - 473

Published: April 28, 2025

With the successful deployment of several mRNA vaccines against SARS-CoV-2, an vaccine RSV (respiratory syncytial virus) and a large pipeline products other infectious diseases, cancers rare it is important to examine whole product lifecycle. technology enables design, testing manufacturing systems be rapidly developed, but these advantages can lost if factors that determine public access are not closely considered. This review analyzes key aspects lifecycle including candidate manufacturing, quality safety storage. Regulatory thinking well advanced in some countries others, more thought on regulation outside pandemic situation as therapeutics individual neoantigen therapies disease treatments needed. Consumer acceptance—the “social license operate” around products—is critical for their uptake, particularly pandemic.

Language: Английский

Citations

Translation efficiency covariation across cell types is a conserved organizing principle of mammalian transcriptomes DOI

Yue Liu, Ian Hoskins,

Michael Geng

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 11, 2024

ABSTRACT Characterization of shared patterns RNA expression between genes across conditions has led to the discovery regulatory networks and novel biological functions. However, it is unclear if such coordination extends translation, a critical step in gene expression. Here, we uniformly analyzed 3,819 ribosome profiling datasets from 117 human 94 mouse tissues cell lines. We introduce concept Translation Efficiency Covariation (TEC), identifying coordinated translation types. nominate potential mechanisms driving regulation. TEC conserved cells helps uncover Moreover, our observations indicate that proteins physically interact are highly enriched for positive covariation at both translational transcriptional levels. Our findings establish as organizing principle mammalian transcriptomes.

Language: Английский

Citations

Comprehensive translational profiling and STE AI uncover rapid control of protein biosynthesis during cell stress DOI

Attila Horváth, Yoshika Janapala,

Katrina Woodward

et al.

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 52(13), P. 7925 - 7946

Published: May 9, 2024

Abstract Translational control is important in all life, but it remains a challenge to accurately quantify. When ribosomes translate messenger (m)RNA into proteins, they attach the mRNA series, forming poly(ribo)somes, and can co-localize. Here, we computationally model new types of co-localized ribosomal complexes on identify them using enhanced translation complex profile sequencing (eTCP-seq) based rapid vivo crosslinking. We detect long disome footprints outside regions non-random elongation stalls show these are linked initiation protein biosynthesis rates. subject disomes other artificial intelligence (AI) analysis construct new, accurate self-normalized measure translation, termed stochastic efficiency (STE). then apply STE investigate changes yeast undergoing glucose depletion. Importantly, that, well beyond tagging stalls, provide rich insight translational mechanisms, polysome dynamics topology. AI ranks cellular mRNAs by absolute rates under given conditions, assist identifying its elements will facilitate development next-generation synthetic biology designs mRNA-based therapeutics.

Language: Английский

Citations

Predicting the translation efficiency of messenger RNA in mammalian cells DOI

Dinghai Zheng, Jun Wang,

Logan Persyn

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 11, 2024

The degree to which translational control is specified by mRNA sequence poorly understood in mammalian cells. Here, we constructed and leveraged a compendium of 3,819 ribosomal profiling datasets, distilling them into transcriptome-wide atlas translation efficiency (TE) measurements encompassing >140 human mouse cell types. We subsequently developed RiboNN, multitask deep convolutional neural network, classic machine learning models predict TEs hundreds types from sequence-encoded features, achieving state-of-the-art performance (r=0.79 r=0.78 for mean TE across types). While the majority earlier solely considered 5′ UTR sequence, RiboNN integrates contributions full-length that UTR, CDS, 3′ respectively possess ~67%, 31%, 2% per-nucleotide information density specification TEs. Interpretation revealed spatial positioning low-level di- tri-nucleotide features (i.e., including codons) largely explain model performance, capturing mechanistic principles such as how processivity tRNA abundance output. predictive behavior base-modified therapeutic RNA, can evolutionary selection pressures UTRs. Finally, it detects common language governing regulatory highlights interconnectedness translation, stability, localization organisms.

Language: Английский

Citations

Optimizing protein expression in the One-Pot PURE System: Insights into reaction composition and translation efficiency DOI

Yan Zhang, Matas Deveikis, Yanping Qiu

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 19, 2024

ABSTRACT The One-Pot PURE ( P rotein synthesis U sing R ecombinant E lements) system simplifies the preparation of traditional systems by co-culturing and purifying 36 essential proteins for gene expression in a single step, thereby improving accessibility affordability widespread laboratory adoption customization. However, replicating this protocol to match productivity can take considerable time effort due uncharacterized variability system’s biochemical composition. In work, we observed unstable protein E. coli strains M15/pREP4 BL21(DE3) addressed using glucose-mediated catabolite repression minimize burdensome background expression. We also identified differences optimal induction timing between these two strains, leading growth incompatibility co-culture, proteolysis expressed M15/pREP4. showed that consolidating all vectors into protease-deficient strain could proteolysis. This single-strain led more uniform cell at induction, stoichiometry critical translation initiation factors reaction efficient production. addition optimizing composition, found variations commercial energy solution formulations compensate suboptimal stoichiometry. Moreover, our study revealed significant capacity commercially available tRNAs, suggesting potential tRNA codons improve translation. Taken together, work highlights complex interplay influencing presents strategies its robustness productivity.

Language: Английский

Citations

Engineering of mRNA vaccine platform with reduced lipids and enhanced efficacy DOI

Tianjiao Ji, Xu Ma, Shaoli Liu

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 8, 2024

Abstract Lipid nanoparticles (LNPs) are the most clinically relevant vehicles for mRNA vaccines. Despite great successes, toxicity caused by high dose of lipid components still represents a challenge. The suboptimal loading efficiency in LNPs not only compromises vaccine’s efficacy but also heightens risk non-specific immune responses, accelerates clearance from bloodstream, and exacerbates side effects associated with carriers. These problems underscore urgent need improving to provide dose-sparing effects. Herein, we developed manganese ion (Mn²⁺) mediated enrichment strategy efficiently form high-density core, termed Mn-mRNA nanoparticle, which is subsequently coated lipids. resulting nanosystem, L@Mn-mRNA, achieved over twice compared conventional vaccine formulations (LNP-mRNA). Remarkably, L@Mn-mRNA demonstrated 2-fold increase cellular uptake LNP-mRNA, attributed enhanced stiffness provided core. By combining improved superior uptake, significantly antigen-specific responses therapeutic as We elucidated mechanism behind construction optimized formulations, this method suitable types lipids mRNAs. Thus, holds significant potential platform next generation lipid-based

Language: Английский

Citations

mRNA疫苗理性设计：从经验到人工智能设计 DOI

Yuxuan Hu,

Chengtao Pu,

Boxiang Liu

et al.

Chinese Science Bulletin (Chinese Version), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 1, 2024

Citations