Investigating the human host - ssRNA virus interaction landscape using the SMEAGOL toolbox

AbstractViruses are intracellular parasites that need their host cell to reproduce. Consequently, they have evolved numerous mechanisms to exploit the molecular machinery of their host cells, including the broad spectrum of host RNA-binding proteins (RBPs). However, the RBP interactome of viral genomes and the consequences of these interactions for infection are still to be mapped for most RNA viruses. To facilitate these efforts we have developed SMEAGOL, a fast and user-friendly toolbox to analyze the enrichment or depletion of RBP binding motifs across RNA sequences (https://github.com/gruber-sciencelab/SMEAGOL). To shed light on the interaction landscape of RNA viruses with human host cell RBPs at a large scale, we applied SMEAGOL to 197 single-stranded RNA (ssRNA) viral genome sequences. We find that the majority of ssRNA virus genomes are significantly enriched or depleted in binding motifs for human RBPs, suggesting selection pressure on these interactions. Our analysis provides an overview of potential virus - RBP interactions, covering the majority of ssRNA viral genomes fully sequenced to date, and represents a rich resource for studying host interactions vital to the virulence of ssRNA viruses. Our resource and the SMEAGOL toolbox will support future studies of virus / host interactions, ultimately feeding into better treatments.

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RNA-Binding Proteins at the Host-Pathogen Interface Targeting Viral Regulatory Elements

Viruses ◽

10.3390/v13060952 ◽

2021 ◽

Vol 13 (6) ◽

pp. 952

Author(s):

Azman Embarc-Buh ◽

Rosario Francisco-Velilla ◽

Encarnacion Martinez-Salas

Keyword(s):

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Rna Viruses ◽

Regulatory Elements ◽

Host Cells ◽

Viral Rnas ◽

Positive Strand ◽

Multiplication Cycle ◽

Positive Strand Rna

Viral RNAs contain the information needed to synthesize their own proteins, to replicate, and to spread to susceptible cells. However, due to their reduced coding capacity RNA viruses rely on host cells to complete their multiplication cycle. This is largely achieved by the concerted action of regulatory structural elements on viral RNAs and a subset of host proteins, whose dedicated function across all stages of the infection steps is critical to complete the viral cycle. Importantly, not only the RNA sequence but also the RNA architecture imposed by the presence of specific structural domains mediates the interaction with host RNA-binding proteins (RBPs), ultimately affecting virus multiplication and spreading. In marked difference with other biological systems, the genome of positive strand RNA viruses is also the mRNA. Here we focus on distinct types of positive strand RNA viruses that differ in the regulatory elements used to promote translation of the viral RNA, as well as in the mechanisms used to evade the series of events connected to antiviral response, including translation shutoff induced in infected cells, assembly of stress granules, and trafficking stress.

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Mycobacterium tuberculosis infection of host cells in space and time

FEMS Microbiology Reviews ◽

10.1093/femsre/fuz006 ◽

2019 ◽

Vol 43 (4) ◽

pp. 341-361 ◽

Cited By ~ 31

Author(s):

Claudio Bussi ◽

Maximiliano G Gutierrez

Keyword(s):

Mycobacterium Tuberculosis ◽

Host Cell ◽

Cell Biology ◽

Current Knowledge ◽

Bacterial Pathogen ◽

Infectious Agent ◽

Host Cells ◽

Cellular Mechanisms ◽

Mycobacterium Tuberculosis Infection ◽

Human Host

ABSTRACTTuberculosis (TB) caused by the bacterial pathogen Mycobacterium tuberculosis (Mtb) remains one of the deadliest infectious diseases with over a billion deaths in the past 200 years (Paulson 2013). TB causes more deaths worldwide than any other single infectious agent, with 10.4 million new cases and close to 1.7 million deaths in 2017. The obstacles that make TB hard to treat and eradicate are intrinsically linked to the intracellular lifestyle of Mtb. Mtb needs to replicate within human cells to disseminate to other individuals and cause disease. However, we still do not completely understand how Mtb manages to survive within eukaryotic cells and why some cells are able to eradicate this lethal pathogen. Here, we summarise the current knowledge of the complex host cell-pathogen interactions in TB and review the cellular mechanisms operating at the interface between Mtb and the human host cell, highlighting the technical and methodological challenges to investigating the cell biology of human host cell-Mtb interactions.

