Structure of a eukaryotic RNase III postcleavage complex reveals a double-ruler mechanism for substrate selection

Caught in the act-Visualizing ribonucleases during eukaryotic ribosome assembly

Ribosomes are essential macromolecular machines responsible for translating the genetic information encoded in mRNAs into proteins. Ribosomes are composed of ribosomal RNAs and proteins (rRNAs and RPs) and the rRNAs fulfill both catalytic and architectural functions. Excision of the mature eukaryotic rRNAs from their precursor transcript is achieved through a complex series of endoribonucleolytic cleavages and exoribonucleolytic processing steps that are precisely coordinated with other aspects of ribosome assembly. Many ribonucleases involved in pre-rRNA processing have been identified and pre-rRNA processing pathways are relatively well defined. However, momentous advances in cryo-electron microscopy have recently enabled structural snapshots of various pre-ribosomal particles from budding yeast (Saccharomyces cerevisiae) and human cells to be captured and, excitingly, these structures not only allow pre-rRNAs to be observed before and after cleavage events, but also enable ribonucleases to be visualized on their target RNAs. These structural views of pre-rRNA processing in action allow a new layer of understanding of rRNA maturation and how it is coordinated with other aspects of ribosome assembly. They illuminate mechanisms of target recognition by the diverse ribonucleases involved and reveal how the cleavage/processing activities of these enzymes are regulated. In this review, we discuss the new insights into pre-rRNA processing gained by structural analyses and the growing understanding of the mechanisms of ribonuclease regulation. This article is categorized under: Translation > Ribosome Biogenesis RNA Processing > rRNA Processing.

Genome-wide identification, characterization and expression analysis of AGO, DCL, and RDR families in Chenopodium quinoa

RNA interference is a highly conserved mechanism wherein several types of non-coding small RNAs regulate gene expression at the transcriptional or post-transcriptional level, modulating plant growth, development, antiviral defence, and stress responses. Argonaute (AGO), DCL (Dicer-like), and RNA-dependent RNA polymerase (RDR) are key proteins in this process. Here, these three protein families were identified in Chenopodium quinoa. Further, their phylogenetic relationships with Arabidopsis, their domains, three-dimensional structure modelling, subcellular localization, and functional annotation and expression were analysed. Whole-genome sequence analysis predicted 21 CqAGO, eight CqDCL, and 11 CqRDR genes in quinoa. All three protein families clustered into phylogenetic clades corresponding to those of Arabidopsis, including three AGO clades, four DCL clades, and four RDR clades, suggesting evolutionary conservation. Domain and protein structure analyses of the three gene families showed almost complete homogeneity among members of the same group. Gene ontology annotation revealed that the predicted gene families might be directly involved in RNAi and other important pathways. Largely, these gene families showed significant tissue-specific expression patterns, RNA-sequencing (RNA-seq) data revealed that 20 CqAGO, seven CqDCL, and ten CqRDR genes tended to have preferential expression in inflorescences. Most of them being downregulated in response to drought, cold, salt and low phosphate stress. To our knowledge, this is the first study to elucidate these key protein families involved in the RNAi pathway in quinoa, which are significant for understanding the mechanisms underlying stress responses in this plant.

Structural basis for Dicer-like function of an engineered RNase III variant and insights into the reaction trajectory of two-Mg2+-ion catalysis

The RNase III family of dsRNA-specific endonucleases is exemplified by prokaryotic RNase III and eukaryotic Rnt1p, Drosha, and Dicer. Structures of Aquifex aeolicus RNase III (AaRNase III) and Saccharomyces cerevisiae Rnt1p (ScRnt1p) show that both enzymes recognize substrates in a sequence-specific manner and propel RNA hydrolysis by two-Mg²⁺-ion catalysis. Previously, we created an Escherichia coli RNase III variant (EcEEQ) by eliminating the sequence specificity via protein engineering and called it bacterial Dicer for the fact that it produces heterogeneous small interfering RNA cocktails. Here, we present a 1.8-Å crystal structure of a postcleavage complex of EcEEQ, representing a reaction state immediately after the cleavage of scissile bond. The structure not only establishes the structure-and-function relationship of EcEEQ, but also reveals the functional role of a third Mg²⁺ ion that is involved in RNA hydrolysis by bacterial RNase III. In contrast, the cleavage site assembly of ScRnt1p does not contain a third Mg²⁺ ion. Instead, it involves two more amino acid side chains conserved among eukaryotic RNase IIIs. We conclude that the EcEEQ structure (this work) represents the cleavage assembly of prokaryotic RNase IIIs and the ScRnt1p structure (PDB: 4OOG), also determined at the postcleavage state, represents the cleavage assembly of eukaryotic RNase IIIs. Together, these two structures provide insights into the reaction trajectory of two-Mg²⁺-ion catalysis by prokaryotic and eukaryotic RNase III enzymes.

