The conserved Tpk1 regulates non-homologous end joining double-strand break repair by phosphorylation of Nej1, a homolog of the human XLF

Jessulat, Matthew; Amin, Shahreen; Hooshyar, M. A.; Malty, Ramy H.; Moutaoufik, Mohamed Taha; Zilocchi, Mara; Istace, Zoe; Phanse, Sadhna; Aoki, Hiroyuki; Omidi, Katayoun; Burnside, Daniel; Samanfar, Bahram; Aly, Khaled A.; Golshani, Ashkan; Babu, M. Madan

doi:10.1093/nar/gkab585

Cited by 5 publications

(4 citation statements)

References 51 publications

(92 reference statements)

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“…Negative genetic interaction (nGI) implies that the simultaneous deletion of two genes produces a more severe phenotypic effect than the phenotypes observed with individual gene deletions alone [ 33 ]. An nGI between two genes suggests a functional association between the two gene functions and has been used as a measure to investigate the activity of various genes in DNA repair [ 42 ], cell cycle [ 43 ], transcription [ 26 ] and translation [ 39 ], etc.…”

Section: Resultsmentioning

confidence: 99%

The Involvement of YNR069C in Protein Synthesis in the Baker’s Yeast, Saccharomyces cerevisiae

Takallou,

Hajikarimlou,

Al-gafari

et al. 2024

Biology

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Maintaining translation fidelity is a critical step within the process of gene expression. It requires the involvement of numerous regulatory elements to ensure the synthesis of functional proteins. The efficient termination of protein synthesis can play a crucial role in preserving this fidelity. Here, we report on investigating a protein of unknown function, YNR069C (also known as BSC5), for its activity in the process of translation. We observed a significant increase in the bypass of premature stop codons upon the deletion of YNR069C. Interestingly, the genomic arrangement of this ORF suggests a compatible mode of expression reliant on translational readthrough, incorporating the neighboring open reading frame. We also showed that the deletion of YNR069C results in an increase in the rate of translation. Based on our results, we propose that YNR069C may play a role in translation fidelity, impacting the overall quantity and quality of translation. Our genetic interaction analysis supports our hypothesis, associating the role of YNR069C to the regulation of protein synthesis.

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Section: Resultsmentioning

confidence: 99%

The Involvement of YNR069C in Protein Synthesis in the Baker’s Yeast, Saccharomyces cerevisiae

Takallou,

Hajikarimlou,

Al-gafari

et al. 2024

Biology

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“…These three Tpks have distinct substrates and different functions in cellular processes 36 . For example, Tpk1, but not Tpk2 and Tpk3 regulates non-homologous end joining double-stranded break repair by phosphorylating Nej1 37 . While Tpk2 activates pseudohyphal growth, Tpk3 inhibits filamentation and Tpk1 has no effect 38 .…”

Section: Resultsmentioning

confidence: 99%

“…The different behavior of Tpk isoforms on Jhd2 is consistent with the study performed by Ptacek et al that three Tpks have distinct substrate specificities and most substrates are recognized by only one of the Tpks 36 . Tpk1, but not Tpk2 and Tpk3 regulates non-homologous end joining double-stranded break repair by phosphorylating Nej1 37 . Tpk2 activates pseudohyphal growth, while Tpk3 inhibits filamentation and Tpk1 has no effect 38 .…”

Section: Discussionmentioning

confidence: 98%

Phosphorylation of Jhd2 by the Ras-cAMP-PKA(Tpk2) pathway regulates histone modifications and autophagy

Gong

Tong

et al. 2022

Nat Commun

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Cells need to coordinate gene expression with their metabolic states to maintain cell homeostasis and growth. How cells transduce nutrient availability to appropriate gene expression remains poorly understood. Here we show that glycolysis regulates histone modifications and gene expression by activating protein kinase A (PKA) via the Ras-cyclic AMP pathway. The catalytic subunit of PKA, Tpk2 antagonizes Jhd2-catalyzed H3K4 demethylation by phosphorylating Jhd2 at Ser321 and Ser340 in response to glucose availability. Tpk2-catalyzed Jhd2 phosphorylation impairs its nuclear localization, reduces its binding to chromatin, and promotes its polyubiquitination and degradation by the proteasome. Tpk2-catalyzed Jhd2 phosphorylation also maintains H3K14 acetylation by preventing the binding of histone deacetylase Rpd3 to chromatin. By phosphorylating Jhd2, Tpk2 regulates gene expression, maintains normal chronological life span and promotes autophagy. These results provide a direct connection between metabolism and histone modifications and shed lights on how cells rewire their biological responses to nutrient signals.