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RNA–protein interactions: disorder, moonlighting and junk contribute to eukaryotic complexity

Open Biology ◽

10.1098/rsob.190096 ◽

2019 ◽

Vol 9 (6) ◽

pp. 190096 ◽

Cited By ~ 14

Author(s):

Anna Balcerak ◽

Alicja Trebinska-Stryjewska ◽

Ryszard Konopinski ◽

Maciej Wakula ◽

Ewa Anna Grzybowska

Keyword(s):

Protein Interactions ◽

Regulatory Networks ◽

Rna Binding ◽

Rna Binding Proteins ◽

Protein Complexes ◽

Binding Motifs ◽

Coding Regions ◽

Regulatory Circuits ◽

Proteins Interactions

RNA–protein interactions are crucial for most biological processes in all organisms. However, it appears that the complexity of RNA-based regulation increases with the complexity of the organism, creating additional regulatory circuits, the scope of which is only now being revealed. It is becoming apparent that previously unappreciated features, such as disordered structural regions in proteins or non-coding regions in DNA leading to higher plasticity and pliability in RNA–protein complexes, are in fact essential for complex, precise and fine-tuned regulation. This review addresses the issue of the role of RNA–protein interactions in generating eukaryotic complexity, focusing on the newly characterized disordered RNA-binding motifs, moonlighting of metabolic enzymes, RNA-binding proteins interactions with different RNA species and their participation in regulatory networks of higher order.

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Picornaviruses and RNA Metabolism: Local and Global Effects of Infection

Journal of Virology ◽

10.1128/jvi.02088-17 ◽

2019 ◽

Vol 93 (21) ◽

Cited By ~ 3

Author(s):

Autumn C. Holmes ◽

Bert L. Semler

Keyword(s):

Host Cell ◽

Rna Binding ◽

Rna Binding Proteins ◽

Foot And Mouth Disease ◽

Rna Metabolism ◽

Cell Nuclei ◽

Cell Functions ◽

Mouth Disease Virus ◽

Wide Range ◽

Positive Strand Rna

ABSTRACT Due to the limiting coding capacity for members of the Picornaviridae family of positive-strand RNA viruses, their successful replication cycles require complex interactions with host cell functions. These interactions span from the down-modulation of many aspects of cellular metabolism to the hijacking of specific host functions used during viral translation, RNA replication, and other steps of infection by picornaviruses, such as human rhinovirus, coxsackievirus, poliovirus, foot-and-mouth disease virus, enterovirus D-68, and a wide range of other human and nonhuman viruses. Although picornaviruses replicate exclusively in the cytoplasm of infected cells, they have extensive interactions with host cell nuclei and the proteins and RNAs that normally reside in this compartment of the cell. This review will highlight some of the more recent studies that have revealed how picornavirus infections impact the RNA metabolism of the host cell posttranscriptionally and how they usurp and modify host RNA binding proteins as well as microRNAs to potentiate viral replication.

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Role of RNA Motifs in RNA Interaction with Membrane Lipid Rafts: Implications for Therapeutic Applications of Exosomal RNAs

International Journal of Molecular Sciences ◽

10.3390/ijms22179416 ◽

2021 ◽

Vol 22 (17) ◽

pp. 9416

Author(s):

Rafał Mańka ◽

Pawel Janas ◽

Karolina Sapoń ◽

Teresa Janas ◽

Tadeusz Janas

Keyword(s):

Lipid Rafts ◽

Rna Binding ◽

Rna Binding Proteins ◽

Membrane Lipid ◽

Rna Aptamers ◽

Target Cells ◽

Rna Motifs ◽

Binding Motifs ◽

Rna Exosome ◽

Rna Interaction

RNA motifs may promote interactions with exosomes (EXO-motifs) and lipid rafts (RAFT-motifs) that are enriched in exosomal membranes. These interactions can promote selective RNA loading into exosomes. We quantified the affinity between RNA aptamers containing various EXO- and RAFT-motifs and membrane lipid rafts in a liposome model of exosomes by determining the dissociation constants. Analysis of the secondary structure of RNA molecules provided data about the possible location of EXO- and RAFT-motifs within the RNA structure. The affinity of RNAs containing RAFT-motifs (UUGU, UCCC, CUCC, CCCU) and some EXO-motifs (CCCU, UCCU) to rafted liposomes is higher in comparison to aptamers without these motifs, suggesting direct RNA-exosome interaction. We have confirmed these results through the determination of the dissociation constant values of exosome-RNA aptamer complexes. RNAs containing EXO-motifs GGAG or UGAG have substantially lower affinity to lipid rafts, suggesting indirect RNA-exosome interaction via RNA binding proteins. Bioinformatics analysis revealed RNA aptamers containing both raft- and miRNA-binding motifs and involvement of raft-binding motifs UCCCU and CUCCC. A strategy is proposed for using functional RNA aptamers (fRNAa) containing both RAFT-motif and a therapeutic motif (e.g., miRNA inhibitor) to selectively introduce RNAs into exosomes for fRNAa delivery to target cells for personalized therapy.

