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  1. Article: Repression of

    Zhang, Fan / Sen, Neelam Dabas / Hinnebusch, Alan G

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Powers et al. recently demonstrated that ... ...

    Abstract Powers et al. recently demonstrated that the
    Language English
    Publishing date 2024-01-31
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.01.30.578007
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Differential requirements for P stalk components in activating yeast protein kinase Gcn2 by stalled ribosomes during stress.

    Gupta, Ritu / Hinnebusch, Alan G

    Proceedings of the National Academy of Sciences of the United States of America

    2023  Volume 120, Issue 16, Page(s) e2300521120

    Abstract: The General Amino Acid Control is a conserved response to amino acid starvation involving activation of protein kinase Gcn2, which phosphorylates eukaryotic initiation factor 2 (eIF2α) with attendant inhibition of global protein synthesis and increased ... ...

    Abstract The General Amino Acid Control is a conserved response to amino acid starvation involving activation of protein kinase Gcn2, which phosphorylates eukaryotic initiation factor 2 (eIF2α) with attendant inhibition of global protein synthesis and increased translation of yeast transcriptional activator
    MeSH term(s) Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Protein Serine-Threonine Kinases/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Ribosomes/metabolism ; eIF-2 Kinase/metabolism ; Transcription Factors/metabolism ; Amino Acids/metabolism ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Carrier Proteins/metabolism ; Eukaryotic Initiation Factor-2/genetics ; Eukaryotic Initiation Factor-2/metabolism ; Phosphorylation
    Chemical Substances Protein Serine-Threonine Kinases (EC 2.7.11.1) ; Saccharomyces cerevisiae Proteins ; eIF-2 Kinase (EC 2.7.11.1) ; Transcription Factors ; Amino Acids ; RNA, Transfer (9014-25-9) ; Carrier Proteins ; Eukaryotic Initiation Factor-2 ; GCN2 protein, S cerevisiae (EC 2.7.11.1)
    Language English
    Publishing date 2023-04-12
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Intramural
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2300521120
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 1148: Show issues Location:
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  3. Article ; Online: Yeast eIF2A has a minimal role in translation initiation and uORF-mediated translational control in vivo.

    Gaikwad, Swati / Ghobakhlou, Fardin / Zhang, Hongen / Hinnebusch, Alan G

    eLife

    2024  Volume 12

    Abstract: Initiating translation of most eukaryotic mRNAs depends on recruitment of methionyl initiator tRNA (Met-tRNAi) in a ternary complex (TC) with GTP-bound eukaryotic initiation factor 2 (eIF2) to the small (40S) ribosomal subunit, forming a 43S ... ...

    Abstract Initiating translation of most eukaryotic mRNAs depends on recruitment of methionyl initiator tRNA (Met-tRNAi) in a ternary complex (TC) with GTP-bound eukaryotic initiation factor 2 (eIF2) to the small (40S) ribosomal subunit, forming a 43S preinitiation complex (PIC) that attaches to the mRNA and scans the 5'-untranslated region (5' UTR) for an AUG start codon. Previous studies have implicated mammalian eIF2A in GTP-independent binding of Met-tRNAi to the 40S subunit and its recruitment to specialized mRNAs that do not require scanning, and in initiation at non-AUG start codons, when eIF2 function is attenuated by phosphorylation of its α-subunit during stress. The role of eIF2A in translation in vivo is poorly understood however, and it was unknown whether the conserved ortholog in budding yeast can functionally substitute for eIF2. We performed ribosome profiling of a yeast deletion mutant lacking eIF2A and isogenic wild-type (WT) cells in the presence or absence of eIF2α phosphorylation induced by starvation for amino acids isoleucine and valine. Whereas starvation of WT confers changes in translational efficiencies (TEs) of hundreds of mRNAs, the
    MeSH term(s) Animals ; Saccharomyces cerevisiae/genetics ; Codon, Initiator/genetics ; Eukaryotic Initiation Factor-2/genetics ; Phosphorylation ; 5' Untranslated Regions ; Guanosine Triphosphate ; Mammals
    Chemical Substances Codon, Initiator ; Eukaryotic Initiation Factor-2 ; 5' Untranslated Regions ; Guanosine Triphosphate (86-01-1)
    Language English
    Publishing date 2024-01-24
    Publishing country England
    Document type Journal Article
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.92916
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Translational regulation by uORFs and start codon selection stringency.

