Cross-species analysis of viral nucleic acid interacting proteins identifies TAOKs as innate immune regulators

AbstractThe cell intrinsic antiviral response of multicellular organisms developed over millions of years and critically relies on the ability to sense and eliminate viral nucleic acids. Here we use an affinity proteomics approach in evolutionary distant species (human, mouse and fly) to identify proteins that are conserved in their ability to associate with diverse viral nucleic acids. This approach shows a core of orthologous proteins targeting viral genetic material and species-specific interactions. Functional characterization of the influence of 181 candidates on replication of 6 distinct viruses in human cells and flies identifies 128 nucleic acid binding proteins with an impact on virus growth. We identify the family of TAO kinases (TAOK1, −2 and −3) as dsRNA-interacting antiviral proteins and show their requirement for type-I interferon induction. Depletion of TAO kinases in mammals or flies leads to an impaired response to virus infection characterized by a reduced induction of interferon stimulated genes in mammals and impaired expression of srg1 and diedel in flies. Overall, our study shows a larger set of proteins able to mediate the interaction between viral genetic material and host factors than anticipated so far, attesting to the ancestral roots of innate immunity and to the lineage-specific pressures exerted by viruses.

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Binding Of Immune Serine Proteases To Nucleic Acids Enhances Their Nuclear Localization and Promotes Their Cleavage Of Nucleic Acid-Binding Protein Substrates

Blood ◽

10.1182/blood.v122.21.3471.3471 ◽

2013 ◽

Vol 122 (21) ◽

pp. 3471-3471

Author(s):

Jennifer Whangbo ◽

Marshall Thomas ◽

Geoffrey McCrossan ◽

Aaron Deutsch ◽

Kimberly Martinod ◽

...

Keyword(s):

Nucleic Acid ◽

Nucleic Acids ◽

Nuclear Localization ◽

Serine Proteases ◽

Rna Binding ◽

Nuclear Accumulation ◽

Target Cells ◽

Nucleic Acid Binding ◽

High Affinity ◽

Nucleic Acid Binding Proteins

Abstract When released from cytotoxic T lymphocytes and natural killer cells, Granzyme (Gzm) serine proteases induce programmed cell death of pathogen-infected cells and tumor cells. The Gzms rapidly accumulate in the target cell nucleus by an unknown mechanism. Many of the known substrates of GzmA and GzmB, the most abundant killer cell proteases, bind to DNA or RNA. Gzm substrates predicted by unbiased proteomics studies are also highly enriched for nucleic acid binding proteins. Here we show by fluorescence polarization assays that Gzms bind DNA and RNA with nanomolar affinity. We hypothesized that Gzm binding to nucleic acids enhances nuclear accumulation in target cells and facilitates their cleavage of nucleic acid-binding substrates. In fact, RNase treatment of cell lysates reduced cleavage of RNA binding protein (RBP) targets by GzmA and GzmB. Moreover, adding RNA to recombinant RBP substrates greatly enhanced in vitro cleavage by GzmB, but adding RNA to non-nucleic acid binding proteins did not. For example, exogenous RNA enhanced GzmB cleavage of recombinant hnRNP C1 (an RBP) but not LMNB1 (a non-RBP). In addition, GzmB cleaved the RNA-binding HuR protein efficiently only when it was bound to an HuR-binding RNA oligonucleotide, but not in the presence of an equal amount of non-binding RNA. Thus, nucleic acids facilitate Gzm cleavage of nucleic acid binding substrates. To evaluate whether nucleic acid binding influences Gzm trafficking in target cells, we incubated fixed target cells with RNase and then added Gzms. RNA degradation in target cells reduced Gzm cytosolic localization and increased nuclear accumulation. Similarly, pre-incubating Gzms with exogenous competitor DNA reduced Gzm nuclear localization. The Gzms form a monophyletic clade with other immune serine proteases including neutrophil elastase (NE) and cathepsin G (CATG). Upon neutrophil activation, NE translocates to the nucleus to drive the formation of neutrophil extracellular traps (NETs). NE and CATG, but not non-immune serine proteases such as trypsin and pancreatic elastase, also bind DNA with high affinity and localize to the nucleus of permeabilized cells. Consistent with this finding, competitor DNA also blocks the nuclear localization of NE. Moreover NE and CATG localization to NETs depends on DNA binding. Thus the antimicrobial activity of NETs may depend in part upon the affinity of these proteases for DNA. Our findings indicate that high affinity nucleic acid binding is a conserved and functionally important property of serine proteases involved in cell-mediated immunity. Disclosures: Lieberman: Alnylam Pharmaceuticals: Membership on an entity’s Board of Directors or advisory committees.

