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Fadel Fakih

@fakih98.bsky.social
76 followers 163 following 67 posts

Fourth year PhD student at Julius Lukes Lab @BiologyCentre Studying tRNAs and translation in protists.

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Fadel Fakih @fakih98.bsky.social · 30/09/2026
What can a PhD student extract from a conference, other than good food? #PhD #PhDlife rnastuff.com/2026/09/29/c...
rnastuff.com
Conferences as a compressed view of science
Last week, I was the at the 30th tRNA conference in Greece. The great food and the soft breeze of the Mediterranean made me lazy to think beyond tRNA business; which is still my main interest never…
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Fadel Fakih @fakih98.bsky.social · 25/09/2026
Structural basis of step II spliced leader RNA trans-splicing in trypanosomatid parasites www.nature.com/articles/s41...
nature.com
Structural basis of step II spliced leader RNA trans-splicing in trypanosomatid parasites - Nature Communications
Trypanosomatid parasites rely on Spliced Leader (SL) RNA trans-splicing to produce every mature mRNA. Here, the authors present cryo-EM structures of the trans spliceosome during SL exon ligation, pro...
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Fadel Fakih @fakih98.bsky.social · 20/09/2026
Just made it to Crete, Greece - not to discuss the law's of Zues, but to discuss tRNAs at the 30th tRNA conference. #tRNA #RNA #PhD
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Fadel Fakih @fakih98.bsky.social · 17/09/2026
Very pround of my student Aknur Temirbayeva who succesfully defended her bachelor thesis today. Supervising her over the past year has been a particularly rewarding experience, especially seeing how much young people can be extremely excited about science. Congratulations, Aknur!! #RNA #RNAsky
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Fadel Fakih @fakih98.bsky.social · 09/09/2026
Alternative genetic codes in bacteria and archaea identified with a fast k-mer–based algorithm www.pnas.org/doi/10.1073/...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Fadel Fakih @fakih98.bsky.social · 07/09/2026
Stop codon readthrough in Trichomonas is a mechanism for gene expression regulation and expanding protein function www.biorxiv.org/content/10.6...
biorxiv.org
Stop codon readthrough in Trichomonas is a mechanism for gene expression regulation and expanding protein function
Trichomonas vaginalis is the causative agent of trichomoniasis, a common sexually transmitted infection among women of reproductive and peri-menopausal age. The parasite has an unusually large genome,...
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Reposted by Fadel Fakih
Ali Haidar @ahaidar.bsky.social · 31/08/2026
Thrilled to have been a part of this amazing paper with beautiful #imaging How does the #oocyte combat cytoplasmic dilution during growth ? #Translation in the Zollo Body is one way Below are our main findings 👇
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Fadel Fakih @fakih98.bsky.social · 28/08/2026
Nonviral delivery of chemically modified tRNA rescues nonsense mutations in cystic fibrosis www.science.org/doi/10.1126/...
science.org
Nonviral delivery of chemically modified tRNA rescues nonsense mutations in cystic fibrosis
Suppressor transfer RNAs (sup-tRNAs) can rescue disease-causing nonsense mutations by promoting readthrough of premature termination codons (PTCs). Their clinical translation is limited by suboptimal ...
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Fadel Fakih @fakih98.bsky.social · 27/08/2026
Evolution of tRNA gene repertoires in photosynthetic organisms link.springer.com/article/10.1...
link.springer.com
From water to land: evolution of tRNA gene repertoires in photosynthetic organisms - The EMBO Journal
Photosynthetic eukaryotes have undergone evolutionary shifts from aquatic to terrestrial habitats, accompanied by changes in genome organization and gene regulation. Yet, the evolution of transfer RNA...
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Fadel Fakih @fakih98.bsky.social · 25/08/2026
Leishmania exosomal tRNA-derived small non-coding RNA fragments modulate host THP-1 derived macrophage proteins journals.plos.org/plosone/arti...
journals.plos.org
Leishmania exosomal tRNA-derived small non-coding RNA fragments modulate host THP-1 derived macrophage proteins: A quantitative proteomic analysis
Protozoan parasites of the genus Leishmania, the causative agents of human leishmaniasis, have evolved mechanisms to manipulate host cell functions to their advantage. Recently, small non-coding RNAs ...
