Talks

Galaxy clusters are visible across the electromagnetic spectrum. Observations of their structure, abundance, and evolution provide constraints to cosmology. We are in a golden age of statistical power for galaxy clusters, where observations will provide multiwavelength data for tens of thousands of galaxy clusters. However, our ability to maximize the use of clusters as cosmology probes is limited by how well we measure cluster masses and quantify systematic effects in galaxy cluster detection and characterization. I will discuss modeling efforts that enable us to test for systematics that arise from both astrophysical and observational effects.

RNA undergoes a variety of chemical modifications after transcription, which are essential for RNA maturation and function. Over 150 RNA modifications have been identified to date, yet only about 16% of them are conserved across all three domains of life—eukaryotes, archaea, and bacteria. The vast majority of RNA modifications are domain- or species-specific, suggesting that RNA modifications have been independently acquired and fixed during evolution to meet diverse environmental challenges. We are engaged in a project to identify novel RNA modifications from various sources, and have reported 18 modifications so far. Taking advantage of mass spec analysis of RNA modifications, we identified more than 50 genes responsible for tRNA modifications, rRNA modifications as well as mRNA modification.
Ribosomal RNAs (rRNAs) contain a wide variety of post-transcriptional modifications which play critical roles in ribosome assembly and function. Recently we discovered two stereoselective rRNA methylations in the peptidyl-transferase center (PTC) of 50S ribosomal subunit in Escherichia coli cultured under anaerobic conditions. We also identified the rlmX gene which encodes a cobalamin-dependent radical SAM methyltransferase responsible for these methylations. Double knockout strain of rlmX and rlhA (responsible for ho5C2501) exhibited anaerobic growth reduction. Biochemical studies showed that protein synthesis and peptide bond formation were promoted by these rRNA modifications. Cryogenic electron microscopy (cryo-EM) structure of E. coli 70S ribosome indicated that these hypoxia-induced rRNA modifications stabilize the P-site and the PTC. These findings demonstrated that ribosomes are activated by the hypoxia-induced rRNA modifications to enhance translational capability, thereby surviving in anaerobic conditions.
The physiological importance of RNA modification is highlighted by human diseases caused by aberrant RNA modification. We previously reported a severe reduction in the frequency of tRNA modifications in mitochondrial disease patients, like MELAS and MERRF. These findings provided the first evidence of RNA modification disorder. We call “RNA modopathy” as a new category of human diseases. Recently, we successfully introduced tRNA modifications into mutant tRNAs by expressing tRNA-modifying enzymes in the MELAS patient cells. In this presentation, I am gonna talk on our efforts toward future gene therapy.

RNA undergoes a variety of chemical modifications after transcription, which are essential for RNA maturation and function. Over 150 RNA modifications have been identified to date, yet only about 16% of them are conserved across all three domains of life—eukaryotes, archaea, and bacteria. The vast majority of RNA modifications are domain- or species-specific, suggesting that RNA modifications have been independently acquired and fixed during evolution to meet diverse environmental challenges. We are engaged in a project to identify novel RNA modifications from various sources, and have reported 18 modifications so far. Taking advantage of mass spec analysis of RNA modifications, we identified more than 50 genes responsible for tRNA modifications, rRNA modifications as well as mRNA modification.
Ribosomal RNAs (rRNAs) contain a wide variety of post-transcriptional modifications which play critical roles in ribosome assembly and function. Recently we discovered two stereoselective rRNA methylations in the peptidyl-transferase center (PTC) of 50S ribosomal subunit in Escherichia coli cultured under anaerobic conditions. We also identified the rlmX gene which encodes a cobalamin-dependent radical SAM methyltransferase responsible for these methylations. Double knockout strain of rlmX and rlhA (responsible for ho5C2501) exhibited anaerobic growth reduction. Biochemical studies showed that protein synthesis and peptide bond formation were promoted by these rRNA modifications. Cryogenic electron microscopy (cryo-EM) structure of E. coli 70S ribosome indicated that these hypoxia-induced rRNA modifications stabilize the P-site and the PTC. These findings demonstrated that ribosomes are activated by the hypoxia-induced rRNA modifications to enhance translational capability, thereby surviving in anaerobic conditions.
The physiological importance of RNA modification is highlighted by human diseases caused by aberrant RNA modification. We previously reported a severe reduction in the frequency of tRNA modifications in mitochondrial disease patients, like MELAS and MERRF. These findings provided the first evidence of RNA modification disorder. We call “RNA modopathy” as a new category of human diseases. Recently, we successfully introduced tRNA modifications into mutant tRNAs by expressing tRNA-modifying enzymes in the MELAS patient cells. In this presentation, I am gonna talk on our efforts toward future gene therapy.

