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  1. Article ; Online: A Simple Method for the Detection of Wybutosine-Modified tRNA

    Nostramo, Regina T / Hopper, Anita K

    Methods in molecular biology (Clifton, N.J.)

    2023  Volume 2666, Page(s) 1–14

    Abstract: tRNAs are highly mobile molecules that are trafficked back and forth between the nucleus and cytoplasm by several proteins. However, characterization of the movement of tRNAs and the proteins mediating these movements can be difficult. Here, we describe ... ...

    Abstract tRNAs are highly mobile molecules that are trafficked back and forth between the nucleus and cytoplasm by several proteins. However, characterization of the movement of tRNAs and the proteins mediating these movements can be difficult. Here, we describe an easy and cost-effective assay to discover genes that are involved in two specific tRNA trafficking events, retrograde nuclear import and nuclear re-export for yeast, Saccharomyces cerevisiae. This assay, referred to as the hydrochloric acid (HCl)/aniline assay, identifies the presence or absence of a unique modification on tRNA
    MeSH term(s) Active Transport, Cell Nucleus ; RNA, Transfer, Phe/metabolism ; Hydrochloric Acid ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Cell Nucleus/genetics ; Cell Nucleus/metabolism
    Chemical Substances RNA, Transfer, Phe ; wybutosine ; Hydrochloric Acid (QTT17582CB) ; RNA, Transfer (9014-25-9) ; Saccharomyces cerevisiae Proteins
    Language English
    Publishing date 2023-05-11
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-3191-1_1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A novel assay provides insight into tRNAPhe retrograde nuclear import and re-export in S. cerevisiae.

    Nostramo, Regina T / Hopper, Anita K

    Nucleic acids research

    2020  Volume 48, Issue 20, Page(s) 11577–11588

    Abstract: In eukaryotes, tRNAs are transcribed in the nucleus and subsequently exported to the cytoplasm where they serve as essential adaptor molecules in translation. However, tRNAs can be returned to the nucleus by the evolutionarily conserved process called ... ...

    Abstract In eukaryotes, tRNAs are transcribed in the nucleus and subsequently exported to the cytoplasm where they serve as essential adaptor molecules in translation. However, tRNAs can be returned to the nucleus by the evolutionarily conserved process called tRNA retrograde nuclear import, before relocalization back to the cytoplasm via a nuclear re-export step. Several important functions of these latter two trafficking events have been identified, yet the pathways are largely unknown. Therefore, we developed an assay in Saccharomyces cerevisiae to identify proteins mediating tRNA retrograde nuclear import and re-export using the unique wybutosine modification of mature tRNAPhe. Our hydrochloric acid/aniline assay revealed that the karyopherin Mtr10 mediates retrograde import of tRNAPhe, constitutively and in response to amino acid deprivation, whereas the Hsp70 protein Ssa2 mediates import specifically in the latter. Furthermore, tRNAPhe is re-exported by Crm1 and Mex67, but not by the canonical tRNA exporters Los1 or Msn5. These findings indicate that the re-export process occurs in a tRNA family-specific manner. Together, this assay provides insights into the pathways for tRNAPhe retrograde import and re-export and is a tool that can be used on a genome-wide level to identify additional gene products involved in these tRNA trafficking events.
    MeSH term(s) Active Transport, Cell Nucleus ; Aniline Compounds ; Cell Nucleus/metabolism ; Genetic Techniques ; HSP70 Heat-Shock Proteins/metabolism ; Hydrochloric Acid ; Karyopherins/metabolism ; Nuclear Proteins/metabolism ; Nucleocytoplasmic Transport Proteins/metabolism ; Nucleosides ; RNA, Transfer, Phe/chemistry ; RNA, Transfer, Phe/metabolism ; RNA-Binding Proteins/metabolism ; Receptors, Cytoplasmic and Nuclear/metabolism ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Exportin 1 Protein
    Chemical Substances Aniline Compounds ; HSP70 Heat-Shock Proteins ; Karyopherins ; MEX67 protein, S cerevisiae ; MTR10 protein, S cerevisiae ; Nuclear Proteins ; Nucleocytoplasmic Transport Proteins ; Nucleosides ; RNA, Transfer, Phe ; RNA-Binding Proteins ; Receptors, Cytoplasmic and Nuclear ; SSA2 protein, S cerevisiae ; Saccharomyces cerevisiae Proteins ; wybutosine ; Hydrochloric Acid (QTT17582CB) ; aniline (SIR7XX2F1K)
    Language English
    Publishing date 2020-10-16
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    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/gkaa879
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  3. Article ; Online: Beyond rRNA and snRNA: tRNA as a 2'-O-methylation target for nucleolar and Cajal body box C/D RNPs.