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“…Cells with defects in the NHEJ pathway are expected to display reduced survival compared to the wt, assessed by the normalized number of colonies formed from transformations with linearized vs circular plasmids for a given yeast strain. YKU80 and the recently discovered TPK1 are known to be important for NHEJ (233,254,258) thus strains yku80∆ and tpk1∆ were used as positive controls. Repair efficiency of 5' overhangs was reduced by approximately 30% in YHI9∆ cells compared to the wt.…”

Section: Efficiency Of Dna Repair By Nhejmentioning

confidence: 99%

Investigation of Novel Gene Functions in Yeast Using Functional Genomics

Jagadeesan

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Systems biology, a diverse and complex field, relies heavily on functional genomics and highthroughput methods to understand the intricacy of cellular and molecular interactions. Through large-scale, comprehensive genome screening experiments, we generate considerable amounts of data, referred to as "big data," that unravel the complex biochemical interactions within living cells. In this context, Saccharomyces cerevisiae, commonly referred to as baker's yeast serves as a pivotal model organism in scientific research. Its widespread utilization is attributed to the readily available high-throughput techniques, substantial genetic similarity to humans, ease of manipulation, and the wealth of genetic and biochemical resources at its disposal. Our research primarily targets the dissection of the intricate molecular machinery involved in the translation initiation pathway, specifically structured messenger RNAs(mRNAs) in Saccharomyces cerevisiae.Recognizing the centrality of translation to cellular functionality and its perturbation in disease conditions, we employ functional genomic strategies and high-throughput techniques to unearth previously unrecognized gene functions within this process. We examine around 5000 nonessential yeast genes for their effect on the translation of reporter genes, unmasking four previously unidentified gene functions: PEX11, RIM20, YRF1-6, and DBP7. These genes significantly modulate the translation of mRNAs that feature structured 5'UTRs.Further, we leverage a functional genomics computational platform to uncover novel genes implicated in the DNA damage pathway. Integrating protein-protein interactions (PPI), genetic interactions, and gene expression data, we identified three unknown gene functions, GAL7, YMR130W, and YHI9, which are associated with double-strand break repair via both homologous and non-homologous end-joining pathways. These genetic associations are further validated through experimental methodologies. Additionally, we aim to elucidate the inhibitory mechanisms of the SARS-CoV-2 NSP1 gene on translation pathway, proposing the involvement of several other proteins and translation initiation factors critical to viral translation.This research provides profound insights into the complexity of the translation initiation iii pathway, integral to cellular functionality and survival. The revelation of new gene functionalities expands our present understanding and paves the way for further exploration of translational perturbations in disease conditions, thus potentially aiding the development of innovative therapeutic strategies. The integration of large-scale functional genomics and computational strategies enhances our ability to simultaneously evaluate thousands of genes, enriching the depth of our investigations. Also, the investigation of SARS-CoV-2 NSP1 translation inhibitory mechanism using functional genomics approach may expose new targets for antiviral interventions. Given the genetic parallels between baker's yeast and humans, our discoveries could significantly i...

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The conserved Tpk1 regulates non-homologous end joining double-strand break repair by phosphorylation of Nej1, a homolog of the human XLF

Cited by 5 publications

References 51 publications

The Involvement of YNR069C in Protein Synthesis in the Baker’s Yeast, Saccharomyces cerevisiae

The Involvement of YNR069C in Protein Synthesis in the Baker’s Yeast, Saccharomyces cerevisiae

Phosphorylation of Jhd2 by the Ras-cAMP-PKA(Tpk2) pathway regulates histone modifications and autophagy

Investigation of Novel Gene Functions in Yeast Using Functional Genomics

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