Molecular ruler mechanism and interfacial catalysis of the integral membrane acyltransferase PatA

Glycolipids are prominent components of bacterial membranes that play critical roles not only in maintaining the structural integrity of the cell but also in modulating host-pathogen interactions. PatA is an essential acyltransferase involved in the biosynthesis of phosphatidyl-myo-inositol mannosides (PIMs), key structural elements and virulence factors of Mycobacterium tuberculosis. We demonstrate by electron spin resonance spectroscopy and surface plasmon resonance that PatA is an integral membrane acyltransferase tightly anchored to anionic lipid bilayers, using a two-helix structural motif and electrostatic interactions. PatA dictates the acyl chain composition of the glycolipid by using an acyl chain selectivity “ruler.” We established this by a combination of structural biology, enzymatic activity, and binding measurements on chemically synthesized nonhydrolyzable acyl–coenzyme A (CoA) derivatives. We propose an interfacial catalytic mechanism that allows PatA to acylate hydrophobic PIMs anchored in the inner membrane of mycobacteria, through the use of water-soluble acyl-CoA donors.

In Vitro Identification and In Vivo Confirmation of Inhibitors for Sweet Potato Chlorotic Stunt Virus RNA Silencing Suppressor, a Viral RNase III

Sweet potato virus disease (SPVD), caused by synergistic infection of Sweet potato chlorotic stunt virus (SPCSV) and Sweet potato feathery mottle virus (SPFMV), is responsible for substantial yield losses all over the world. However, there are currently no approved treatments for this severe disease. The crucial role played by RNase III of SPCSV (CSR3) as an RNA silencing suppressor during the viruses' synergistic interaction in sweetpotato makes it an ideal drug target for developing antiviral treatment. In this study, high-throughput screening (HTS) of small molecular libraries targeting CSR3 was initiated by a virtual screen using Glide docking, allowing the selection of 6,400 compounds out of 136,353. We subsequently developed and carried out kinetic-based HTS using fluorescence resonance energy transfer technology, which isolated 112 compounds. These compounds were validated with dose-response assays including kinetic-based HTS and binding affinity assays using surface plasmon resonance and microscale thermophoresis. Finally, the interference of the selected compounds with viral accumulation was verified in planta In summary, we identified five compounds belonging to two structural classes that inhibited CSR3 activity and reduced viral accumulation in plants. These results provide the foundation for developing antiviral agents targeting CSR3 to provide new strategies for controlling sweetpotato virus diseases.IMPORTANCE We report here a high-throughput inhibitor identification method that targets a severe sweetpotato virus disease caused by coinfection with two viruses (SPCSV and SPFMV). The disease is responsible for up to 90% yield losses. Specifically, we targeted the RNase III enzyme encoded by SPCSV, which plays an important role in suppressing the RNA silencing defense system of sweetpotato plants. Based on virtual screening, laboratory assays, and confirmation in planta, we identified five compounds that could be used to develop antiviral drugs to combat the most severe sweetpotato virus disease.

A ribonuclease III involved in virulence of Mucorales fungi has evolved to cut exclusively single-stranded RNA

Members of the ribonuclease III (RNase III) family regulate gene expression by processing double-stranded RNA (dsRNA). This family includes eukaryotic Dicer and Drosha enzymes that generate small dsRNAs in the RNA interference (RNAi) pathway. The fungus Mucor lusitanicus, which causes the deadly infection mucormycosis, has a complex RNAi system encompassing a non-canonical RNAi pathway (NCRIP) that regulates virulence by degrading specific mRNAs. In this pathway, Dicer function is replaced by R3B2, an atypical class I RNase III, and small single-stranded RNAs (ssRNAs) are produced instead of small dsRNA as Dicer-dependent RNAi pathways. Here, we show that R3B2 forms a homodimer that binds to ssRNA and dsRNA molecules, but exclusively cuts ssRNA, in contrast to all known RNase III. The dsRNA cleavage inability stems from its unusual RNase III domain (RIIID) because its replacement by a canonical RIIID allows dsRNA processing. A crystal structure of R3B2 RIIID resembles canonical RIIIDs, despite the low sequence conservation. However, the groove that accommodates dsRNA in canonical RNases III is narrower in the R3B2 homodimer, suggesting that this feature could be responsible for the cleavage specificity for ssRNA. Conservation of this activity in R3B2 proteins from other mucormycosis-causing Mucorales fungi indicates an early evolutionary acquisition.

Structural and mechanistic insight into stem-loop RNA processing by yeast Pichia stipitis Dicer

Dicer is a member of the ribonuclease III enzyme family and processes double-stranded RNA into small functional RNAs. The variation in the domain architecture of Dicer among different species whilst preserving its biological dicing function is intriguing. Here, we describe the structure and function of a novel catalytically active RNase III protein, a non-canonical Dicer (PsDCR1), found in budding yeast Pichia stipitis. The structure of the catalytically active region (the catalytic RNase III domain and double-stranded RNA-binding domain 1 [dsRBD1]) of DCR1 showed that RNaseIII domain is structurally similar to yeast RNase III (Rnt1p) but uniquely presents dsRBD1 in a diagonal orientation, forming a catalytic core made of homodimer and large RNA-binding surface. The second dsRNA binding domain at C-terminus, which is absent in Rnt1, enhances the RNA cleavage activity. Although the cleavage pattern of PsDCR1 anchors an apical loop similar to Rnt1, the cleavage activity depended on the sequence motif at the lower stem, not the apical loop, of hairpin RNA. Through RNA sequencing and RNA mutations, we showed that RNA cleavage by PsDCR1 is determined by the stem-loop structure of the RNA substrate, suggesting the possibility that stem-loop RNA-guided gene silencing pathway exists in budding yeast.

Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation

Restriction endonucleases naturally target DNA duplexes. Systematic screening has identified a small minority of these enzymes that can also cleave RNA/DNA heteroduplexes and that may therefore be useful as tools for RNA biochemistry. We have chosen AvaII (G↓GWCC, where W stands for A or T) as a representative of this group of restriction endonucleases for detailed characterization. Here, we report crystal structures of AvaII alone, in specific complex with partially cleaved dsDNA, and in scanning complex with an RNA/DNA hybrid. The specific complex reveals a novel form of semi-specific dsDNA readout by a hexa-coordinated metal cation, most likely Ca²⁺ or Mg²⁺. Substitutions of residues anchoring this non-catalytic metal ion severely impair DNA binding and cleavage. The dsDNA in the AvaII complex is in the A-like form. This creates space for 2′-OH groups to be accommodated without intra-nucleic acid steric conflicts. PD-(D/E)XK restriction endonucleases of known structure that bind their dsDNA targets in the A-like form cluster into structurally similar groups. Most such enzymes, including some not previously studied in this respect, cleave RNA/DNA heteroduplexes. We conclude that A-form dsDNA binding is a good predictor for RNA/DNA cleavage activity.

Development of FRET-based high-throughput screening for viral RNase III inhibitors

The class 1 ribonuclease III (RNase III) encoded by Sweet potato chlorotic stunt virus (CSR3) suppresses RNA silencing in plant cells and thereby counters the host antiviral response by cleaving host small interfering RNAs, which are indispensable components of the plant RNA interference (RNAi) pathway. The synergy between sweet potato chlorotic stunt virus and sweet potato feathery mottle virus can reduce crop yields by 90%. Inhibitors of CSR3 might prove efficacious to counter this viral threat, yet no screen has been carried out to identify such inhibitors. Here, we report a novel high-throughput screening (HTS) assay based on fluorescence resonance energy transfer (FRET) for identifying inhibitors of CSR3. For monitoring CSR3 activity via HTS, we used a small interfering RNA substrate that was labelled with a FRET-compatible dye. The optimized HTS assay yielded 109 potential inhibitors of CSR3 out of 6,620 compounds tested from different small-molecule libraries. The three best inhibitor candidates were validated with a dose-response assay. In addition, a parallel screen of the selected candidates was carried out for a similar class 1 RNase III enzyme from Escherichia coli (EcR3), and this screen yielded a different set of inhibitors. Thus, our results show that the CSR3 and EcR3 enzymes were inhibited by distinct types of molecules, indicating that this HTS assay could be widely applied in drug discovery of class 1 RNase III enzymes.

Dicer's Helicase Domain: A Meeting Place for Regulatory Proteins

The function of Dicer’s helicase domain has been enigmatic since its discovery. Why do only some Dicers require ATP, despite a high degree of sequence conservation in their helicase domains? We discuss evolutionary considerations based on differences between vertebrate and invertebrate antiviral defense, and how the helicase domain has been co-opted in extant organisms as the binding site for accessory proteins. Many accessory proteins are double-stranded RNA binding proteins, and we propose models for how they modulate Dicer function and catalysis.

The molecular mechanism of dsRNA processing by a bacterial Dicer

Members of the ribonuclease (RNase) III family regulate gene expression by processing dsRNAs. It was previously shown that Escherichia coli (Ec) RNase III recognizes dsRNA with little sequence specificity and the cleavage products are mainly 11 nucleotides (nt) long. It was also shown that the mutation of a glutamate (EcE38) to an alanine promotes generation of siRNA-like products typically 22 nt long. To fully characterize substrate specificity and product size of RNase IIIs, we performed in vitro cleavage of dsRNAs by Ec and Aquifex aeolicus (Aa) enzymes and delineated their products by next-generation sequencing. Surprisingly, we found that both enzymes cleave dsRNA at preferred sites, among which a guanine nucleotide was enriched at a specific position (+3G). Based on sequence and structure analyses, we conclude that RNase IIIs recognize +3G via a conserved glutamine (EcQ165/AaQ161) side chain. Abolishing this interaction by mutating the glutamine to an alanine eliminates the observed +3G preference. Furthermore, we identified a second glutamate (EcE65/AaE64), which, when mutated to alanine, also enhances the production of siRNA-like products. Based on these findings, we created a bacterial Dicer that is ideally suited for producing heterogeneous siRNA cocktails to be used in gene silencing studies.

Study of the role of Mg2+ in dsRNA processing mechanism by bacterial RNase III through QM/MM simulations

The ribonuclease III (RNase III) cleaves dsRNA in specific positions generating mature RNAs. RNase III enzymes play important roles in RNA processing, post-transcriptional gene expression, and defense against viral infection. The enzyme's active site contains Mg²⁺ ions bound by a network of acidic residues and water molecules, but there is a lack of information about their specific roles. In this work, multiple steered molecular dynamics simulations at QM/MM level were performed to explore the hydrolysis reaction carried out by the enzyme. Free energy profiles modifying the features of the active site are obtained and the role of Mg²⁺ ions, the solvent molecules and the residues of the active site are discussed in detail. Our results show that Mg²⁺ ions carry out different roles in the hydrolysis process positioning the substrate for the attack from a coordinated nucleophile and activating it to perform hydrolysis reaction, cleaving the dsRNA backbone in a S_N2 substitution. In addition, water molecules present in the active site lower the energy barrier of the process. RNase III hydrolyzes dsRNA to generate mature RNAs. For this purpose, its active site contains Mg²⁺ which has an important role during the reaction. Results show that the Mg²⁺ activates the solvent molecule that produces the nucleophilic attack and the surrounding waters contribute significantly to the hydrolysis process.