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Fadel Fakih @fakih98.bsky.social · 19/08/2026
Codon optimization depletes stop codons in alternative reading frames of protein-coding nucleic acid therapeutics www.pnas.org/doi/abs/10.1...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Fadel Fakih @fakih98.bsky.social · 18/08/2026
RNA Cis-Elements Involved in Animal Virus Stop Codon Readthrough: Stop Codon Context and Downstream RNA Structures www.mdpi.com/1999-4915/18...
mdpi.com
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Fadel Fakih @fakih98.bsky.social · 13/08/2026
Trypanosomal MICOS Is Assembled on Non-Respiring Mitochondrial Crista Precursors and Associates With Two Integral Microproteins onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
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Fadel Fakih @fakih98.bsky.social · 13/08/2026
Stop codon reassignment to tryptophan in members of the bacterial phylum Actinomycetota www.microbiologyresearch.org/content/jour...
microbiologyresearch.org
Stop codon reassignment to tryptophan in members of the bacterial phylum Actinomycetota
Reassignment of stop codons is a significant evolutionary event with recoding of UGA to tryptophan being previously identified in only three bacterial phyla, the Bacillota, Pseudomonadota and Verrucom...
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Fadel Fakih @fakih98.bsky.social · 07/08/2026
MiaA-mediated tRNA modifications couple tryptophan attenuation and changes in tRNA abundance to complex phenotypes in Pseudomonas aeruginosa academic.oup.com/nar/article/...
academic.oup.com
MiaA-mediated tRNA modifications couple tryptophan attenuation and changes in tRNA abundance to complex phenotypes in Pseudomonas aeruginosa
Abstract. Transfer RNA (tRNA)-modifying enzymes are emerging as key regulators of bacterial physiology. MiaA, a tRNA isopentenyltransferase, is well studie
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Fadel Fakih @fakih98.bsky.social · 05/08/2026
Anticodon nucleotide modifications affect translational tuning by the ribosomal CAR surface www.biorxiv.org/content/10.6...
biorxiv.org
Anticodon nucleotide modifications affect translational tuning by the ribosomal CAR surface
Nucleotide modifications of the tRNA anticodon can affect protein translation fidelity and speed. Chemical modifications of the anticodon nucleotide 34 are regulated under cellular stress and associat...
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Fadel Fakih @fakih98.bsky.social · 04/08/2026
A p32 family RNA editing factor acts in mitochondrial ribosome biogenesis www.biorxiv.org/content/10.6...
biorxiv.org
A p32 family RNA editing factor acts in mitochondrial ribosome biogenesis
Biogenesis of mitochondrial ribosomes (mitoribosomes) in the unicellular parasite Trypanosoma brucei requires an exceptionally large toolkit of assembly factors, identified in stable precursors of lar...
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Fadel Fakih @fakih98.bsky.social · 03/08/2026
Reassigning an amber codon to selenocysteine using a functional cysteine suppression pair in Escherichia coli www.sciencedirect.com/science/arti...
sciencedirect.com
Reassigning an amber codon to selenocysteine using a functional cysteine suppression pair in Escherichia coli
Selenoproteins, characterized by the presence of selenocysteine (Sec) residues, are widely distributed across all domains of life. The unique attribut…
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Fadel Fakih @fakih98.bsky.social · 31/07/2026
Dietary arginine drives codon-dependent MHC class I translation and improves immunity in colon tumorigenesis and respiratory viral infection www.cell.com/cell/abstrac...
cell.com
Dietary arginine drives codon-dependent MHC class I translation and improves immunity in colon tumorigenesis and respiratory viral infection
Arginine availability regulates arginyl tRNA levels and codon-dependent translation of MHC class I, tuning antigen presentation and shaping anti-viral and anti-tumor immunity.