    Dever, Thomas E / Ivanov, Ivaylo P / Hinnebusch, Alan G

    Genes & development

    2023  Volume 37, Issue 11-12, Page(s) 474–489

    Abstract: In addition to the main, protein-coding, open reading frame (mORF), many eukaryotic mRNAs contain upstream ORFs (uORFs) initiated at AUG or near-cognate codons residing 5' of the mORF start site. Whereas translation of uORFs generally represses ... ...

    Abstract In addition to the main, protein-coding, open reading frame (mORF), many eukaryotic mRNAs contain upstream ORFs (uORFs) initiated at AUG or near-cognate codons residing 5' of the mORF start site. Whereas translation of uORFs generally represses translation of the mORFs, a subset of uORFs serves as a nexus for regulating translation of the mORF. In this review, we summarize the mechanisms by which uORFs can repress or stimulate mRNA translation, highlight uORF-mediated translational repression involving ribosome queuing, and critically evaluate recently described alternatives to the delayed reinitiation model for uORF-mediated regulation of the
    MeSH term(s) Codon, Initiator/genetics ; Protein Biosynthesis ; Codon/metabolism ; Ribosomes/genetics ; Ribosomes/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Open Reading Frames/genetics
    Chemical Substances Codon, Initiator ; Codon ; RNA, Messenger
    Language English
    Publishing date 2023-07-11
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, N.I.H., Intramural
    ZDB-ID 806684-x
    ISSN 1549-5477 ; 0890-9369
    ISSN (online) 1549-5477
    ISSN 0890-9369
    DOI 10.1101/gad.350752.123
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 2292: Show issues Location:
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    Zs.MG 54: Show issues

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  5. Article: Transcriptome-wide analysis of the function of Ded1 in translation preinitiation complex assembly in a reconstituted in vitro system.

    Zhou, Fujun / Bocetti, Julie M / Hou, Meizhen / Qin, Daoming / Hinnebusch, Alan G / Lorsch, Jon R

    bioRxiv : the preprint server for biology

    2024  

    Abstract: We have developed a deep sequencing-based approach, Rec-Seq, that allows simultaneous monitoring of ribosomal 48S pre-initiation complex (PIC) formation on every mRNA in the translatome in an in vitro reconstituted system. Rec-Seq isolates key early ... ...

    Abstract We have developed a deep sequencing-based approach, Rec-Seq, that allows simultaneous monitoring of ribosomal 48S pre-initiation complex (PIC) formation on every mRNA in the translatome in an in vitro reconstituted system. Rec-Seq isolates key early steps in translation initiation in the absence of all other cellular components and processes. Using this approach we show that the DEAD-box ATPase Ded1 promotes 48S PIC formation on the start codons of >1000 native mRNAs, most of which have long, structured 5'-untranslated regions (5'UTRs). Remarkably, initiation measured in Rec-Seq was enhanced by Ded1 for most mRNAs previously shown to be highly Ded1-dependent by ribosome profiling of
    Language English
    Publishing date 2024-02-05
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.10.16.562452
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Transcriptome-wide analysis of the function of Ded1 in translation preinitiation complex assembly in a reconstituted in vitro system.

    Zhou, Fujun / Bocetti, Julie M / Hou, Meizhen / Qin, Daoming / Hinnebusch, Alan G / Lorsch, Jon R

    eLife

    2024  Volume 13

    Abstract: We have developed a deep sequencing-based approach, Rec-Seq, that allows simultaneous monitoring of ribosomal 48S preinitiation complex (PIC) formation on every mRNA in the translatome in an in vitro reconstituted system. Rec-Seq isolates key early steps ...