Conformational adaptation of UNCG loops upon crowding

If the A-form helix is the major structural motif found in RNA, the loops that cap them constitute the second most important family of motifs. Among those, two are overrepresented, GNRA and UNCG tetraloops. Recent surveys of RNA structures deposited in the PDB show that GNRA and UNCG tetraloops can adopt tertiary folds that are very different from their canonical conformations, characterized by the presence of a U-turn of a Z-turn, respectively. Crystallographic data from both a lariat-capping (LC) ribozyme and a group II intron ribozyme reveal that a given UUCG tetraloop can adopt a distinct fold depending on its structural environment. Specifically, when the crystal packing applies relaxed constraints on the loop, the canonical Z-turn conformation is observed. In contrast, a highly packed environment induces "squashing" of the tetraloop by distorting its sugar-phosphate backbone in a specific way that expels the first and fourth nucleobases out of the loop, and falls in van der Waals distance of the last base pair of the helix, taking the place of the pair formed between the first and fourth residues in Z-turn loops. The biological relevance of our observations is supported by the presence of similarly deformed loops in the highly packed environment of the ribosome and in a complex between a dsRNA and a RNase III. The finding that Z-turn loops change conformation under higher molecular packing suggests that, in addition to their demonstrated role in stabilizing RNA folding, they may contribute to the three-dimensional structure of RNA by mediating tertiary interactions with distal residues.

Molecular basis for transfer RNA recognition by the double-stranded RNA-binding domain of human dihydrouridine synthase 2

Double stranded RNA-binding domain (dsRBD) is a ubiquitous domain specialized in the recognition of double-stranded RNAs (dsRNAs). Present in many proteins and enzymes involved in various functional roles of RNA metabolism, including RNA splicing, editing, and transport, dsRBD generally binds to RNAs that lack complex structures. However, this belief has recently been challenged by the discovery of a dsRBD serving as a major tRNA binding module for human dihydrouridine synthase 2 (hDus2), a flavoenzyme that catalyzes synthesis of dihydrouridine within the complex elbow structure of tRNA. We here unveil the molecular mechanism by which hDus2 dsRBD recognizes a tRNA ligand. By solving the crystal structure of this dsRBD in complex with a dsRNA together with extensive characterizations of its interaction with tRNA using mutagenesis, NMR and SAXS, we establish that while hDus2 dsRBD retains a conventional dsRNA recognition capability, the presence of an N-terminal extension appended to the canonical domain provides additional residues for binding tRNA in a structure-specific mode of action. Our results support that this extension represents a feature by which the dsRBD specializes in tRNA biology and more broadly highlight the importance of structural appendages to canonical domains in promoting the emergence of functional diversity.

A three-dimensional RNA motif mediates directional trafficking of Potato spindle tuber viroid from epidermal to palisade mesophyll cells in Nicotiana benthamiana

Potato spindle tuber viroid (PSTVd) is a circular non-coding RNA of 359 nucleotides that replicates and spreads systemically in host plants, thus all functions required to establish an infection are mediated by sequence and structural elements in the genome. The PSTVd secondary structure contains 26 Watson-Crick base-paired stems and 27 loops. Most of the loops are believed to form three-dimensional (3D) structural motifs through non-Watson-Crick base pairing, base stacking, and other local interactions. Homology-based prediction using the JAR3D online program revealed that loop 27 (nucleotides 177-182) most likely forms a 3D structure similar to the loop of a conserved hairpin located in the 3' untranslated region of histone mRNAs in animal cells. This stem-loop, which is involved in 3'-end maturation, is not found in polyadenylated plant histone mRNAs. Mutagenesis showed that PSTVd genomes containing base substitutions in loop 27 predicted by JAR3D to disrupt the 3D structure were unable to replicate in Nicotiana benthamiana leaves following mechanical rub inoculation, with one exception: a U178G/U179G double mutant was replication-competent and able to spread within the upper epidermis of inoculated leaves, but was confined to this cell layer. Remarkably, direct delivery of the U178G/U179G mutant into the vascular system by needle puncture inoculation allowed it to spread systemically and enter mesophyll cells and epidermal cells of upper leaves. These findings highlight the importance of RNA 3D structure for PSTVd replication and intercellular trafficking and indicate that loop 27 is required for epidermal exit, but not epidermal entry or transit between other cell types. Thus, requirements for RNA trafficking between epidermal and underlying palisade mesophyll cells are unique and directional. Our findings further suggest that 3D structure and RNA-protein interactions constrain RNA sequence evolution, and validate JAR3D as a tool to predict RNA 3D structure.

