Biology subjects

Saba, J. A.

Publications and source records attributed to Saba, J. A..

4 recordsLinked to original sources

bioRxiv2026

The LARP1 RRM functions as a ribosome responsive regulator of TOP mRNAs

Ribosome concentration varies across cell type, state, and disease, yet the mechanism by which mammalian cells sense ribosome levels to regulate ribosome synthesis remains unknown. Previous studies implicate LARP1 in binding ribosomes and, separately, in repressing mRNAs containing TOP motifs (TOPs), which encode all ribosomal proteins as well as several translation factors. Here, we show that ribosome binding is the essential licensing event for LARP1-mediated TOP repression. Phylogenetic analysis reveals that LARP1's ribosome binding region is part of a highly conserved RNA recognition motif (RRM) which is predicted to directly interact with its TOP-binding HEAT repeat domain. Ribosome binding activates the HEAT repeats to bind and repress TOPs, thereby repressing TOP translation and ribosome synthesis. Mutants which uncouple the coordinated functions of these domains constitutively repress TOPs and compromise cell fitness. These data reveal an unprecedented ribosome sensing function of LARP1, orchestrated through the unique coordinating role of its RRM, unveiling the mechanism by which mammalian cells tune ribosome synthesis to demand across diverse contexts.

molecular biology↗

bioRxiv2023

LARP1 senses free ribosomes to coordinate supply and demand of ribosomal proteins

Terminal oligopyrimidine motif-containing mRNAs (TOPs) encode all ribosomal proteins in mammals and are regulated to tune ribosome synthesis to cell state. Previous studies implicate LARP1 in 40S- or 80S-ribosome complexes that repress and stabilize TOPs. However, a mechanistic understanding of how LARP1 and TOPs interact with these complexes to coordinate TOP outcomes is lacking. Here, we show that LARP1 senses the cellular supply of ribosomes by directly binding non-translating ribosomal subunits. Cryo-EM structures reveal a previously uncharacterized domain of LARP1 bound to and occluding the 40S mRNA channel. Free cytosolic ribosomes induce sequestration of TOPs in repressed 80S-LARP1-TOP complexes independent of alterations in mTOR signaling. Together, this work demonstrates a general ribosome-sensing function of LARP1 that allows it to tune ribosome protein synthesis to cellular demand. One-Sentence SummaryLARP1 directly binds free ribosomal subunits to repress TOP mRNAs

molecular biology↗

bioRxiv2023

Conserved cardiolipin-mitochondrial ADP/ATP carrier interactions assume distinct structural and functional roles that are clinically relevant

The mitochondrial phospholipid cardiolipin (CL) promotes bioenergetics via oxidative phosphorylation (OXPHOS). Three tightly bound CLs are evolutionarily conserved in the ADP/ATP carrier (AAC in yeast; adenine nucleotide translocator, ANT in mammals) which resides in the inner mitochondrial membrane and exchanges ADP and ATP to enable OXPHOS. Here, we investigated the role of these buried CLs in the carrier using yeast Aac2 as a model. We introduced negatively charged mutations into each CL-binding site of Aac2 to disrupt the CL interactions via electrostatic repulsion. While all mutations disturbing the CL-protein interaction destabilized Aac2 monomeric structure, transport activity was impaired in a pocket-specific manner. Finally, we determined that a disease-associated missense mutation in one CL-binding site in ANT1 compromised its structure and transport activity, resulting in OXPHOS defects. Our findings highlight the conserved significance of CL in AAC/ANT structure and function, directly tied to specific lipid-protein interactions.

biochemistry↗

bioRxiv2022

Bursting Translation on Single mRNAs in Live Cells

Stochasticity has emerged as a mechanism to control gene expression. Much of this so-called "noise" has been attributed to bursting transcription. However, the stochasticity of translation has not similarly been investigated due to a lack of enabling imaging technologies. We developed techniques to track single mRNAs and their translation in live cells for hours, allowing measurement of previously uncharacterized translation dynamics. We applied genetic and pharmacological perturbations to control translation kinetics. Like transcription, translation is not a constitutive process but instead cycles between inactive and active states or "bursts". But unlike transcription, which is largely frequency modulated, complex structure in the 5-untranslated region alters burst amplitude. Bursting frequency can be controlled through cap-proximal sequences and trans-acting factors such as eIF4F. We coupled single molecule imaging with stochastic modeling to deduce the fundamental kinetic parameters of translational bursting, a new dimension of translational control. HighlightsO_LILong-term tracking of single mRNAs reveals multi-state, bursting translation C_LIO_LIStructure in the 5-untranslated region modulates translational burst amplitude C_LIO_LI5-cap proximal sequences modulate translational burst frequency C_LIO_LImTOR signaling adjusts translation bursting to respond to environmental cues C_LI

molecular biology↗