    Abstract We have developed a deep sequencing-based approach, Rec-Seq, that allows simultaneous monitoring of ribosomal 48S preinitiation complex (PIC) formation on every mRNA in the translatome in an in vitro reconstituted system. Rec-Seq isolates key early steps in translation initiation in the absence of all other cellular components and processes. Using this approach, we show that the DEAD-box ATPase Ded1 promotes 48S PIC formation on the start codons of >1000 native mRNAs, most of which have long, structured 5'-untranslated regions (5'UTRs). Remarkably, initiation measured in Rec-Seq was enhanced by Ded1 for most mRNAs previously shown to be highly Ded1-dependent by ribosome profiling of
    MeSH term(s) 5' Untranslated Regions ; Codon, Initiator ; Transcriptome ; RNA, Messenger/genetics ; DEAD-box RNA Helicases
    Chemical Substances 5' Untranslated Regions ; Codon, Initiator ; RNA, Messenger ; DEAD-box RNA Helicases (EC 3.6.4.13)
    Language English
    Publishing date 2024-04-04
    Publishing country England
    Document type Journal Article
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.93255
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  7. Article ; Online: uS5/Rps2 residues at the 40S ribosome entry channel enhance initiation at suboptimal start codons in vivo.

    Dong, Jinsheng / Hinnebusch, Alan G

    Genetics

    2021  Volume 220, Issue 1

    Abstract: The eukaryotic 43S pre-initiation complex (PIC) containing Met-tRNAiMet in a ternary complex (TC) with eIF2-GTP scans the mRNA leader for an AUG codon in favorable "Kozak" context. AUG recognition triggers rearrangement of the PIC from an open ... ...

    Abstract The eukaryotic 43S pre-initiation complex (PIC) containing Met-tRNAiMet in a ternary complex (TC) with eIF2-GTP scans the mRNA leader for an AUG codon in favorable "Kozak" context. AUG recognition triggers rearrangement of the PIC from an open conformation to a closed state with more tightly bound Met-tRNAiMet. Yeast ribosomal protein uS5/Rps2 is located at the mRNA entry channel of the 40S subunit in the vicinity of mRNA nucleotides downstream from the AUG codon or rRNA residues that communicate with the decoding center, but its participation in start codon recognition was unknown. We found that nonlethal substitutions of conserved Rps2 residues in the entry channel reduce bulk translation initiation and increase discrimination against poor initiation codons. A subset of these substitutions suppress initiation at near-cognate UUG start codons in a yeast mutant with elevated UUG initiation, and also increase discrimination against AUG codons in suboptimal Kozak context, thus resembling previously described substitutions in uS3/Rps3 at the 40S entry channel or initiation factors eIF1 and eIF1A. In contrast, other Rps2 substitutions selectively discriminate against either near-cognate UUG codons, or poor Kozak context of an AUG or UUG start codon. These findings suggest that different Rps2 residues are involved in distinct mechanisms involved in discriminating against different features of poor initiation sites in vivo.
    MeSH term(s) Saccharomyces cerevisiae
    Language English
    Publishing date 2021-09-15
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Intramural
    ZDB-ID 2167-2
    ISSN 1943-2631 ; 0016-6731
    ISSN (online) 1943-2631
    ISSN 0016-6731
    DOI 10.1093/genetics/iyab176
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    Zs.B 767: Show issues Location:
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  8. Article: Yeast eIF2A has a minimal role in translation initiation and uORF-mediated translational control

    Gaikwad, Swati / Ghobakhlou, Fardin / Zhang, Hongen / Hinnebusch, Alan G

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Initiating translation of most eukaryotic mRNAs depends on recruitment of methionyl initiator tRNA (Met-tRNAi) in a ternary complex (TC) with GTP-bound eukaryotic initiation factor 2 (eIF2) to the small (40S) ribosomal subunit, forming a 43S ... ...

    Abstract Initiating translation of most eukaryotic mRNAs depends on recruitment of methionyl initiator tRNA (Met-tRNAi) in a ternary complex (TC) with GTP-bound eukaryotic initiation factor 2 (eIF2) to the small (40S) ribosomal subunit, forming a 43S preinitiation complex (PIC) that attaches to the mRNA and scans the 5'-untranslated region (5' UTR) for an AUG start codon. Previous studies have implicated mammalian eIF2A in GTP-independent binding of Met-tRNAi to the 40S subunit and its recruitment to specialized mRNAs that do not require scanning, and in initiation at non-AUG start codons, when eIF2 function is attenuated by phosphorylation of its α-subunit during stress. The role of eIF2A in translation
    Language English
    Publishing date 2023-12-09
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.10.06.561292
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  9. Article ; Online: Differential requirements for Gcn5 and NuA4 HAT activities in the starvation-induced versus basal transcriptomes.

