Identification and characterization of human Mex-3 proteins, a novel family of evolutionarily conserved RNA-binding proteins differentially localized to processing bodies

ABSTRACTRNA-binding proteins (RBPs) have been established as core components of several post-transcriptional gene regulation mechanisms. Experimental techniques such as cross-linking and co-immunoprecipitation have enabled the identification of RBPs, RNA-binding domains (RBDs), and their regulatory roles in the eukaryotic species such as human and yeast in large-scale. In contrast, our knowledge of the number and potential diversity of RBPs in bacteria is poorer due to the technical challenges associated with the existing global screening approaches.We introduce APRICOT, a computational pipeline for the sequence-based identification and characterization of proteins using RBDs known from experimental studies. The pipeline identifies functional motifs in protein sequences using Position Specific Scoring Matrices and Hidden Markov Models of the functional domains and statistically scores them based on a series of sequence-based features. Subsequently, APRICOT identifies putative RBPs and characterizes them by several biological properties. Here we demonstrate the application and adaptability of the pipeline on large-scale protein sets, including the bacterial proteome of Escherichia coli. APRICOT showed better performance on various datasets compared to other existing tools for the sequence-based prediction of RBPs by achieving an average sensitivity and specificity of 0.90 and 0.91 respectively. The command-line tool and its documentation are available at https://pypi.python.org/pypi/bio-apricot

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Characterization of Viral Double-Stranded RNA-Binding Proteins

Methods ◽

10.1006/meth.1998.0626 ◽

1998 ◽

Vol 15 (3) ◽

pp. 225-232 ◽

Cited By ~ 11

Author(s):

Bertram L. Jacobs ◽

Jeffrey O. Langland ◽

Teresa Brandt

Keyword(s):

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Double Stranded Rna

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Discovery of RNA-binding proteins and characterization of their dynamic responses by enhanced RNA interactome capture

Nature Communications ◽

10.1038/s41467-018-06557-8 ◽

2018 ◽

Vol 9 (1) ◽

Cited By ~ 40

Author(s):

Joel I. Perez-Perri ◽

Birgit Rogell ◽

Thomas Schwarzl ◽

Frank Stein ◽

Yang Zhou ◽

...

Keyword(s):

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Jurkat Cells ◽

Dynamic Responses ◽

Capture Probe ◽

Signal To Noise ◽

Low Background ◽

Detailed Composition

AbstractFollowing the realization that eukaryotic RNA-binding proteomes are substantially larger than anticipated, we must now understand their detailed composition and dynamics. Methods such as RNA interactome capture (RIC) have begun to address this need. However, limitations of RIC have been reported. Here we describe enhanced RNA interactome capture (eRIC), a method based on the use of an LNA-modified capture probe, which yields numerous advantages including greater specificity and increased signal-to-noise ratios compared to existing methods. In Jurkat cells, eRIC reduces the rRNA and DNA contamination by >10-fold compared to RIC and increases the detection of RNA-binding proteins. Due to its low background, eRIC also empowers comparative analyses of changes of RNA-bound proteomes missed by RIC. For example, in cells treated with dimethyloxalylglycine, which inhibits RNA demethylases, eRIC identifies m6A-responsive RNA-binding proteins that escape RIC. eRIC will facilitate the unbiased characterization of RBP dynamics in response to biological and pharmacological cues.

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Characterization of glycine-rich RNA-binding proteins inBrassica napusunder stress conditions

Physiologia Plantarum ◽

10.1111/j.1399-3054.2012.01628.x ◽

2012 ◽

Vol 146 (3) ◽

pp. 297-307 ◽

Cited By ~ 12

Author(s):

Min Kyung Kim ◽

Hyun Ju Jung ◽

Dong Hyun Kim ◽

Hunseung Kang

Keyword(s):

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Stress Conditions

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Two Yeast La Motif-containing Proteins Are RNA-binding Proteins that Associate with Polyribosomes

Molecular Biology of the Cell ◽

10.1091/mbc.10.11.3849 ◽

1999 ◽

Vol 10 (11) ◽

pp. 3849-3862 ◽

Cited By ~ 36

Author(s):

Suzanne G. Sobel ◽

Sandra L. Wolin

Keyword(s):

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Rna Polymerase Iii ◽

Mrna Translation ◽

Protein Synthesis Inhibitors ◽

La Protein ◽

Evolutionarily Conserved ◽

Synthetically Lethal ◽

Type Strains

We have characterized two Saccharomyces cerevisiaeproteins, Sro9p and Slf1p, which contain a highly conserved motif found in all known La proteins. Originally described as an autoantigen in patients with rheumatic disease, the La protein binds to newly synthesized RNA polymerase III transcripts. In yeast, the La protein homologue Lhp1p is required for the normal pathway of tRNA maturation and also stabilizes newly synthesized U6 RNA. We show that deletions in both SRO9 and SLF1 are not synthetically lethal with a deletion in LHP1, indicating that the three proteins do not function in a single essential process. Indirect immunofluorescence microscopy reveals that although Lhp1p is primarily localized to the nucleus, Sro9p is cytoplasmic. We demonstrate that Sro9p and Slf1p are RNA-binding proteins that associate preferentially with translating ribosomes. Consistent with a role in translation, strains lacking either Sro9p or Slf1p are less sensitive than wild-type strains to certain protein synthesis inhibitors. Thus, Sro9p and Slf1p define a new and possibly evolutionarily conserved class of La motif-containing proteins that may function in the cytoplasm to modulate mRNA translation.

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