Jamie H. D. Cate

tRNA-derived second messengers confer bacterial immunity

The paper identifies a bacterial immune pathway where tRNA cleavage generates second messengers that trigger cell death via RNA-guided nuclease activity.

Improving RNA Secondary Structure Prediction Through Expanded Training Data

The paper improves RNA secondary structure prediction by training a deep learning model on a new dataset of RNA sequences and structures, showing better generalization to unseen RNA families.

Enzymatic formation of a conserved isoaspartate in ribosomal protein uS11

The paper identifies an enzymatic pathway for isoaspartate formation in bacterial ribosomal protein uS11, showing its conservation and structural importance.

Structure and evolution-guided design of minimal RNA-guided nucleases

The paper designs active RNA-guided nucleases using AI and structure-guided methods, validated by cryo-EM and functional testing across species.

A family of archaeal hibernation factors that bind in tandem and protect ribosomes in dormant cells

This study identifies a family of archaeal hibernation factors that bind to ribosomes in tandem and protect them during dormancy.

eIF3 interactions with miRNAs involved in translational control of early T cell activation

The paper investigates eIF3 interactions with miRNAs during early T cell activation, finding that eIF3 binds miR-17~92 cluster miRNAs and that their disruption affects T cell activation markers.

Altering the ribosome exit tunnel to improve consecutive incorporation of challenging monomers

This study shows that an A2062U mutation in 23S rRNA improves ribosome activity for translating sequences with challenging monomers like proline and β2-hydroxy acids.

Translational Downregulation of 5' TOP mRNAs During T Cell Exhaustion

The paper identifies translational repression of 5' TOP mRNAs in exhausted human CD8+ T cells despite elevated mTOR activity.

Overcoming the eIF2α Brake in Human Cell-Derived Translation Systems

This paper identifies eIF2 phosphorylation as a major barrier to translation in human cell-derived systems and presents strategies to overcome it through genome editing or expression-based rescue.

Structure of an Archaeal Ribosome with a Divergent Active Site

The paper identifies divergent ribosomal RNA sequences in the PTC of archaea and determines their structure, revealing sequence variation and a novel hibernation factor.

miRNA-Mediated Regulation of Gene Expression During Early Activation in Jurkat Cells

The paper analyzes miRNA-mediated gene regulation during early T cell activation using multi-omics data, revealing distinct regulatory patterns based on translation efficiency and miRNA binding site density.

Circular 23S rRNA within archaeal ribosomes

The paper identifies circular 23S rRNA in archaeal ribosomes, showing they are more abundant than linear forms and confirms their structure through sequencing and modeling.

eIF3 engages with 3'-UTR termini of highly translated mRNAs

The paper shows eIF3 binds to 3'-UTR termini of highly translated mRNAs, suggesting a general role in translation regulation and mRNA circularization.

Role of ribosomal protein bS1 in orthogonal mRNA start codon selection

This study investigates the role of ribosomal protein bS1 in start codon selection by engineering E. coli ribosomes lacking bS1 and finding that bS1 binding is not essential for orthogonality.

RNA language models predict mutations that improve RNA function

The paper develops an RNA language model to predict mutations that enhance RNA thermostability using a new database of RNA sequences linked to environmental temperatures.

RNA elements required for the high efficiency of West Nile Virus-induced ribosomal frameshifting

This study identifies RNA elements critical for high-efficiency ribosomal frameshifting in West Nile Virus, revealing structural and sequence requirements and implications for antiviral strategies.

JUN mRNA Translation Regulation is Mediated by Multiple 5' UTR and Start Codon Features

This study identifies sequence and structural features in the JUN 5' UTR that regulate translation, showing the involvement of eIF4A and multiple start codons.

Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates

The paper uses atomistic simulations to identify structural criteria for substrates that can be efficiently incorporated by the E. coli ribosome.

Robust T cell activation requires an eIF3-driven burst in T cell receptor translation

This study identifies eIF3's role in regulating TCR translation via 3-UTR binding, enhancing CAR-T cell efficacy in vitro.

The N-terminal and central domains of CoV-2 nsp1 play key functional roles in suppression of cellular gene expression and preservation of viral gene expression

This study identifies key residues in SARS-CoV-2 nsp1 that regulate host and viral mRNA translation, revealing functional differences between these mRNA types.

crispr2vec: Machine Learning Model Predicts Off-Target Cuts of CRISPR systems

crispr2vec predicts off-target cuts of CRISPR systems using a deep metric learning model trained on sgRNA sequences.

A burst in T cell receptor translation mediated by eIF3 interactions with T cell receptor mRNAs

The paper identifies eIF3's role in enhancing TCR translation during T cell activation through interactions with 3-UTRs of TCR mRNAs.

Repression of ferritin light chain translation by human eIF3

The paper identifies eIF3 as a repressor of FTL mRNA translation and shows that SNPs causing hyperferritinemia disrupt this repression.

Phazolicin - a Novel Thiazole/Oxazole-Modified Peptide Inhibiting the Bacterial Ribosome in a Species-Specific Way.

The paper discovers a new LAP antibiotic, phazolicin, which inhibits bacterial ribosomes in a species-specific manner by blocking the exit tunnel.

PTBP1 mRNA isoforms and regulation of their translation

The paper identifies PTBP1 mRNA isoforms and shows their cell cycle-dependent regulation by eIF3, affecting PTBP1 protein levels and downstream processes.

Cellular response to small molecules that selectively stall protein synthesis by the ribosome

The paper identifies genetic modifiers of cell growth in response to a PCSK9 translational inhibitor and reveals their roles in ribosome quality control.

Kluyveromyces marxianus as a robust synthetic biology platform host

This paper engineers Kluyveromyces marxianus to create a synthetic biology platform with enhanced traits for industrial applications.

Role for Ribosome-Associated Complex and Stress-Seventy subfamily B (RAC-Ssb) in integral membrane protein translation

The paper identifies a new quality control pathway for integral membrane proteins involving RAC-Ssb that couples translation rate to the unfolded protein response.

Screening and directed evolution of transporters to improve xylodextrin utilization in the yeast Saccharomyces cerevisiae

The paper identifies and evaluates transporters for improved xylodextrin utilization in yeast and discusses challenges in directed evolution.

Cellobiose consumption uncouples extracellular glucose sensing and glucose metabolism in Saccharomyces cerevisiae

The paper uncouples glucose sensing from metabolism in yeast by using a cellobiose pathway, revealing new regulatory mechanisms for ATP management and energy homeostasis.