Structural insights into DNA degradation by human mitochondrial nuclease MGME1

Mitochondrial nucleases play important roles in accurate maintenance and correct metabolism of mtDNA, the own genetic materials of mitochondria that are passed exclusively from mother to child. MGME1 is a highly conserved DNase that was discovered recently. Mutations in MGME1-coding gene lead to severe mitochondrial syndromes characterized by external ophthalmoplegia, emaciation, and respiratory failure in humans. Unlike many other nucleases that are distributed in multiple cellular organelles, human MGME1 is a mitochondria-specific nuclease; therefore, it can serve as an ideal target for treating related syndromes. Here, we report one HsMGME1-Mn2+ complex and three different HsMGME1-DNA complex structures. In combination with in vitro cleavage assays, our structures reveal the detailed molecular basis for substrate DNA binding and/or unwinding by HsMGME1. Besides the conserved two-cation-assisted catalytic mechanism, structural analysis of HsMGME1 and comparison with homologous proteins also clarified substrate binding and cleavage directionalities of the DNA double-strand break repair complexes RecBCD and AddAB.

Improved foot-and-mouth disease vaccine, O TWN-R, protects pigs against SEA topotype virus occurred in South Korea

Foot-and-mouth disease (FMD) is a highly contagious disease and causes economic damage at a national level. In particular, the type O FMD virus (FMDV) is a serotype that causes FMD outbreaks most frequently in the world. In recent years, Southeast Asia (SEA), Middle East-South Asia (ME-SA), and Cathay topotype-mediated FMD are prevalent in Asia, among which the SEA and ME-SA topotypes cause a majority of the outbreaks. The SEA topotype virus is more likely to infect both cattle and pigs simultaneously, thereby resulting in more severe damages; thus, it is necessary to study the protection ability of the candidate vaccines of this topotype after immunization. In this study, an experimental vaccine for pigs was produced using a vaccine strain that contains the structural protein of the O Taiwan97 strain, which was derived from the Cathay topotype, and its effect was evaluated. In the immunization test in pigs and cattle, the antibody titers were found to be elevated two weeks after immunization and very high titers of neutralizing antibodies were formed after four weeks. After the second inoculation, very high titers of neutralizing antibodies were produced in both species in the fourth week after immunization, and the antibodies maintained for up to six months and three months in cattle and pigs, respectively. No significant immunological difference in antibody production was observed in cattle and pigs. This study confirmed that complete protection from the challenge of the SEA topotype virus (O/Jincheon/SKR/2014), although the antibody titers against O/Jincheon/SKR/2014 strain were not that high, was achieved through immunization with the newly developed Cathay topotype vaccine in pigs.

Promoter-dependent nuclear RNA degradation ensures cell cycle-specific gene expression

Cell cycle progression depends on phase-specific gene expression. Here we show that the nuclear RNA degradation machinery plays a lead role in promoting cell cycle-dependent gene expression by triggering promoter-dependent co-transcriptional RNA degradation. Single molecule quantification of RNA abundance in different phases of the cell cycle indicates that relative curtailment of gene expression in certain phases is attained even when transcription is not completely inhibited. When nuclear ribonucleases are deleted, transcription of the Saccharomyces cerevisiae G1-specific axial budding gene AXL2 is detected throughout the cell cycle and its phase-specific expression is lost. Promoter replacement abolished cell cycle-dependent RNA degradation and rendered the RNA insensitive to the deletion of nuclear ribonucleases. Together the data reveal a model of gene regulation whereby RNA abundance is controlled by promoter-dependent induction of RNA degradation.

Structure and function of Rnt1p: An alternative to RNAi for targeted RNA degradation

The double-stranded RNA-binding protein (dsRBP) family controls RNA editing, stability, and function in all eukaryotes. The central feature of this family is the recognition of a generic RNA duplex using highly conserved double-stranded RNA-binding domain (dsRBD) that recognizes the characteristic distance between the minor grooves created by the RNA helix. Variations on this theme that confer species and functional specificities have been reported but most dsRBPs retain their capacity to bind generic dsRNA. The ribonuclease III (RNase III) family members fall into four classes, represented by bacterial RNase III, yeast Rnt1p, human Drosha, and human Dicer, respectively. Like all dsRBPs and most members of the RNase III family, Rnt1p has a dsRBD, but unlike most of its kin, it poorly binds to generic RNA helices. Instead, Rnt1p, the only known RNase III expressed in Saccharomyces cerevisiae that lacks the RNAi (RNA interference) machinery, recognizes a specific class of stem-loop structures. To recognize the specific substrates, the dsRBD of Rnt1p is specialized, featuring a αβββααα topology and a sequence-specific RNA-binding motif at the C-terminus. Since the discovery of Rnt1p in 1996, significant progress has been made in studies of its genetics, function, structure, and mechanism of action, explaining the reasons and mechanisms for the increased specificity of this enzyme and its impact on the mechanism of RNA degradation. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Processing > Processing of Small RNAs RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.