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SBSA: an online service for somatic binding sequence annotation

Nucleic Acids Research ◽

10.1093/nar/gkab877 ◽

2021 ◽

Author(s):

Limin Jiang ◽

Fei Guo ◽

Jijun Tang ◽

Hui Yu ◽

Scott Ness ◽

...

Keyword(s):

Somatic Mutation ◽

Rna Binding ◽

Rna Binding Proteins ◽

Human Subjects ◽

Specific Factor ◽

Single Nucleotide ◽

Binding Motifs ◽

Genomic Variants ◽

Full Capacity ◽

Binding Sequence

Abstract Efficient annotation of alterations in binding sequences of molecular regulators can help identify novel candidates for mechanisms study and offer original therapeutic hypotheses. In this work, we developed Somatic Binding Sequence Annotator (SBSA) as a full-capacity online tool to annotate altered binding motifs/sequences, addressing diverse types of genomic variants and molecular regulators. The genomic variants can be somatic mutation, single nucleotide polymorphism, RNA editing, etc. The binding motifs/sequences involve transcription factors (TFs), RNA-binding proteins, miRNA seeds, miRNA-mRNA 3′-UTR binding target, or can be any custom motifs/sequences. Compared to similar tools, SBSA is the first to support miRNA seeds and miRNA-mRNA 3′-UTR binding target, and it unprecedentedly implements a personalized genome approach that accommodates joint adjacent variants. SBSA is empowered to support an indefinite species, including preloaded reference genomes for SARS-Cov-2 and 25 other common organisms. We demonstrated SBSA by annotating multi-omics data from over 30,890 human subjects. Of the millions of somatic binding sequences identified, many are with known severe biological repercussions, such as the somatic mutation in TERT promoter region which causes a gained binding sequence for E26 transformation-specific factor (ETS1). We further validated the function of this TERT mutation using experimental data in cancer cells. Availability:http://innovebioinfo.com/Annotation/SBSA/SBSA.php.

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SARS-CoV-2 nucleocapsid protein undergoes liquid-liquid phase separation stimulated by RNA and partitions into phases of human ribonucleoproteins

10.1101/2020.06.09.141101 ◽

2020 ◽

Cited By ~ 12

Author(s):

Theodora Myrto Perdikari ◽

Anastasia C. Murthy ◽

Veronica H. Ryan ◽

Scott Watters ◽

Mandar T. Naik ◽

...

Keyword(s):

Phase Separation ◽

Liquid Phase ◽

Nucleocapsid Protein ◽

Rna Binding ◽

Rna Binding Proteins ◽

Liquid Phase Separation ◽

Host Protein ◽

Host Cells ◽

Liquid Liquid Phase Separation

AbstractTightly packed complexes of nucleocapsid protein and genomic RNA form the core of viruses and may assemble within viral factories, dynamic compartments formed within the host cells. Here, we examine the possibility that the multivalent RNA-binding nucleocapsid protein (N) from the severe acute respiratory syndrome coronavirus (SARS-CoV-2) compacts RNA via protein-RNA liquid-liquid phase separation (LLPS) and that N interactions with host RNA-binding proteins are mediated by phase separation. To this end, we created a construct expressing recombinant N fused to a N-terminal maltose binding protein tag which helps keep the oligomeric N soluble for purification. Using in vitro phase separation assays, we find that N is assembly-prone and phase separates avidly. Phase separation is modulated by addition of RNA and changes in pH and is disfavored at high concentrations of salt. Furthermore, N enters into in vitro phase separated condensates of full-length human hnRNPs (TDP-43, FUS, and hnRNPA2) and their low complexity domains (LCs). However, N partitioning into the LC of FUS, but not TDP-43 or hnRNPA2, requires cleavage of the solubilizing MBP fusion. Hence, LLPS may be an essential mechanism used for SARS-CoV-2 and other RNA viral genome packing and host protein co-opting, functions necessary for viral replication and hence infectivity.

