Biology subjects

Ramakrishnan, V.

Publications and source records attributed to Ramakrishnan, V..

14 recordsLinked to original sources

bioRxiv2026

Molecular Architecture of the Human GCN1-ABCF3 Ribosome Collision Sensor

The Integrated Stress Response is a critical eukaryotic signaling pathway that maintains cellular proteostasis. During amino acid scarcity, the yeast kinase Gcn2 (GCN2 in humans) and its activators Gcn1/Gcn20 phosphorylate eIF2 to reprogram translation, but how GCN2 senses nutrient stress in mammals is not known. Ribosome collisions serve as a major physiological trigger. Here we report a cryo-EM structure of human GCN1 bound to collided di-ribosomes. GCN1 specifically recognizes and rigidifies the flexible interface of the collided di-ribosome. Binding is mediated by contacts with both ribosomal P-stalks and a conserved segment that "pinches" the beak of the 40S subunit of the trailing ribosome. Functional assays confirm that multivalent Gcn1 contacts with collided ribosomes are essential for full Gcn2 activation in stressed yeast cells. Using nanobody-based proteomics in cells deprived of prolyl-tRNA, we identify ABCF3 as the primary mammalian ortholog of yeast Gcn20 recruited to ribosomes during amino acid starvation.

biochemistry↗

bioRxiv2026

Sequence-Specific Reduction of Interlimb Accuracy Asymmetry Reveals Preserved Motor Learning Dynamics in Chronic Stroke: Insights from Lesion-Aware fMRI

Background: People with chronic stroke retain the capacity to learn new motor skills, yet how preserved motor learning is expressed during practice remains incompletely understood. Sequence learning provides a useful model for examining these within-session learning dynamics and their neural basis after stroke. Objective: To characterize a temporally resolved behavioral phenotype of motor sequence learning in chronic stroke and establish its neural context using task-based functional MRI (fMRI). Methods: Twenty-four individuals with chronic stroke and 14 neurologically healthy controls performed a bimanual force-tracking sequence-learning task during functional MRI. Performance convergence was defined as the sequence-specific reduction in the accuracy difference between the paretic and less-affected hands across practice. Neural activity was evaluated using whole-brain, region-of-interest, and functional-connectivity analyses following preprocessing tailored to structurally heterogeneous stroke lesions. Results: Stroke participants demonstrated significant performance convergence despite persistent motor impairment, indicating preserved expression of sequence learning during practice that was not detected by conventional behavioral measures. Lesion-aware fMRI identified robust task-related activation and preserved stage-dependent modulation within cerebellar, premotor, and striatal learning networks, together with reduced bilateral putaminal activity after stroke. However, preregistered analyses found no reproducible associations between individual differences in performance convergence and learning-related activation or functional connectivity. Conclusions: Performance convergence provides a sensitive, temporally resolved behavioral phenotype of preserved motor sequence learning in chronic stroke that complements conventional endpoint measures. Together, performance convergence and task-based functional MRI provide a framework for investigating individual differences in motor learning capacity and their implications for rehabilitation responsiveness.

neuroscience↗

bioRxiv2025

Molecular architecture and diversity of StopGo/2A translational recoding

Viral 2A sequences trigger a co-translational peptide bond formation "skipping" event, termed "StopGo", to generate two separate proteins from a single open reading frame without classical termination. To investigate the mechanism of StopGo, we determined the cryo-EM structure of a mammalian ribosome positioned at the foot-and-mouth disease virus 2A (F2A) site. The structure shows how interactions between the F2A nascent chain (NC) and the ribosomal exit tunnel induce a conformational change in the peptidyl transferase center that precludes further translation elongation but instead pre-exposes the P-tRNA:F2A-NC ester bond for hydrolysis and NC release. Additionally, we bioinformatically characterized variation and host association across nearly 10,000 StopGo sequences identified in virus genomes. We expanded the canonical core motif to (D/G/C/N)(V/I)ExNPGP and identified additional rare but functional variants. We also revealed several distinct upstream motifs that we showed biochemically to be important for StopGo activity. Interestingly, although StopGo is known to be functionally active in plants, we found no evidence for natural utilization of StopGo by plant viruses. Overall, these findings provide valuable insights into a unique translation recoding mechanism, and lay foundations for further optimization of multi-gene expression in biotechnology.