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Fadel Fakih @fakih98.bsky.social · 30/07/2026
A newly described role for tRNA: an architectural scaffold that helps organize the mitochondrial RNA-editing machinery of trypanosomes. #RNA #rnasky #phd #biology rnastuff.com/2026/07/30/a...
rnastuff.com
A tRNA as an Architectural Scaffold in the Trypanosome Editosome
A transfer RNA (tRNA) was originally seen as a boring adaptor that brings amino acids to the ribosome during protein translation. A tRNA, with its distinct 2D cloverleaf structure, has an amino aci…
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Reposted by Fadel Fakih
Nature Reviews Molecular Cell Biology @natrevmcb.nature.com · 27/07/2026
ICYMI: New Online! Mitochondrial tRNA biogenesis, modifications and disease relevance
dlvr.it
Mitochondrial tRNA biogenesis, modifications and disease relevance
Nature Reviews Molecular Cell Biology, Published online: 24 July 2026; doi:10.1038/s41580-026-00999-5Mitochondrial tRNA (mt-tRNA) biogenesis has evolved to support a degenerate mt-tRNA structure and a simplified genetic code. Liu and colleagues provide a fascinating overview of mt-tRNA biology, discuss how mt-tRNA-associated perturbations directly cause disease, and examine how emerging knowledge will lead to targeted therapeutics.
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Fadel Fakih @fakih98.bsky.social · 28/07/2026
Structural basis of the RNA-editing cascade in trypanosome mitochondria www.nature.com/articles/s41...
nature.com
Structural basis of the RNA-editing cascade in trypanosome mitochondria - Nature
Cryo-electron microscopy sheds light on the architecture of the Trypanosoma brucei mitochondrial editosome and reveals how this assembly mediates mRNA editing through the insertion and deletion of uri...
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Fadel Fakih @fakih98.bsky.social · 27/07/2026
Cryo-EM reveals that Escherichia coli tRNA-transglycosylase can bind and act upon two tRNAs www.pnas.org/doi/abs/10.1...
pnas.org
Cryo-EM reveals that Escherichia coli tRNA-transglycosylase can bind and act upon two tRNAs | PNAS
Bacterial tRNA-guanine transglycosylases (TGT) are essential enzymes involved in tRNA modification, contributing to the virulence of multiple patho...
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Reposted by Fadel Fakih
RNA Society Journal @rnajournal.bsky.social · 24/07/2026
The 3′ UTR isn’t just a tail. Shorter regions boost translation termination, longer ones can hinder it — but structured elements rescue the process by bringing key factors together at the ribosome bit.ly/3QfcEyh
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Reposted by Fadel Fakih
Bloodsucking Parasites @bloodsparasites.bsky.social · 25/07/2026
Structural basis for emetine inhibition of ribosome translocation in Toxoplasma gondii bioRxivpreprint
dlvr.it
Structural basis for emetine inhibition of ribosome translocation in Toxoplasma gondii
Apicomplexan parasites, including Toxoplasma gondii and Plasmodium falciparum, are major human pathogens that cause toxoplasmosis and malaria, respectively. The existing structures of T. gondii translational machinery are from empty ribosomes that lack several key components, including ribosomal protein RACK1 (Receptor for Activated C Kinase 1). Here, we used cryo-electron microscopy (cryoEM) to determine high-resolution structures of T. gondii ribosomal complexes, including a translating 80S ribosome bound to mRNA and tRNA. These structures reveal that RACK1 occupies the conserved binding site on the 40S subunit observed in other eukaryotic ribosomes. We also determined the architecture of the ribosomal P-stalk and identified the ribosomal proteins uL10 and uL11, which were not observed in previous T. gondii ribosome structures. In addition, we determined structures of the 80S ribosome bound to mRNA, tRNA, and the translation inhibitor emetine in two distinct conformational states. These snapshots reveal two mechanisms by which emetine inhibits the translocation step of mRNA translation: either by dislodging the mRNA from the E-site of the ribosome or by acting as a molecular glue within the E-site, thereby stalling translocation. Together, these findings provide new insights into the molecular basis of protein synthesis in apicomplexan parasites and establish a structural framework for the development of future antiparasitic therapeutics.