    Zheng, Qiaoyun / Qiu, Hongfang / Zhang, Hongen / Hinnebusch, Alan G

    Nucleic acids research

    2023  Volume 51, Issue 8, Page(s) 3696–3721

    Abstract: The histone acetyltransferase (HAT) subunit of coactivator complex SAGA, Gcn5, stimulates eviction of promoter nucleosomes at certain highly expressed yeast genes, including those activated by transcription factor Gcn4 in amino acid-deprived cells; ... ...

    Abstract The histone acetyltransferase (HAT) subunit of coactivator complex SAGA, Gcn5, stimulates eviction of promoter nucleosomes at certain highly expressed yeast genes, including those activated by transcription factor Gcn4 in amino acid-deprived cells; however, the importance of other HAT complexes in this process was poorly understood. Analyzing mutations that disrupt the integrity or activity of HAT complexes NuA4 or NuA3, or HAT Rtt109, revealed that only NuA4 acts on par with Gcn5, and functions additively, in evicting and repositioning promoter nucleosomes and stimulating transcription of starvation-induced genes. NuA4 is generally more important than Gcn5, however, in promoter nucleosome eviction, TBP recruitment, and transcription at most other genes expressed constitutively. NuA4 also predominates over Gcn5 in stimulating TBP recruitment and transcription of genes categorized as principally dependent on the cofactor TFIID versus SAGA, except for the most highly expressed subset including ribosomal protein genes, where Gcn5 contributes strongly to PIC assembly and transcription. Both SAGA and NuA4 are recruited to promoter regions of starvation-induced genes in a manner that might be feedback controlled by their HAT activities. Our findings reveal an intricate interplay between these two HATs in nucleosome eviction, PIC assembly, and transcription that differs between the starvation-induced and basal transcriptomes.
    MeSH term(s) Histone Acetyltransferases/genetics ; Histone Acetyltransferases/metabolism ; Nucleosomes/genetics ; Nucleosomes/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Transcriptome
    Chemical Substances GCN5 protein, S cerevisiae (EC 2.3.1.48) ; Histone Acetyltransferases (EC 2.3.1.48) ; NuA4 protein, S cerevisiae (EC 2.3.1.48) ; Nucleosomes ; Saccharomyces cerevisiae Proteins ; Transcription Factors
    Language English
    Publishing date 2023-03-02
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Intramural
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkad099
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    Zs.A 1067: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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  10. Article: Structural Insights into the Mechanism of Scanning and Start Codon Recognition in Eukaryotic Translation Initiation.

    Hinnebusch, Alan G

    Trends in biochemical sciences

    2017  Volume 42, Issue 8, Page(s) 589–611

    Abstract: Initiation of translation on eukaryotic mRNAs generally follows the scanning mechanism, wherein a preinitiation complex (PIC) assembled on the small (40S) ribosomal subunit and containing initiator methionyl ... ...

    Abstract Initiation of translation on eukaryotic mRNAs generally follows the scanning mechanism, wherein a preinitiation complex (PIC) assembled on the small (40S) ribosomal subunit and containing initiator methionyl tRNA
    MeSH term(s) Codon, Initiator/genetics ; Eukaryotic Initiation Factors/metabolism ; Peptide Chain Initiation, Translational ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Ribosomes/chemistry ; Ribosomes/genetics ; Ribosomes/metabolism
    Chemical Substances Codon, Initiator ; Eukaryotic Initiation Factors ; RNA, Messenger
    Language English
    Publishing date 2017-08
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 194216-5
    ISSN 1362-4326 ; 0968-0004 ; 0376-5067
    ISSN (online) 1362-4326
    ISSN 0968-0004 ; 0376-5067
    DOI 10.1016/j.tibs.2017.03.004
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    Zs.A 1207: Show issues Location:
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