molecular biology↗

bioRxiv2025

Mechanism of translation initiation on endogenous eukaryotic circular RNAs

Eukaryotic circular RNAs (circRNAs) perform a wide variety of functions. A subset of circRNAs has been demonstrated to undergo translation in vivo. However, few insights exist on the underlying translation mechanisms. Here, we elucidate the basis of translation initiation in two naturally occurring circular RNAs, circMbl and circSfl. We show that in vitro prepared versions of both circRNAs are translated in eukaryotic cell lysates and cells. Initiation depends on the untranslated region (UTR) and can be reconstituted using only the 43S pre-initiation complex, eukaryotic initiation factors 4G, 4A, 4B, and, for circSfl, the RNA helicase DHX29. Functional assays and structural analysis of the initiation complexes suggest that scanning until recognition of the start codon follows initial ribosome landing occurring on AU-rich, accessible UTR patches upstream of the initiation sites. Together, these results provide key insights into how eukaryotic ribosomes engage with and initiate translation on circular endogenous transcripts.

molecular biology↗

bioRxiv2025

Multi Omics Driven Polypharmacology for Osteoarthritis Joint Regeneration

Osteoarthritis (OA) is a common degenerative condition of major joints with no effective cure. Yograj Guggulu (YG) is a well-established polyherbal formulation in Indian traditional medicine for the management of joint disorders. However, its mode of action remains unclear. We integrated multi omics network analysis with a rat model to investigate the effects of oral administration of YG on osteoarthritic joints. YG administration significantly alleviated pain and improved joint function. Imaging and histological analyses reveal that YG protects against structural degeneration in the joint with OA. Proteomic and metabolomic profiling, along with network analysis, uncovered that multiple components of YG alter protein expression in key pathways related to inflammation and cartilage degradation, thus validating the observed clinical effects. The efficacy of YG seems to be the result of the synergistic action of its diverse constituents. Our findings support the use of YG as a multitarget therapy for OA and encourage efforts for the potential repurposing of its active components.

systems biology↗

bioRxiv2025

Identification of Novel Marine-based Inhibitors against Tetracycline Destructase in Acinetobacter Baumannii using Computational Approaches

Tetracyclines are indispensable antibiotics employed to treat a broad spectrum of bacterial infections. However, the emergence of clinical pathogens exhibiting significant resistance to these drugs has posed a formidable challenge in managing bacterial diseases effectively. This resistance is attributed to the proliferation and diversity of resistance genes and various mechanisms that render tetracyclines inactive. A prevalent mechanism of resistance is enzymatic inactivation by tetracycline destructases, which compromises the efficacy of tetracyclines. Consequently, there is a pressing need to discover novel molecules capable of inhibiting tetracycline destructases activity and thereby enhancing the drugs potency. In this study, we identify novel inhibitors for tetracycline destructase (TDase) in Acinetobacter Baumannii, utilizing compounds derived from marine environments. Through a high-throughput virtual screening approach, we have investigated the potent natural marine compounds interaction and dynamic behaviour of tetracycline destructase through molecular simulations. These findings hold promise for the development of novel and efficacious therapeutics against bacterial infections.

bioinformatics↗

bioRxiv2024

Human tumor suppressor protein Pdcd4 binds at the mRNA entry channel in 40S small ribosomal subunit

Translation is regulated mainly in the initiation step, and its dysregulation is implicated in many human diseases. Several proteins have been found to regulate translational initiation, including Pdcd4 (programmed cell death gene 4). Pdcd4 is a tumor suppressor protein that prevents cell growth, invasion, and metastasis. It is downregulated in most tumor cells, while global translation in the cell is upregulated. To understand the mechanisms underlying translational control by Pdcd4, we used single-particle cryo-electron microscopy to determine the structure of human Pdcd4 bound to 40S small ribosomal subunit, including Pdcd4-40S and Pdcd4-40S-eIF4A-eIF3-eIF1 complexes. The structures reveal the binding site of Pdcd4 at the mRNA entry site in the 40S, where the C-terminal domain (CTD) interacts with eIF4A at the mRNA entry site, while the N-terminal domain (NTD) is inserted into the mRNA channel and decoding site. The structures, together with quantitative binding and in vitro translation assays, shed light on the critical role of the NTD for the recruitment of Pdcd4 to the ribosomal complex and suggest a model whereby Pdcd4 blocks the eIF4F-independent role of eIF4A during recruitment and scanning of the 5' UTR of mRNA.

biochemistry↗

bioRxiv2022

The structure of a human translation initiation complex reveals two independent roles for the helicase eIF4A