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Reposted by Fadel Fakih
Bloodsucking Parasites @bloodsparasites.bsky.social · 24/07/2026
Trypanosomal MICOS is assembled on non-respiring mitochondrial crista precursors and associates with two integral microproteins bioRxivpreprint
dlvr.it
Trypanosomal MICOS is assembled on non-respiring mitochondrial crista precursors and associates with two integral microproteins
The mitochondrial contact site and cristae organizing system (MICOS) is a multiprotein complex that shapes crista junctions and maintains inner and outer membrane contacts. MICOS coordinates the assembly of electron transport chain complexes, a prerequisite for cellular respiration. Indeed, MICOS is lost in eukaryotes that dispensed with cellular respiration, suggesting that its assembly depends on the presence of an active respiratory chain. Trypanosoma brucei provides a unique system to test this hypothesis as its mitochondrion undergoes developmentally regulated remodeling. In the insect stage, the mitochondrion contains cristae with an active electron transport chain, whereas the mammalian bloodstream form possesses precursor cristae with stub-like morphology that lack respiratory activity. MICOS has been characterized in the insect stage but remains unexamined in the bloodstream form. Here, we demonstrate that all MICOS subunits assemble onto precursor cristae, retaining conserved interactions with both outer and inner membrane protein machineries. This is somewhat unexpected given the co-occurrence of MICOS with active cellular respiration in nature. Furthermore, we identify novel MICOS-associated proteins that are dispensable for its stability, suggesting auxiliary rather than core roles in MICOS function. Together, our findings establish that MICOS assembly precedes cellular respiratory competence and expand its interaction landscape in trypanosomatids.
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Reposted by Fadel Fakih
bioRxiv Genetics @biorxiv-genetic.bsky.social · 24/07/2026
Single anticodon-edited tRNA therapy targeting highly prevalent Arg>Ter premature termination codons causing inherited retinal diseases www.biorxiv.org/content/10.64898/20…
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Fadel Fakih @fakih98.bsky.social · 23/07/2026
elifesciences.org/articles/109...
elifesciences.org
Profiling of terminating ribosomes reveals translational control at stop codons
Systematic characterization of terminating ribosomes uncovers sequence features influencing ribosome dynamics at stop codons with direct implications in 3' UTR translation.
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Reposted by Fadel Fakih
bioRxiv Genomics @biorxiv-genomic.bsky.social · 16/07/2026
The genetic architecture of human programmed stop codon readthrough www.biorxiv.org/content/10.64898/20…
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Reposted by Fadel Fakih
PLOS Biology @plosbiology.org · 20/07/2026
Regulation of gene expression in the #parasite #Leishmania is largely post-transcriptional, but how is it controlled? This study shows that modification of tRNAs by #quenosine influences codon-biased translation and contributes to Leishmania virulence @plosbiology.org 🧪 plos.io/4bwvAjs
Model illustrating the role of queuosine (Q) tRNA modification in the virulence of L. mexicana. Q-tRNA levels increase significantly during the differentiation from the procyclic promastigotes (insect stage) to the axenic amastigotes (mammalian stage), underscoring the importance of Q-tRNA modification for parasite adaptation and infectivity. Loss of Q modification via LmxTGT2 knockout disrupts codon-biased translational control, leading to substantial changes in the proteome. Specifically, downregulated proteins were enriched in NAU codons decoded by Q-tRNA, while upregulated proteins predominantly contained NAC codons. The resulting codon-specific imbalance impairs the parasite’s ability to establish infection and maintain virulence. These findings demonstrate that Q modification functions as a novel post-transcriptional regulatory mechanism that fine-tunes translation during Leishmania life cycle, compensating for the lack of classical transcriptional control and promoting adaptation to the host environment.