Conserved Proteins of the RNA Interference System in the Arbuscular Mycorrhizal Fungus Rhizoglomus irregulare Provide New Insight into the Evolutionary History of Glomeromycota

Horizontal gene transfer (HGT) is an important mechanism in the evolution of many living organisms particularly in Prokaryotes where genes are frequently dispersed between taxa. Although, HGT has been reported in Eukaryotes, its accumulative effect and its frequency has been questioned. Arbuscular mycorrhizal fungi (AMF) are an early diverged fungal lineage belonging to phylum Glomeromycota, whose phylogenetic position is still under debate. The history of AMF and land plant symbiosis dates back to at least 460 Ma. However, Glomeromycota are estimated to have emerged much earlier than land plants. In this study, we surveyed genomic and transcriptomic data of the model arbuscular mycorrhizal fungus Rhizoglomus irregulare (synonym Rhizophagus irregularis) and its relatives to search for evidence of HGT that occurred during AMF evolution. Surprisingly, we found a signature of putative HGT of class I ribonuclease III protein-coding genes that occurred from autotrophic cyanobacteria genomes to R. irregulare. At least one of two HGTs was conserved among AMF species with high levels of sequence similarity. Previously, an example of intimate symbiosis between AM fungus and cyanobacteria was reported in the literature. Ribonuclease III family enzymes are important in small RNA regulation in Fungi together with two additional core proteins (Argonaute/piwi and RdRP). The eukaryotic RNA interference system found in AMF was conserved and showed homology with high sequence similarity in Mucoromycotina, a group of fungi closely related to Glomeromycota. Prior to this analysis, class I ribonuclease III has not been identified in any eukaryotes. Our results indicate that a unique acquisition of class I ribonuclease III in AMF is due to a HGT event that occurred from cyanobacteria to Glomeromycota, at the latest before the divergence of the two Glomeromycota orders Diversisporales and Glomerales.

The siRNA suppressor RTL1 is redox-regulated through glutathionylation of a conserved cysteine in the double-stranded-RNA-binding domain

RNase III enzymes cleave double stranded (ds)RNA. This is an essential step for regulating the processing of mRNA, rRNA, snoRNA and other small RNAs, including siRNA and miRNA. Arabidopsis thaliana encodes nine RNase III: four DICER-LIKE (DCL) and five RNASE THREE LIKE (RTL). To better understand the molecular functions of RNase III in plants we developed a biochemical assay using RTL1 as a model. We show that RTL1 does not degrade dsRNA randomly, but recognizes specific duplex sequences to direct accurate cleavage. Furthermore, we demonstrate that RNase III and dsRNA binding domains (dsRBD) are both required for dsRNA cleavage. Interestingly, the four DCL and the three RTL that carry dsRBD share a conserved cysteine (C230 in Arabidopsis RTL1) in their dsRBD. C230 is essential for RTL1 and DCL1 activities and is subjected to post-transcriptional modification. Indeed, under oxidizing conditions, glutathionylation of C230 inhibits RTL1 cleavage activity in a reversible manner involving glutaredoxins. We conclude that the redox state of the dsRBD ensures a fine-tune regulation of dsRNA processing by plant RNase III.

Comparison of preribosomal RNA processing pathways in yeast, plant and human cells - focus on coordinated action of endo- and exoribonucleases

Proper regulation of ribosome biosynthesis is mandatory for cellular adaptation, growth and proliferation. Ribosome biogenesis is the most energetically demanding cellular process, which requires tight control. Abnormalities in ribosome production have severe consequences, including developmental defects in plants and genetic diseases (ribosomopathies) in humans. One of the processes occurring during eukaryotic ribosome biogenesis is processing of the ribosomal RNA precursor molecule (pre-rRNA), synthesized by RNA polymerase I, into mature rRNAs. It must not only be accurate but must also be precisely coordinated with other phenomena leading to the synthesis of functional ribosomes: RNA modification, RNA folding, assembly with ribosomal proteins and nucleocytoplasmic RNP export. A multitude of ribosome biogenesis factors ensure that these events take place in a correct temporal order. Among them are endo- and exoribonucleases involved in pre-rRNA processing. Here, we thoroughly present a wide spectrum of ribonucleases participating in rRNA maturation, focusing on their biochemical properties, regulatory mechanisms and substrate specificity. We also discuss cooperation between various ribonucleolytic activities in particular stages of pre-rRNA processing, delineating major similarities and differences between three representative groups of eukaryotes: yeast, plants and humans.

Structural and functional studies of a noncanonical Dicer from Entamoeba histolytica

RNaseIII proteins are dsRNA-specific endonucleases involved in many important biological processes, such as small RNA processing and maturation in eukaryotes. Various small RNAs have been identified in a protozoan parasite Entamoeba histolytica. EhRNaseIII is the only RNaseIII endonuclease domain (RIIID)-containing protein in E. histolytica. Here, we present three crystal structures that reveal several unique structural features of EhRNaseIII, especially the interactions between the two helixes (α1 and α7) flanking the RIIID core domain. Structure and sequence analysis indicate that EhRNaseIII is a noncanonical Dicer and it lacks a dsRBD in the C-terminal region (CTR). In vitro studies suggest that EhRNaseIII prefers to bind and cleave longer dsRNAs, generating products around 25 nucleotides in length. Truncation of the CTR or attaching the dsRBD of Aquifex aeolicus RNaseIII can enhance the binding and cleavage activities of EhRNaseIII. In combination with in vitro crosslinking assay, our results suggested that EhRNaseIII functions in a cooperative mode. We speculate that some partner proteins may exist in E. histolytica and regulates the activity of EhRNaseIII through interaction with its CTR. Our studies support that EhRNaseIII plays an important role in producing small RNAs in E. histolytica.