SummaryInitiation of mRNA translation is a key regulatory step in gene expression in all eukaryotes. Canonical initiation of translation in eukaryotes involves recruitment of the 43S preinitiation complex to the 5' end of mRNA by the cap-binding complex eIF4F to form the 48S initiation complex (48S), followed by scanning along the mRNA until the start codon is selected.1-8 We have previously shown that eIF4F binds near the mRNA channel exit site of the 43S, leaving an open question about how mRNA secondary structure is removed as it enters the mRNA binding channel on the other side of the 40S subunit.4 Here we describe a human 48S positioned at the start codon that shows that in addition to the eIF4A that is part of eIF4F, there is a second eIF4A helicase bound to the mRNA entry site. The entry channel bound eIF4A is positioned through interactions with eIF3 and the 40S subunit to enable its ATP-dependent helicase activity to directly unwind secondary structure located downstream of the scanning 48S complex. The structure also reveals universally conserved interactions between eIF4F and the 48S, likely explaining how this complex can promote mRNA recruitment in all eukaryotes. mRNA translation has emerged as an important tool for developing innovative therapies, yet several fundamental aspects of its regulation remain unknown. This work sheds light on the critical regulatory roles of eIF4A and eIF4F during the recruitment and scanning of the 5' UTR of mRNA.

molecular biology↗

bioRxiv2022

Signatures for Viral Infection and Inflammation in the Proximal Olfactory System in Familial Alzheimer's Disease

ObjectiveAlzheimers disease (AD) is characterized by loss of smell and olfactory system pathology that precedes the diagnosis of dementia. Understanding these early processes can potentially identify diagnostic and therapeutic targets to slow AD progression. Here we analyzed differential gene and protein expression in the olfactory bulb (OB) and olfactory tract (OT) of familial AD (FAD) individuals carrying the autosomal dominant presenilin 1 E280A paisa mutation and age-matched controls. MethodsFormalin-fixed, paraffin-embedded sections containing both the OB and OT from 6 FAD individuals and 6 age-matched controls were obtained. Tissue morphology and composition were characterized by immunohistochemistry using antibodies against the myelin marker proteolipid protein (PLP), amyloid-beta (A{beta}), and microglia/macrophage markers Iba1 and CD68, respectively. OB and OT were analyzed separately by targeted RNA sequencing of the whole human transcriptome (BioSpyder TempO-Seq); ingenuity pathway analysis and R-computational program were used to identify differentially expressed genes and pathways between groups. The nanoString spatial proteomics assay for 88 proteins, including markers for AD and immune responses, was used to complement gene expression findings. ResultsCompared to control OT, FAD OT had significantly increased immunostaining for A{beta} and CD68 in the high and low myelinated regions, as well as increased immunostaining for Iba1 in the high myelinated region only; both control and FAD OT samples had similar total area of high and low myelinated regions. In FAD samples, RNA sequencing showed a transcription profile consistent with: (1) viral infection in the OB; (2) inflammation in the OT that carries information via entorhinal cortex from the OB to hippocampus, a brain region essential for learning and memory; and (3) decreased oligodendrocyte deconvolved transcripts, indicating dysregulation of myelination. Interestingly, spatial proteomic analysis confirmed altered myelination in the OT of FAD individuals, implying dysfunction of communication between the OB and hippocampus. ConclusionsThese findings raise the possibility that viral infection and associated inflammation and dysregulation of myelination of the olfactory system may disrupt downstream hippocampal function, contributing to acceleration of FAD progression.

neuroscience↗

bioRxiv2021

Visualising formation of the ribosomal active site in mitochondria

Ribosome assembly is an essential and complex process that is regulated at each step by specific biogenesis factors. Using cryo-electron microscopy, we identify and order major steps in the formation of the highly conserved peptidyl transferase centre (PTC) and tRNA binding sites in the large subunit of the human mitochondrial ribosome (mitoribosome). The conserved GTPase GTPBP7 regulates the folding and incorporation of core 16S ribosomal RNA (rRNA) helices and the ribosomal protein bL36m, and ensures that the PTC base U3039 has been 2'-O-methylated. Additionally, GTPBP7 binds the RNA methyltransferase NSUN4 and MTERF4, which facilitate earlier steps by sequestering H68-71 of the 16S rRNA and allowing biogenesis factors to access the maturing PTC. Consistent with the central role of NSUN4*MTERF4 and GTPBP7 during mitoribosome biogenesis, in vivo mutagenesis designed to disrupt binding of their Caenorhabditis elegans orthologs to the large subunit potently activates mitochondrial stress responses and results in severely reduced viability, developmental delays and sterility. Next-generation RNA sequencing reveals widespread gene expression changes in these mutant animals that are indicative of mitochondrial stress response activation. We also answer the long-standing question of why NSUN4 but not its enzymatic activity, is indispensable for mitochondrial protein synthesis in metazoans.

