RNA recognition motifs involved in nuclear import of RNA-binding proteins

Control of gene expression in trypanosomes relies almost exclusively on post-transcriptional mechanisms. Trypanosomes have the normal enzymes for mRNA decay: both the exosome and a 5′–3′-exoribonuclease are important in the degradation of very unstable transcripts, whereas the CAF1/NOT complex plays a major role in the degradation of all mRNAs tested. Targeted RNA interference screening was used to identify RNA-binding proteins that regulate mRNA degradation, and it revealed roles for proteins with RNA recognition motifs or pumilio domains.

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Genome-wide identification and phylogenetic analysis of plant RNA binding proteins comprising both RNA recognition motifs and contiguous glycine residues

Molecular Genetics and Genomics ◽

10.1007/s00438-015-1144-1 ◽

2015 ◽

Vol 291 (2) ◽

pp. 763-773 ◽

Cited By ~ 7

Author(s):

Martin Lewinski ◽

Armin Hallmann ◽

Dorothee Staiger

Keyword(s):

Phylogenetic Analysis ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Rna Recognition ◽

Rna Recognition Motifs ◽

Genome Wide ◽

Recognition Motifs

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Domain necessary for Drosophila ELAV nuclear localization: function requires nuclear ELAV

Journal of Cell Science ◽

10.1242/jcs.112.24.4501 ◽

1999 ◽

Vol 112 (24) ◽

pp. 4501-4512 ◽

Cited By ~ 1

Author(s):

Y.M. Yannoni ◽

K. White

Keyword(s):

Nuclear Localization ◽

Rna Binding ◽

Rna Binding Proteins ◽

Nuclear Localization Sequence ◽

Rna Recognition ◽

Rna Recognition Motifs ◽

Mutant Proteins ◽

Localization Sequence ◽

Recognition Motifs

The neuron specific Drosophila ELAV protein belongs to the ELAV family of RNA binding proteins which are characterized by three highly conserved RNA recognition motifs, an N-terminal domain, and a hinge region between the second and third RNA recognition motifs. Despite their highly conserved RNA recognition motifs the ELAV family members are a group of proteins with diverse posttranscriptional functions including splicing regulation, mRNA stability and translatability and have a variety of subcellular localizations. The role of the ELAV hinge in localization and function was examined using transgenes encoding ELAV hinge deletions, in vivo. Subcellular localization of the hinge mutant proteins revealed that residues between amino acids 333–374 are necessary for nuclear localization. This delineated sequence has no significant homology to classical nuclear localization sequences, but it is similar to the recently characterized nucleocytoplasmic shuttling sequence, the HNS, from a human ELAV family member, HuR. This defined sequence, however, was insufficient for nuclear localization as tested using hinge-GFP fusion proteins. Functional assays revealed that mutant proteins that fail to localize to the nucleus are unable to provide ELAV vital function, but their function is significantly restored when translocated into the nucleus by a heterologous nuclear localization sequence tag.

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The Sam68 nuclear body is composed of two RNase-sensitive substructures joined by the adaptor HNRNPL

The Journal of Cell Biology ◽

10.1083/jcb.201601024 ◽

2016 ◽

Vol 214 (1) ◽

pp. 45-59 ◽

Cited By ~ 34

Author(s):

Taro Mannen ◽

Seisuke Yamashita ◽

Kozo Tomita ◽

Naoki Goshima ◽

Tetsuro Hirose

Keyword(s):

Cell Nucleus ◽

Rna Binding ◽

Rna Binding Proteins ◽

Nuclear Body ◽

Nuclear Bodies ◽

Cdna Clones ◽

Rna Recognition ◽

Rna Recognition Motifs ◽

Rnase Treatment ◽

Recognition Motifs

The mammalian cell nucleus contains membraneless suborganelles referred to as nuclear bodies (NBs). Some NBs are formed with an architectural RNA (arcRNA) as the structural core. Here, we searched for new NBs that are built on unidentified arcRNAs by screening for ribonuclease (RNase)-sensitive NBs using 32,651 fluorescently tagged human cDNA clones. We identified 32 tagged proteins that required RNA for their localization in distinct nuclear foci. Among them, seven RNA-binding proteins commonly localized in the Sam68 nuclear body (SNB), which was disrupted by RNase treatment. Knockdown of each SNB protein revealed that SNBs are composed of two distinct RNase-sensitive substructures. One substructure is present as a distinct NB, termed the DBC1 body, in certain conditions, and the more dynamic substructure including Sam68 joins to form the intact SNB. HNRNPL acts as the adaptor to combine the two substructures and form the intact SNB through the interaction of two sets of RNA recognition motifs with the putative arcRNAs in the respective substructures.