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Reposted by Fadel Fakih
bioRxiv Biochemistry @biorxiv-biochem.bsky.social · 01/07/2026
Distinct roles of three trypanosomal Oxa1 insertases in biogenesis of mitochondrial membrane complexes www.biorxiv.org/content/10.64898/20…
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Reposted by Fadel Fakih
Ali Haidar @ahaidar.bsky.social · 24/06/2026
Whether condensates have real biological functions has long been debated. Our new Molecular Cell Perspective argues translation is a core one, not just repression. Next: live high-res imaging + probing condensate dynamics should let us get at where translation starts and how condensates shape it.
https://www.sciencedirect.com/science/article/pii/S1097276526003758
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Fadel Fakih @fakih98.bsky.social · 17/06/2026
A PhD gives you stuff beyond the sections of your CV. Check out my post on the importance of socializing with senior scientists. #PhD #biology #science rnastuff.com/2026/06/12/t...
rnastuff.com
The Invisible Education of PhD Life
Over dinner with a distinguished parasitologist, our PI told us that something very important about science is that it makes you meet very interesting people. The formal PhD experience is generally…
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Fadel Fakih @fakih98.bsky.social · 17/06/2026
A symbiotic origin of the ribosome? academic.oup.com/pnasnexus/ar...
academic.oup.com
A symbiotic origin of the ribosome?
Abstract. The origin of life is one of the great mysteries of science. Of the multiple unsolved problems, the origin of the translation system (the means b
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Reposted by Fadel Fakih
STCmicrobeblog @stcmicrobeblog.bsky.social · 20/05/2026
#RNASky
nachrichten.idw-online.de
New tool decodes the structures and motifs of RNA
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Fadel Fakih @fakih98.bsky.social · 11/05/2026
Do experiments in model organisms reveal universal biological rules, or only local regularities shaped by evolutionary history? Here is a short synthesis, inspired by our work, on how comparative genomics helps us distinguish between the two. #PhD #Biology #RNA rnastuff.com/2026/05/10/c...
rnastuff.com
Comparative Genomics, and the Boundaries of Molecular Rules
The evolution of life on Earth is a history of countless successes and failures. The variations arise through chance, but within physical, chemical, and biological organization and limitations. Nat…
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Reposted by Fadel Fakih
Faculty of Science, University of South Bohemia @fscusb.bsky.social · 07/05/2026
New research shows bacteria can redefine stop codons by shortening tRNA anticodon stems. This "extended superwobble" proves tRNAs aren't passive—they're active drivers that can evolve entirely new genetic codes! doi.org/10.1093/nar/...
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Reposted by Fadel Fakih
bioRxivpreprint @biorxivpreprint.bsky.social · 05/05/2026
A threonine-to-aspartate ACA codon reassignment in uncultivated Acidimicrobiales bacteria www.biorxiv.org/content/10.64898/20…
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Fadel Fakih @fakih98.bsky.social · 05/05/2026
We have a new preprint on a rare sense-to-sense genetic code reassignment in uncultivated Acidimicrobiales bacteria. We report evidence that ACA, normally a threonine codon, is reassigned to aspartate in a RAAP-2 lineage. #tRNA #PhD #evolution Link: www.biorxiv.org/content/10.6...
biorxiv.org
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Fadel Fakih @fakih98.bsky.social · 04/05/2026
On DRT3: a fascinating discovery that makes us rethink textbook diagrams, but does it really break the central dogma of molecular biology? #RNA #PhD #Science rnastuff.com/2026/05/04/d...
rnastuff.com
DRT3 and the Creativity of Molecular Biology
A recent Science paper described an extremely strange antiphage reverse transcriptase system, DRT3. DRT3 is made up of two RT-like proteins, DRT3a and DRT3b, and a non-coding RNA. These assemble in…
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Reposted by Fadel Fakih
Michal Kolář @mhko.bsky.social · 20/04/2026
Our latest contribution is out! In this highly collaborative paper, we show that tRNAs with a 4-base-pair anticodon stem are surprisingly frequent across organisms. Our atomistic MD simulations reveal the role of the 5th base pair. academic.oup.com/nar/article/...