biochemistry↗

bioRxiv2018

Structural basis for the inhibition of translation through eIF2α phosphorylation

One of the responses to stress by eukaryotic cells is the down-regulation of protein synthesis by phosphorylation of translation initiation factor eIF2. Phosphorylation results in low availability of the eIF2 ternary complex (eIF2-GTP-tRNAi) by affecting its interaction with its GTP-GDP exchange factor eIF2B. We have determined the cryo-EM structure of eIF2B in complex with phosphorylated eIF2 at an overall resolution of 4.15 [A]. Two eIF2 molecules bind opposite sides of an eIF2B hetero-decamer through eIF2-D1, which contains the phosphorylated Ser51. eIF2-D1 is mainly inserted between the N-terminal helix bundle domains of {delta} and subunits of eIF2B. Phosphorylation of Ser51 enhances binding to eIF2B through direct interactions of phosphate groups with residues in eIF2B and indirectly by inducing contacts of eIF2 helix 58-63 with eIF2B{delta} leading to a competition with Met-tRNAi.

biophysics↗

bioRxiv2018

The beta propellers of eIF3b and eIF3i relocate together to the ribosomal intersubunit interface during translation initiation

During eukaryotic translational initiation, the 48S ribosomal pre-initiation complex (PIC) scans the 5 untranslated region of mRNA until it encounters a start codon. We present a single particle electron cryomicroscopy (cryo-EM) reconstruction of a yeast 48S PIC in an open scanning-competent state in which eIF3b is observed bound on the 40S subunit interface. eIF3b is re-located with eIF3i from their solvent-interface locations observed in other PIC structures; however, eIF3i is not in contact with the 40S. Re-processing of micrographs of our previous 48S PIC in a closed state using currently available tools reveal a similar re-location of eIF3b and eIF3i from the solvent to subunit interface. Genetic analysis indicates that high fidelity initiation in vivo depends strongly on eIF3b interactions at the subunit interface that either promote the closed conformation of the PIC on start codon selection or facilitate subsequent relocation back to the solvent side of the 40S subunit.

molecular biology↗

bioRxiv2018

Translational initiation factor eIF5 replaces eIF1 on the 40S ribosomal subunit to promote start-codon recognition

In eukaryotic translation initiation AUG recognition of the mRNA requires accommodation of Met-tRNAi in a \"PIN\" state, which is antagonized by the factor eIF1. eIF5 is a GTPase activating protein (GAP) of eIF2 that additionally promotes stringent AUG selection, but the molecular basis of its dual function was unknown. We present a cryo-electron microscopy (cryo-EM) reconstruction of a 48S pre-initiation complex (PIC), at an overall resolution of 3.0 [A], featuring the N-terminal domain (NTD) of eIF5 bound to the 40S subunit at the location vacated by eIF1. eIF5 interacts with and allows a more accommodated orientation of Met-tRNAi. Substitutions of eIF5 residues involved in the eIF5-NTD/tRNAi interaction influenced initiation at near-cognate UUG codons in vivo, and the closed/open PIC conformation in vitro, consistent with direct stabilization of the codon:anticodon duplex by the wild-type eIF5-NTD. The present structure reveals the basis for a key role of eIF5 in start-codon selection.

biophysics↗

bioRxiv2017

GTP Hydrolysis by eIF5B in the Last Step of Translation Initiation Is Activated by a Rotation of the Small Ribosomal Subunit.

Placement of an initiator aminoacyl-tRNA [(f)Met-tRNA[Formula]] base paired with the AUG initiation codon of a messenger RNA (mRNA) is the first step of translation. The eukaryotic translation factor eIF5B or its bacerial homologue IF2 facilitate the correct positioning of initiator tRNA in the P site of the ribosome. We report the electron cryomicroscopy (cryoEM) structure of a stabilized intermediate state of a yeast 80S/tRNAiMet/eIF5B complex at 3.6 [A] resolution. The structure shows how a universally conserved tyrosine couples the rotational state of the small ribosomal subunit with GTP hydrolysis.

biochemistry↗