The Functional Cycle of Rnt1p: Five Consecutive Steps of Double-Stranded RNA Processing by a Eukaryotic RNase III

Double-stranded RNA (dsRNA)-specific RNase III proteins are required for RNA maturation and gene regulation. The mechanism of prokaryotic RNase IIIs has been well characterized, but how eukaryotic RNase IIIs (exemplified by Rnt1p, Drosha, and Dicer) work is less clear. Recently, we reported the crystal structure of Rnt1p in complex with RNA, revealing a double-ruler mechanism for substrate selection. Here, we present more structures of Rnt1p, either RNA free or RNA bound, featuring two major conformations of the enzyme. Using these structures with existing data, we describe the functional cycle of Rnt1p in five steps, selecting, loading, locking, cleavage, and releasing. We also describe atomic details of the two-Mg2+-ion catalytic mechanism that is applicable to all eukaryotic RNase III enzymes. Overall, our results indicate that substrate selection is achieved independent of cleavage, allowing the recognition of substrates with different structures while preserving the basic mechanism of cleavage.

Modeling of the catalytic core of Arabidopsis thaliana Dicer-like 4 protein and its complex with double-stranded RNA

Plant Dicer-like proteins (DCLs) belong to the Ribonuclease III (RNase III) enzyme family. They are involved in the regulation of gene expression and antiviral defense through RNA interference pathways. A model plant, Arabidopsis thaliana encodes four DCL proteins (AtDCL1-4) that produce different classes of small regulatory RNAs. Our studies focus on AtDCL4 that processes double-stranded RNAs (dsRNAs) into 21 nucleotide trans-acting small interfering RNAs. So far, little is known about the structures of plant DCLs and the complexes they form with dsRNA. In this work, we present models of the catalytic core of AtDCL4 and AtDCL4-dsRNA complex constructed by computational methods. We built a homology model of the catalytic core of AtDCL4 comprising Platform, PAZ, Connector helix and two RNase III domains. To assemble the AtDCL4-dsRNA complex two modeling approaches were used. In the first method, to establish conformations that allow building a consistent model of the complex, we used Normal Mode Analysis for both dsRNA and AtDCL4. The second strategy involved template-based approach for positioning of the PAZ domain and manual arrangement of the Connector helix. Our results suggest that the spatial orientation of the Connector helix, Platform and PAZ relative to the RNase III domains is crucial for measuring dsRNA of defined length. The modeled complexes provide information about interactions that may contribute to the relative orientations of these domains and to dsRNA binding. All these information can be helpful for understanding the mechanism of AtDCL4-mediated dsRNA recognition and binding, to produce small RNA of specific size.

Fail-safe transcription termination: Because one is never enough

Termination of RNA polymerase II (RNAPII) transcription is a fundamental step of gene expression that involves the release of the nascent transcript and dissociation of RNAPII from the DNA template. As transcription termination is intimately linked to RNA 3' end processing, termination pathways have a key decisive influence on the fate of the transcribed RNA. Quite remarkably, when reaching the 3' end of genes, a substantial fraction of RNAPII fail to terminate transcription, requiring the contribution of alternative or "fail-safe" mechanisms of termination to release the polymerase. This point of view covers redundant mechanisms of transcription termination and how they relate to conventional termination models. In particular, we expand on recent findings that propose a reverse torpedo model of termination, in which the 3'5' exonucleolytic activity of the RNA exosome targets transcription events associated with paused and backtracked RNAPII.

The catalytic efficiency of yeast ribonuclease III depends on substrate specific product release rate

Members of the ribonuclease III (RNase III) family regulate gene expression by triggering the degradation of double stranded RNA (dsRNA). Hundreds of RNase III cleavage targets have been identified and their impact on RNA maturation and stability is now established. However, the mechanism defining substrates’ reactivity remains unclear. In this study, we developed a real-time FRET assay for the detection of dsRNA degradation by yeast RNase III (Rnt1p) and characterized the kinetic bottlenecks controlling the reactivity of different substrates. Surprisingly, the results indicate that Rnt1p cleavage reaction is not only limited by the rate of catalysis but can also depend on base-pairing of product termini. Cleavage products terminating with paired nucleotides, like the degradation signals found in coding mRNA sequence, were less reactive and more prone to inhibition than products having unpaired nucleotides found in non-coding RNA substrates. Mutational analysis of U5 snRNA and Mig2 mRNA confirms the pairing of the cleavage site as a major determinant for the difference between cleavage rates of coding and non-coding RNA. Together the data indicate that the base-pairing of Rnt1p substrates encodes reactivity determinants that permit both constitutive processing of non-coding RNA while limiting the rate of mRNA degradation.

Functions of double-stranded RNA-binding domains in nucleocytoplasmic transport

The double-stranded RNA-binding domain (dsRBD) is a small protein domain found in eukaryotic, prokaryotic and viral proteins, whose central property is to bind to double-stranded RNA (dsRNA). Aside from this major function, recent examples of dsRBDs involved in the regulation of the sub-cellular localization of proteins, suggest that the participation of dsRBDs in nucleocytoplasmic trafficking is likely to represent a widespread auxiliary function of this type of RNA-binding domain. Overall, dsRBDs from proteins involved in many different biological processes have been reported to be implicated in nuclear import and export, as well as cytoplasmic, nuclear and nucleolar retention. Interestingly, the function of dsRBDs in nucleocytoplasmic trafficking is often regulated by their dsRNA-binding capacity, which can either enhance or impair the transport from one compartment to another. Here, we present and discuss the emerging function of dsRBDs in nucleocytoplasmic transport.