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ProbeRating: a recommender system to infer binding profiles for nucleic acid-binding proteins

Bioinformatics ◽

10.1093/bioinformatics/btaa580 ◽

2020 ◽

Vol 36 (18) ◽

pp. 4797-4804

Author(s):

Shu Yang ◽

Xiaoxi Liu ◽

Raymond T Ng

Keyword(s):

Nucleic Acid ◽

Nucleic Acids ◽

Recommender System ◽

Binding Proteins ◽

Rna Binding ◽

Supplementary Information ◽

Sequence Information ◽

Nucleic Acid Binding ◽

Binding Data ◽

Nucleic Acid Binding Proteins

Abstract Motivation The interaction between proteins and nucleic acids plays a crucial role in gene regulation and cell function. Determining the binding preferences of nucleic acid-binding proteins (NBPs), namely RNA-binding proteins (RBPs) and transcription factors (TFs), is the key to decipher the protein–nucleic acids interaction code. Today, available NBP binding data from in vivo or in vitro experiments are still limited, which leaves a large portion of NBPs uncovered. Unfortunately, existing computational methods that model the NBP binding preferences are mostly protein specific: they need the experimental data for a specific protein in interest, and thus only focus on experimentally characterized NBPs. The binding preferences of experimentally unexplored NBPs remain largely unknown. Results Here, we introduce ProbeRating, a nucleic acid recommender system that utilizes techniques from deep learning and word embeddings of natural language processing. ProbeRating is developed to predict binding profiles for unexplored or poorly studied NBPs by exploiting their homologs NBPs which currently have available binding data. Requiring only sequence information as input, ProbeRating adapts FastText from Facebook AI Research to extract biological features. It then builds a neural network-based recommender system. We evaluate the performance of ProbeRating on two different tasks: one for RBP and one for TF. As a result, ProbeRating outperforms previous methods on both tasks. The results show that ProbeRating can be a useful tool to study the binding mechanism for the many NBPs that lack direct experimental evidence. and implementation Availability and implementation The source code is freely available at <https://github.com/syang11/ProbeRating>. Supplementary information Supplementary data are available at Bioinformatics online.

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Leukocyte Protease Binding to Nucleic Acids Promotes Nuclear Localization and Cleavage of Nucleic Acid Binding Proteins

The Journal of Immunology ◽

10.4049/jimmunol.1303296 ◽

2014 ◽

Vol 192 (11) ◽

pp. 5390-5397 ◽

Cited By ~ 24

Author(s):

Marshall P. Thomas ◽

Jennifer Whangbo ◽

Geoffrey McCrossan ◽

Aaron J. Deutsch ◽

Kimberly Martinod ◽

...

Keyword(s):

Nucleic Acid ◽

Nucleic Acids ◽

Nuclear Localization ◽

Binding Proteins ◽

Nucleic Acid Binding ◽

Nucleic Acid Binding Proteins

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Amino Acid Composition in Various Types of Nucleic Acid-Binding Proteins

International Journal of Molecular Sciences ◽

10.3390/ijms22020922 ◽

2021 ◽

Vol 22 (2) ◽

pp. 922

Author(s):

Martin Bartas ◽

Jiří Červeň ◽

Simona Guziurová ◽

Kristyna Slychko ◽

Petr Pečinka

Keyword(s):

Amino Acid ◽

Nucleic Acid ◽

Nucleic Acids ◽

Amino Acid Composition ◽

Acid Composition ◽

Binding Proteins ◽

Current Knowledge ◽

Special Focus ◽

Nucleic Acid Binding ◽

Nucleic Acid Binding Proteins

Nucleic acid-binding proteins are traditionally divided into two categories: With the ability to bind DNA or RNA. In the light of new knowledge, such categorizing should be overcome because a large proportion of proteins can bind both DNA and RNA. Another even more important features of nucleic acid-binding proteins are so-called sequence or structure specificities. Proteins able to bind nucleic acids in a sequence-specific manner usually contain one or more of the well-defined structural motifs (zinc-fingers, leucine zipper, helix-turn-helix, or helix-loop-helix). In contrast, many proteins do not recognize nucleic acid sequence but rather local DNA or RNA structures (G-quadruplexes, i-motifs, triplexes, cruciforms, left-handed DNA/RNA form, and others). Finally, there are also proteins recognizing both sequence and local structural properties of nucleic acids (e.g., famous tumor suppressor p53). In this mini-review, we aim to summarize current knowledge about the amino acid composition of various types of nucleic acid-binding proteins with a special focus on significant enrichment and/or depletion in each category.

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Snapshot blotting: The transfer of nucleic acids and nucleoprotein complexes from electrophoresis gels to EM grids

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100124215 ◽

1992 ◽

Vol 50 (1) ◽

pp. 762-763

Author(s):

Stephen D. Jett

Keyword(s):

Nucleic Acid ◽

Nucleic Acids ◽

Nucleic Acid Binding ◽

Mobility Shift ◽

Carbon Coated ◽

Nucleoprotein Complexes ◽

Mobility Shift Assay ◽

Protein Nucleic Acid ◽

Gel Mobility Shift ◽

Nucleic Acid Interactions

The electrophoresis gel mobility shift assay is a popular method for the study of protein-nucleic acid interactions. The binding of proteins to DNA is characterized by a reduction in the electrophoretic mobility of the nucleic acid. Binding affinity, stoichiometry, and kinetics can be obtained from such assays; however, it is often desirable to image the various species in the gel bands using TEM. Present methods for isolation of nucleoproteins from gel bands are inefficient and often destroy the native structure of the complexes. We have developed a technique, called “snapshot blotting,” by which nucleic acids and nucleoprotein complexes in electrophoresis gels can be electrophoretically transferred directly onto carbon-coated grids for TEM imaging.

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