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Novel Protocol for Estimating Viruses Specifically Infecting the Marine Planktonic Diatoms

Diversity ◽

10.3390/d12060225 ◽

2020 ◽

Vol 12 (6) ◽

pp. 225

Author(s):

Yuji Tomaru ◽

Kei Kimura

Keyword(s):

Culture Method ◽

Host Cells ◽

Natural Sediment ◽

Viral Genomes ◽

Planktonic Diatoms ◽

Ecological Relationships ◽

Ssrna Virus ◽

Single Host ◽

Complete Lysis ◽

Ssdna Viruses

Since their discovery, at least 15 diatom viruses have been isolated and characterised using a culture method with two cycles of extinction dilution. However, the method is time consuming and laborious, and it isolates only the most dominant virus in a water sample. Recent studies have suggested inter-species host specificity of diatom viruses. Here, we describe a new protocol to estimate previously unrecognised host-virus relationships. Host cell cultures after inoculation of natural sediment pore water samples were obtained before complete lysis. The proliferated viral genomes in the host cells were amplified using degenerate primer pairs targeting protein replication regions of single-stranded RNA (ssRNA) and single-stranded DNA (ssDNA) viruses, and then sequenced. Diverse ssRNA virus types within known diatom virus group were detected from inoculated Chaetoceros tenuissimus and C. setoensis cells. A previously unknown ssDNA virus type was detected in inoculated C. tenuissimus cells, but not in C. setoensis cells. Despite the possible protocol biases, for example non-specific adsorptions of virions onto the host cells, the present method helps to estimate the viruses infectious to a single host species. Further improvements to this protocol targeting the proliferated viral genomes might reveal unexpected diatom–virus ecological relationships.

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Viral Life History Traits

Quantitative Viral Ecology ◽

10.23943/princeton/9780691161549.003.0002 ◽

2016 ◽

Author(s):

Joshua S. Weitz

Keyword(s):

Life History ◽

Mortality Rate ◽

Host Cell ◽

Life History Traits ◽

Viral Infections ◽

Burst Size ◽

Host Cells ◽

Viral Genomes ◽

Life History Stages ◽

Viral Progeny

This chapter discusses a number of key commonalities and differences among viral life history traits. Viruses have two key life history stages: inside and outside a host cell. Viral infections of microbes often lead to the death of host cells and the release of viral progeny. Viral infections can also lead to the integration of viral genomes with those of their hosts; induction of these genomes can result in subsequent lysis and release of viral progeny. Viruses are distinguished not only by the host they infect but also by the quantitative rates and levels at which these interactions take place. Viral life history traits reflect the combined interactions of viruses and hosts; that is, they are not encoded solely by viral genomes. Viral life history traits can also vary by orders of magnitude, whether for time to lysis, burst size, probability of lysogeny, rate of induction, adsorption rate, or mortality rate.

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A yeast RNA-binding protein shuttles between the nucleus and the cytoplasm.

Molecular and Cellular Biology ◽

10.1128/mcb.14.12.8399 ◽

1994 ◽

Vol 14 (12) ◽

pp. 8399-8407 ◽

Cited By ~ 109

Author(s):

J Flach ◽

M Bossie ◽

J Vogel ◽

A Corbett ◽

T Jinks ◽

...

Keyword(s):

Nuclear Protein ◽

Rna Binding ◽

Rna Binding Proteins ◽

Rna Binding Protein ◽

Wild Type ◽

Yeast Saccharomyces Cerevisiae ◽

Binding Motifs ◽

C Terminus ◽

N Terminus ◽

Heterogeneous Nuclear Ribonucleoproteins

RNA-binding proteins have been suggested to move in association with RNA as it leaves the nucleus. The NPL3 gene of the yeast Saccharomyces cerevisiae encodes in nuclear protein with consensus RNA-binding motifs and similarity to heterogeneous nuclear ribonucleoproteins and members of the S/R protein family. We show that although Npl3 is located in the nucleus, it can shuttle between nuclei in yeast heterokaryons. In contrast, other nucleus-targeted proteins do not leave the nucleus under similar conditions. Mutants missing the RNA-binding motifs or the N terminus are still capable of shuttling in and out of the nucleus. Npl3 mutants missing the C terminus fail to localize to the nucleus. Overproduction of Npl3 in wild-type cells shows cell growth. This toxicity depends on the presence of series of unique repeats in the N terminus and localization to the nucleus. We suggest that the properties of Npl3 are consistent with it being involved in export of RNAs from the nucleus.

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