RNA undergoes a variety of chemical modifications after transcription, which are essential for RNA maturation and function. Over 150 RNA modifications have been identified to date, yet only about 16% of them are conserved across all three domains of life—eukaryotes, archaea, and bacteria. The vast majority of RNA modifications are domain- or species-specific, suggesting that RNA modifications have been independently acquired and fixed during evolution to meet diverse environmental challenges. We are engaged in a project to identify novel RNA modifications from various sources, and have reported 18 modifications so far. Taking advantage of mass spec analysis of RNA modifications, we identified more than 50 genes responsible for tRNA modifications, rRNA modifications as well as mRNA modification. Ribosomal RNAs (rRNAs) contain a wide variety of post-transcriptional modifications which play critical roles in ribosome assembly and function. Recently we discovered two stereoselective rRNA methylations in the peptidyl-transferase center (PTC) of 50S ribosomal subunit in Escherichia coli cultured under anaerobic conditions. We also identified the rlmX gene which encodes a cobalamin-dependent radical SAM methyltransferase responsible for these methylations. Double knockout strain of rlmX and rlhA (responsible for ho5C2501) exhibited anaerobic growth reduction. Biochemical studies showed that protein synthesis and peptide bond formation were promoted by these rRNA modifications. Cryogenic electron microscopy (cryo-EM) structure of E. coli 70S ribosome indicated that these hypoxia-induced rRNA modifications stabilize the P-site and the PTC. These findings demonstrated that ribosomes are activated by the hypoxia-induced rRNA modifications to enhance translational capability, thereby surviving in anaerobic conditions. The physiological importance of RNA modification is highlighted by human diseases caused by aberrant RNA modification. We previously reported a severe reduction in the frequency of tRNA modifications in mitochondrial disease patients, like MELAS and MERRF. These findings provided the first evidence of RNA modification disorder. We call “RNA modopathy” as a new category of human diseases. Recently, we successfully introduced tRNA modifications into mutant tRNAs by expressing tRNA-modifying enzymes in the MELAS patient cells. In this presentation, I am gonna talk on our efforts toward future gene therapy.

Ribosome collisions activate the ribotoxic stress response (RSR) mediated by the MAP3K ZAKα (ZAK), which in turn regulates downstream phosphorylation of the MAPKs JNK and p38 and cell fate consequences. Previous in vivo studies have shown that ZAK associates with ribosomes and that this interaction likely occurs through the highly negatively charged C-terminal ribosome binding region. Upon widespread ribosome collisions, ZAK becomes phosphorylated and is released from ribosomes. Despite its central role in cell fate decisions during cellular stress, a structural understanding of the ZAK-ribosome interaction and how this interaction leads to ZAK-activation has remained elusive. Here, we combine biochemistry with structural studies to dissect ZAK interactions with ribosomes in various states both in vivo and in vitro. We identify regions of ZAK necessary for binding to ribosomes under untreated conditions. We discover how interactions between ZAK and the collision-interface mediate ZAK activation. Further, we provide insight into how this process is negatively regulated to prevent constitutive ZAK activation. Collectively, we show that ZAK directly binds at the collided ribosome interface giving molecular insight into kinase regulation at the ribosome.

Ribosome collisions activate the ribotoxic stress response (RSR) mediated by the MAP3K ZAKα (ZAK), which in turn regulates downstream phosphorylation of the MAPKs JNK and p38 and cell fate consequences. Previous in vivo studies have shown that ZAK associates with ribosomes and that this interaction likely occurs through the highly negatively charged C-terminal ribosome binding region. Upon widespread ribosome collisions, ZAK becomes phosphorylated and is released from ribosomes. Despite its central role in cell fate decisions during cellular stress, a structural understanding of the ZAK-ribosome interaction and how this interaction leads to ZAK-activation has remained elusive. Here, we combine biochemistry with structural studies to dissect ZAK interactions with ribosomes in various states both in vivo and in vitro. We identify regions of ZAK necessary for binding to ribosomes under untreated conditions. We discover how interactions between ZAK and the collision-interface mediate ZAK activation. Further, we provide insight into how this process is negatively regulated to prevent constitutive ZAK activation. Collectively, we show that ZAK directly binds at the collided ribosome interface giving molecular insight into kinase regulation at the ribosome.

The rate and accuracy of protein synthesis (translation) is an important determinant of bacterial growth. Ribosomal RNAs (rRNAs), transfer RNAs (tRNAs) and tRNA-modifying enzymes (MEs) are among the key components of the translation repertoire. In rapidly growing bacteria, these components are often present in multiple gene copies (e.g. tRNAs) and exhibit functional backups (e.g. tRNAs and tRNA MEs). However, the costs and consequences of this redundancy are not fully understood. Here, we conducted experimental evolution on 17 E. coli ancestral strains with targeted deletions of distinct translation components and varying extent of translational redundancy. The adaptation strategies observed across 102 independent adaptation lines ranged from phenotypic modulations to point mutations and gene duplications. Strains with large and redundant ancestral translational repertoires potentially adapted via upregulation of the backup components and showed minimal genomic changes. In contrast, strains with a compromised translational repertoire adapted via duplication or overexpression of backup genes. However, the strains with compromised translation repertoires —and no gene-copy backups— often failed to adapt or declined in fitness. Overall, our results unravel how the redundancy of translational repertoire influences bacterial growth and adaptation.

Bacterial translation is quite redundant, with multiple copies of key RNAs and functional redundancies across components. But the degree of redundancy varies across species, and has puzzled scientists for a long time. In this talk I will describe how this problem was approached, what we now know, and what mysteries remain.

Bio for Luis Serrano:

Luis Serrano did his undergraduate and masters in math at the University of Waterloo, his PhD in algebraic combinatorics at the University of Michigan, and a postdoctoral fellowship at the University of Quebec at Montreal. He then went to industry, working in AI at Google, Apple, in large language models at Cohere, and in quantum AI at Zapata Computing. He has taught courses in AI at platforms like Udacity and Coursera, and hosts the popular YouTube channel Serrano Academy with over 180 thousand subscribers. He’s also the author of the Amazon bestseller Grokking Machine Learning.