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Phylogeny of the sex-determining gene Sex-lethal in insects

Genome ◽

10.1139/g05-107 ◽

2006 ◽

Vol 49 (3) ◽

pp. 254-262 ◽

Cited By ~ 34

Author(s):

Walther Traut ◽

Teruyuki Niimi ◽

Kazuho Ikeo ◽

Ken Sahara

Keyword(s):

Drosophila Melanogaster ◽

Rna Binding ◽

Rna Binding Proteins ◽

Mrna Splicing ◽

Rna Recognition ◽

Rna Recognition Motifs ◽

The Family ◽

Mosquito Anopheles Gambiae ◽

Sex Lethal ◽

Recognition Motifs

The Sex-lethal (SXL) protein belongs to the family of RNA-binding proteins and is involved in the regulation of pre-mRNA splicing. SXL has undergone an obvious change of function during the evolution of the insect clade. The gene has acquired a pivotal role in the sex-determining pathway of Drosophila, although it does not act as a sex determiner in non-drosophilids. We collected SXL sequences of insect species ranging from the pea aphid (Acyrtho siphom pisum) to Drosophila melanogaster by searching published articles, sequencing cDNAs, and exploiting homology searches in public EST and whole-genome databases. The SXL protein has moderately conserved N- and C-terminal regions and a well-conserved central region including 2 RNA recognition motifs. Our phylogenetic analysis shows that a single orthologue of the Drosophila Sex-lethal (Sxl) gene is present in the genomes of the malaria mosquito Anopheles gambiae, the honeybee Apis mellifera, the silkworm Bombyx mori, and the red flour beetle Tribolium castaneum. The D. melanogaster, D. erecta, and D. pseudoobscura genomes, however, contain 2 paralogous genes, Sxl and CG3056, which are orthologous to the Anopheles, Apis, Bombyx, and Tribolium Sxl. Hence, a duplication in the fly clade generated Sxl and CG3056. Our hypothesis maintains that one of the genes, Sxl, adopted the new function of sex determiner in Drosophila, whereas the other, CG3056, continued to serve some or all of the yet-unknown ancestral functions.Key words: sex determination, Sxl, CG3056, Bombyx, Apis, Anopheles, Aedes, Acyrtosiphon, Megaselia, Lucilia, Musca, Drosophila, Tribolium, Sciarids, Drosophila melanogaster, Drosophila erecta, Drosophila pseudoobscura, gene duplication.

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Structural basis for terminal loop recognition and processing of pri-miRNA-18a by hnRNP A1

10.1101/178855 ◽

2017 ◽

Cited By ~ 1

Author(s):

Hamed Kooshapur ◽

Nila Roy Choudhury ◽

Bernd Simon ◽

Max Mühlbauer ◽

Alexander Jussupow ◽

...

Keyword(s):

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Structural Basis ◽

Mirna Biogenesis ◽

Rna Recognition ◽

Hnrnp A1 ◽

Sequence Motifs ◽

Terminal Loop ◽

Recognition Motifs

Post-transcriptional mechanisms play a predominant role in the control of microRNA (miRNA) production. Recognition of the terminal loop of precursor miRNAs by RNA-binding proteins (RBPs) influences their processing; however, the mechanistic and structural basis for how levels of individual or subsets of miRNAs are regulated is mostly unexplored. We previously described a role for hnRNP A1, an RBP implicated in many aspects of RNA processing, as an auxiliary factor that promotes the Microprocessor-mediated processing of pri-mir-18a. Here, we reveal the mechanistic basis for this stimulatory role of hnRNP A1 by combining integrative structural biology with biochemical and functional assays. We demonstrate that hnRNP A1 forms a 1:1 complex with pri-mir-18a that involves binding of both RNA recognition motifs (RRMs) to cognate RNA sequence motifs in the conserved terminal loop of pri-mir-18a. Terminal loop binding induces an allosteric destabilization of base-pairing in the pri-mir-18a stem that promotes its down-stream processing. Our results highlight terminal loop RNA recognition by RNA-binding proteins as a general principle of miRNA biogenesis and regulation.

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The RNA-Binding Motif Protein Family in Cancer: Friend or Foe?

Frontiers in Oncology ◽

10.3389/fonc.2021.757135 ◽

2021 ◽

Vol 11 ◽

Author(s):

Zhigang Li ◽

Qingyu Guo ◽

Jiaxin Zhang ◽

Zitong Fu ◽

Yifei Wang ◽

...

Keyword(s):

Rna Binding ◽

Rna Binding Proteins ◽

Binding Motif ◽

Rna Recognition ◽

Aberrant Expression ◽

Rna Recognition Motifs ◽

Binding Domains ◽

Cancer Occurrence ◽

Recognition Motifs

The RNA-binding motif (RBM) proteins are a class of RNA-binding proteins named, containing RNA-recognition motifs (RRMs), RNA-binding domains, and ribonucleoprotein motifs. RBM proteins are involved in RNA metabolism, including splicing, transport, translation, and stability. Many studies have found that aberrant expression and dysregulated function of RBM proteins family members are closely related to the occurrence and development of cancers. This review summarizes the role of RBM proteins family genes in cancers, including their roles in cancer occurrence and cell proliferation, migration, and apoptosis. It is essential to understand the mechanisms of these proteins in tumorigenesis and development, and to identify new therapeutic targets and prognostic markers.

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