    Nostramo, Regina T / Hopper, Anita K

    Genes & development

    2019  Volume 33, Issue 13-14, Page(s) 739–740

    Abstract: Box C/D small nucleolar RNAs (snoRNAs) and small Cajal body (CB) RNAs (scaRNAs) form ribonucleoprotein (RNP) complexes to mediate 2'-O-methylation of rRNAs and small nuclear RNAs (snRNAs), respectively. The site of methylation is determined by antisense ... ...

    Abstract Box C/D small nucleolar RNAs (snoRNAs) and small Cajal body (CB) RNAs (scaRNAs) form ribonucleoprotein (RNP) complexes to mediate 2'-O-methylation of rRNAs and small nuclear RNAs (snRNAs), respectively. The site of methylation is determined by antisense elements in the box C/D RNAs that are complementary to sequences in target RNAs. However, numerous box C/D RNAs in mammalian cells lack antisense elements to rRNAs or snRNAs; thus, their targets remain unknown. In this issue of
    MeSH term(s) Animals ; Coiled Bodies ; Cytidine ; Humans ; Methylation ; RNA, Small Nucleolar ; RNA, Transfer, Met ; Ribonucleoproteins
    Chemical Substances RNA, Small Nucleolar ; RNA, Transfer, Met ; Ribonucleoproteins ; Cytidine (5CSZ8459RP)
    Language English
    Publishing date 2019-09-06
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review ; Comment
    ZDB-ID 806684-x
    ISSN 1549-5477 ; 0890-9369
    ISSN (online) 1549-5477
    ISSN 0890-9369
    DOI 10.1101/gad.328443.119
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    Zs.MG 54: Show issues

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  4. Article: tRNA Processing and Subcellular Trafficking Proteins Multitask in Pathways for Other RNAs.

    Hopper, Anita K / Nostramo, Regina T

    Frontiers in genetics

    2019  Volume 10, Page(s) 96

    Abstract: This article focuses upon gene products that are involved in tRNA biology, with particular emphasis upon post-transcriptional RNA processing and nuclear-cytoplasmic subcellular trafficking. Rather than analyzing these proteins solely from a tRNA ... ...

    Abstract This article focuses upon gene products that are involved in tRNA biology, with particular emphasis upon post-transcriptional RNA processing and nuclear-cytoplasmic subcellular trafficking. Rather than analyzing these proteins solely from a tRNA perspective, we explore the many overlapping functions of the processing enzymes and proteins involved in subcellular traffic. Remarkably, there are numerous examples of conserved gene products and RNP complexes involved in tRNA biology that multitask in a similar fashion in the production and/or subcellular trafficking of other RNAs, including small structured RNAs such as snRNA, snoRNA, 5S RNA, telomerase RNA, and SRP RNA as well as larger unstructured RNAs such as mRNAs and RNA-protein complexes such as ribosomes. Here, we provide examples of steps in tRNA biology that are shared with other RNAs including those catalyzed by enzymes functioning in 5' end-processing, pseudoU nucleoside modification, and intron splicing as well as steps regulated by proteins functioning in subcellular trafficking. Such multitasking highlights the clever mechanisms cells employ for maximizing their genomes.
    Language English
    Publishing date 2019-02-20
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2019.00096
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  5. Article: tRNA dynamics between the nucleus, cytoplasm and mitochondrial surface: Location, location, location.