academic.oup.com
Frequent occurrence and predicted functions of tRNAs with 4-base-pair anticodon stems in bacteria: extended superwobble hypothesis
Abstract. Recently, a tRNATrpCCA with a 4-base-pair (bp) anticodon stem (AS) was shown to efficiently recognize a near-cognate UGA codon in unicellular euk
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Fadel Fakih @fakih98.bsky.social · 21/04/2026
Check out my new post! It is a short and accessible digest of our recently published work in Nucleic Acids Research, highlighting the main findings and the broader implications of the study. #RNA #RNAsky #evolution #science #PhD rnastuff.com/2026/04/20/t...
rnastuff.com
The 4-bp anticodon stem tRNA: an anarchist of the genetic code
In our genetics 101, we often learn that the genetic code is a strict dictionary. But biology, as we know it, is the wonderland of exceptions. In fact, the genetic code can only be called “nearly u…
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Fadel Fakih @fakih98.bsky.social · 20/04/2026
My first author paper is published in @narjournal.bsky.social , co-led with Satish Nandipati and Ambar Kachale. In this work, we build on the implications of the unusual genetic code features of Blastocrithidia nonstop... #RNAsky #RNA #evolution #molecular academic.oup.com/nar/article/...
academic.oup.com
Validate User
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Fadel Fakih @fakih98.bsky.social · 26/03/2026
Subcellular proteomics reveals a blueprint for endosymbiont integration in trypanosomatid Angomonas deanei. www.nature.com/articles/s41...
nature.com
Subcellular proteomics reveals a blueprint for endosymbiont integration in trypanosomatid Angomonas deanei - Nature Communications
The flagellated protist Angomonas deanei harbours a bacterial endosymbiont. Here, Hammond et al. report a high-confidence subcellular proteome, localising 5,796 proteins of the protist and its endosym...
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Fadel Fakih @fakih98.bsky.social · 20/03/2026
The origin of life challenge is about finding the right corridor of usefull disorder. What does QT45 tell us about that? Check the latest post on my blog! #RNA #PhD rnastuff.com/2026/03/19/w...
rnastuff.com
Why evolution needs noise: in the light of QT45 ribozyme
A violet amethyst crystal, while beautiful on the outside, is a highly ordered structure at the microscopic level, and therefore cannot evolve. In contrast, a gas is highly random and cannot store …
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Fadel Fakih @fakih98.bsky.social · 06/11/2025
We just got an ERC synergy to work on our beloved tRNAs and see what nature could tell us! Very happy and excited to be part of this mission! Congratulations to all the 4 labs! More in this link: erc.europa.eu/news-events/... #ERC #synergy_grants #RNA #rnasky
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Fadel Fakih @fakih98.bsky.social · 04/09/2025
Day 2 of #EMBLProtein meeting in Heidelberg, great talks and discussions with pioneers in the field. Also, if you're interested in tRNAs and their role in codon re-assignment visit my poster (nb 108) #rnasky
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Fadel Fakih @fakih98.bsky.social · 06/08/2025
You can go your own way: The targeting signals of trypanosomatid parasites journals.plos.org/plospathogen...
journals.plos.org
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Fadel Fakih @fakih98.bsky.social · 31/07/2025
A preprint from Paris lab showing a novel layer of gene expression regulation in leishmania. #rna #rnasky www.biorxiv.org/content/10.1...
biorxiv.org
Codon biased translation mediated by Queuosine tRNA modification is essential for the virulence of Leishmania mexicana
The complex life cycle of the human parasite Leishmania mexicana requires rapid translational adaptation for survival in two distinct environments: the insect vector and the mammalian host. These medi...
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Fadel Fakih @fakih98.bsky.social · 31/07/2025
Blastocrithidia-A Genetic Alien from the Planet Earth pubmed.ncbi.nlm.nih.gov/40721315/
pubmed.ncbi.nlm.nih.gov
Blastocrithidia-A Genetic Alien from the Planet Earth - PubMed
The standard genetic code, which applies almost without exception, is the key to our understanding of molecular biological processes. Although it is close to impossible to imagine that sparse code cha...
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