iCodon customizes gene expression based on the codon composition

Diez, Michay; Medina-Muñoz, Santiago G.; Castellano, Luciana Andrea; Pescador, Gabriel da Silva; Wu, Qiushuang; Bazzini, Ariel

doi:10.1038/s41598-022-15526-7

Cited by 24 publications

(25 citation statements)

References 65 publications

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“…The Trichoplax adhaerens AKDF 19383 sequence was established by additional genome annotation of the Genbank TRIADDRAFT_19383 sequence (described in Fig. S4 legend), codon-optimized for Xenopus laevis in iCodon 69 , and commercially synthesized and cloned into a modified pSP64-poly(A) vector (full sequence in Supplemental text).…”

Section: Plasmids and Molecular Biologymentioning

confidence: 99%

Constitutive activity of ionotropic glutamate receptors via hydrophobic substitutions in the ligand-binding domain

Seljeset

Sintsova

Wang

et al. 2023

Preprint

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Neurotransmitter ligands electrically excite neurons by activating ionotropic glutamate receptor (iGluR) ion channels. Knowledge of the iGluR amino acid residues that dominate ligand-induced activation would enable the prediction of function from sequence. We therefore explored determinants of activity in rat NMDA-type iGluRs (NMDA receptors), complex heteromeric iGluRs comprising two glycine-binding GluN1 and two glutamate-binding GluN2 subunits, using amino acid sequence analysis, mutagenesis, and electrophysiology. We find that a broadly conserved aspartate residue controls both ligand potency and channel activity, to the extent that certain substitutions at this position bypass the need for ligand-binding in GluN1 subunits, generating NMDA receptors activated solely by glutamate. Furthermore, we identify a homomeric iGluR from the placozoanTrichoplax adhaerensthat has utilized this crucial residue to evolve into a leak channel that is inhibited by neurotransmitter binding, pointing to a dominant role of this residue throughout the iGluR superfamily.

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Section: Plasmids and Molecular Biologymentioning

confidence: 99%

Constitutive activity of ionotropic glutamate receptors via hydrophobic substitutions in the ligand-binding domain

Seljeset

Sintsova

Wang

et al. 2023

Preprint

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“…For mRNA production, vectors were linearized with NotI (NEB) and in vitro transcribed using mMessage mMachine SP6 kit (Ambion). A DNA fragment for mScarlet-i3 46 was codon-optimized using iCodon 57 , purchased from IDT as GBlocks and cloned into pCS2+ NbALFA as described above. pCS2+mNeonGreen-C Cloning Vector was a gift from Ken-Ichi Takemaru (http://n2t.net/addgene:128144; RRID:Addgene_128144 Degron GEAR adapters and degron reporters Zebrafish fbxw11b ORF was amplified from pCS2+ zGrad (Addgene plasmid # 119716) and cloned into pCS2+ GEAR binder clones to replace EGFP ORF using InFusion enzyme (Takara).…”

Section: Molecular Cloningmentioning

confidence: 99%

Genetically encoded affinity reagents (GEARs): A toolkit for visualizing and manipulating endogenous protein functionin vivo

Boswell,

Hoppe,

Sherrard

et al. 2023

Preprint

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Probing endogenous protein localization and function in vivo remains challenging due to laborious gene targeting and monofunctional alleles. Here, we develop a multifunctional, universal, and adaptable toolkit based on genetically encoded affinity reagents (GEARs). GEARs use nanobodies and single chain variable fragments (scFv), which recognize small epitopes, enabling fluorescent visualization and selective degradation of protein targets in vivo. Furthermore, we delineate a CRISPR/Cas9-based epitope tagging pipeline to demonstrate its utility for producing knock-in alleles that have broad multifunctionality. We use GEARs to examine the native behaviour of the pioneer transcription factor Nanog and the planar cell polarity protein Vangl2 during early zebrafish development. Together, this toolkit provides a versatile system for probing and perturbing endogenous protein function while circumventing challenges associated with conventional gene targeting and is broadly available to the model organism community.

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“…The mRNA stability of the zebrafish genes was predicted from the protein-coding sequences using iCodon algorithm [69]. Only sequences with a length multiple of three were used for the analysis.…”

Section: Mrna Stability Prediction By Icodonmentioning

confidence: 99%

“…In addition to nascent peptides held in ribosomes, codon sequences also affect the ribosome traversal [68]. Interestingly, genome-wide prediction of mRNA stability by iCodon, which accounts for the effect of codons on mRNA stability, revealed that mRNAs encoding zinc finger transcription factors are significantly unstable in humans [69]. Moreover, iCodon predicted that zebrafish C2H2-ZF genes were significantly unstable, and C2H2-ZF genes upregulated in MZznf598 were predicted to be even less stable (Supplemental Figure 5I).…”

Section: Sequence Features That Induce Ribosome Stalling At C2h2-zfmentioning

confidence: 99%

Translation of zinc finger domains induces ribosome collision and Znf598-dependent mRNA decay in vertebrates

Ishibashi

Shichino

Han

et al. 2023

Preprint

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Quality control of translation is crucial for maintaining cellular and organismal homeostasis. Obstacles in translation elongation induce ribosome collision, which is monitored by multiple sensor mechanisms. The E3 ubiquitin ligase ZNF598 recognizes collided ribosomes, triggering ribosome-associated quality control (RQC) to rescue stalled ribosomes and no-go decay (NGD) to degrade stall-prone mRNAs in eukaryotes. However, the role of RQC and NGD in maintaining the translational homeostasis of endogenous mRNAs has remained largely unclear. In this study, we investigated endogenous substrate mRNAs of NGD using the maternal-to-zygotic transition (MZT) of zebrafish embryos as a model system. Combining RNA-Seq analysis of znf598 mutant embryos with disome profiling and reporter assays, we revealed that mRNAs encoding the C2H2-type zinc finger domain (C2H2-ZF) frequently cause ribosome collisions and induce NGD during the MZT. Furthermore, we showed that mRNAs encoding C2H2-ZF are degraded by ZNF598 in human cells. Our results suggest that NGD maintains the quality of the translatome during protein evolution and animal development by mitigating the risk of ribosome collision at the abundantly present C2H2-ZF mRNA sequences.

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iCodon customizes gene expression based on the codon composition

Cited by 24 publications

References 65 publications

Constitutive activity of ionotropic glutamate receptors via hydrophobic substitutions in the ligand-binding domain

Constitutive activity of ionotropic glutamate receptors via hydrophobic substitutions in the ligand-binding domain

Genetically encoded affinity reagents (GEARs): A toolkit for visualizing and manipulating endogenous protein functionin vivo

Translation of zinc finger domains induces ribosome collision and Znf598-dependent mRNA decay in vertebrates

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