    Chatterjee, Kunal / Nostramo, Regina T / Wan, Yao / Hopper, Anita K

    Biochimica et biophysica acta. Gene regulatory mechanisms

    2017  Volume 1861, Issue 4, Page(s) 373–386

    Abstract: Although tRNAs participate in the essential function of protein translation in the cytoplasm, tRNA transcription and numerous processing steps occur in the nucleus. This subcellular separation between tRNA biogenesis and function requires that tRNAs be ... ...

    Abstract Although tRNAs participate in the essential function of protein translation in the cytoplasm, tRNA transcription and numerous processing steps occur in the nucleus. This subcellular separation between tRNA biogenesis and function requires that tRNAs be efficiently delivered to the cytoplasm in a step termed "primary tRNA nuclear export". Surprisingly, tRNA nuclear-cytoplasmic traffic is not unidirectional, but, rather, movement is bidirectional. Cytoplasmic tRNAs are imported back to the nucleus by the "tRNA retrograde nuclear import" step which is conserved from budding yeast to vertebrate cells and has been hijacked by viruses, such as HIV, for nuclear import of the viral reverse transcription complex in human cells. Under appropriate environmental conditions cytoplasmic tRNAs that have been imported into the nucleus return to the cytoplasm via the 3rd nuclear-cytoplasmic shuttling step termed "tRNA nuclear re-export", that again is conserved from budding yeast to vertebrate cells. We describe the 3 steps of tRNA nuclear-cytoplasmic movements and their regulation. There are multiple tRNA nuclear export and import pathways. The different tRNA nuclear exporters appear to possess substrate specificity leading to the tantalizing possibility that the cellular proteome may be regulated at the level of tRNA nuclear export. Moreover, in some organisms, such as budding yeast, the pre-tRNA splicing heterotetrameric endonuclease (SEN), which removes introns from pre-tRNAs, resides on the cytoplasmic surface of the mitochondria. Therefore, we also describe the localization of the SEN complex to mitochondria and splicing of pre-tRNA on mitochondria, which occurs prior to the participation of tRNAs in protein translation. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.
    MeSH term(s) Animals ; Biological Transport ; Cell Nucleus/metabolism ; Cytoplasm/metabolism ; Endoribonucleases/metabolism ; Evolution, Molecular ; Fungal Proteins/metabolism ; HSP70 Heat-Shock Proteins/metabolism ; Mitochondrial Membranes/metabolism ; Nuclear Pore Complex Proteins/metabolism ; Nucleocytoplasmic Transport Proteins/metabolism ; Plant Proteins/metabolism ; RNA Precursors/metabolism ; RNA Processing, Post-Transcriptional ; RNA, Transfer/metabolism ; RNA-Binding Proteins/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Transcription, Genetic ; Vertebrates/metabolism ; Yeasts/metabolism
    Chemical Substances Fungal Proteins ; HSP70 Heat-Shock Proteins ; MTR10 protein, S cerevisiae ; Nuclear Pore Complex Proteins ; Nucleocytoplasmic Transport Proteins ; Plant Proteins ; RNA Precursors ; RNA-Binding Proteins ; SSA2 protein, S cerevisiae ; Saccharomyces cerevisiae Proteins ; RNA, Transfer (9014-25-9) ; Endoribonucleases (EC 3.1.-)
    Language English
    Publishing date 2017-11-28
    Publishing country Netherlands
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 60-7
    ISSN 1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 1874-9399 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439
    ISSN (online) 1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
    ISSN 1874-9399 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439
    DOI 10.1016/j.bbagrm.2017.11.007
    Database MEDical Literature Analysis and Retrieval System OnLINE

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