mRNA maturation in giant viruses: variation on a theme

Giant viruses from the Mimiviridae family replicate entirely in their host cytoplasm where their genes are transcribed by a viral transcription apparatus. mRNA polyadenylation uniquely occurs at hairpin-forming palindromic sequences terminating viral transcripts. Here we show that a conserved gene cluster both encode the enzyme responsible for the hairpin cleavage and the viral polyA polymerases (vPAP). Unexpectedly, the vPAPs are homodimeric and uniquely self-processive. The vPAP backbone structures exhibit a symmetrical architecture with two subdomains sharing a nucleotidyltransferase topology, suggesting that vPAPs originate from an ancestral duplication. A Poxvirus processivity factor homologue encoded by Megavirus chilensis displays a conserved 5'-GpppA 2'O methyltransferase activity but is also able to internally methylate the mRNAs' polyA tails. These findings elucidate how the arm wrestling between hosts and their viruses to access the translation machinery is taking place in Mimiviridae.

Transcriptome wide annotation of eukaryotic RNase III reactivity and degradation signals

Detection and validation of the RNA degradation signals controlling transcriptome stability are essential steps for understanding how cells regulate gene expression. Here we present complete genomic and biochemical annotations of the signals required for RNA degradation by the dsRNA specific ribonuclease III (Rnt1p) and examine its impact on transcriptome expression. Rnt1p cleavage signals are randomly distributed in the yeast genome, and encompass a wide variety of sequences, indicating that transcriptome stability is not determined by the recurrence of a fixed cleavage motif. Instead, RNA reactivity is defined by the sequence and structural context in which the cleavage sites are located. Reactive signals are often associated with transiently expressed genes, and their impact on RNA expression is linked to growth conditions. Together, the data suggest that Rnt1p reactivity is triggered by malleable RNA degradation signals that permit dynamic response to changes in growth conditions.

RNA degradation is essential for gene regulation. The amount and timing of protein synthesis is determined, at least in part, by messenger RNA stability. Although RNA stability is determined by specific structural and sequence motif, the distribution of the degradation signals in eukaryotic genomes remains unclear. In this study, we describe the genomic distribution of the RNA degradation signals required for selective nuclear degradation in yeast. The results indicate that most RNAs in the yeast transcriptome are predisposed for degradation, but only few are catalytically active. The catalytic reactivity of messenger RNAs were mostly determined by the overall structural context of the degradation signals. Strikingly, most active RNA degradation signals are found in genes associated with respiration and fermentation. Overall, the findings reported here demonstrate how certain RNA are selected for cleavage and illustrated the importance of this selective RNA degradation for fine tuning gene expression in response to changes in growth condition.

Stress-induced nuclear RNA degradation pathways regulate yeast bromodomain factor 2 to promote cell survival

Bromodomain proteins are key regulators of gene expression. How the levels of these factors are regulated in specific environmental conditions is unknown. Previous work has established that expression of yeast Bromodomain factor 2 (BDF2) is limited by spliceosome-mediated decay (SMD). Here we show that BDF2 is subject to an additional layer of post-transcriptional control through RNase III-mediated decay (RMD). We found that the yeast RNase III Rnt1p cleaves a stem-loop structure within the BDF2 mRNA to down-regulate its expression. However, these two nuclear RNA degradation pathways play distinct roles in the regulation of BDF2 expression, as we show that the RMD and SMD pathways of the BDF2 mRNA are differentially activated or repressed in specific environmental conditions. RMD is hyper-activated by salt stress and repressed by hydroxyurea-induced DNA damage while SMD is inactivated by salt stress and predominates during DNA damage. Mutations of cis-acting signals that control SMD and RMD rescue numerous growth defects of cells lacking Bdf1p, and show that SMD plays an important role in the DNA damage response. These results demonstrate that specific environmental conditions modulate nuclear RNA degradation pathways to control BDF2 expression and Bdf2p-mediated gene regulation. Moreover, these results show that precise dosage of Bromodomain factors is essential for cell survival in specific environmental conditions, emphasizing their importance for controlling chromatin structure and gene expression in response to environmental stress.

Cells adapt to changes in the environment through modulating gene expression at both the RNA and protein levels. RNA degradation plays a central role in this adaption response, by controlling the stability of specific mRNAs to optimize protein production in different conditions. In this study, we show that the gene encoding Bromodomain Factor 2 (BDF2) is tightly regulated according to environmental conditions by two distinct RNA degradation mechanisms. We show that these RNA degradation pathways are critical for cell growth in specific conditions. Our study suggests that environmental modulation of nuclear RNA degradation pathways is a previously unappreciated aspect of gene expression control.

'Black sheep' that don't leave the double-stranded RNA-binding domain fold

The canonical double-stranded RNA (dsRNA)-binding domain (dsRBD) is composed of an α1-β1-β2-β3-α2 secondary structure that folds in three dimensions to recognize dsRNA. Recently, structural and functional studies of divergent dsRBDs revealed adaptations that include intra- and/or intermolecular protein interactions, sometimes in the absence of detectable dsRNA-binding ability. We describe here how discrete dsRBD components can accommodate pronounced amino-acid sequence changes while maintaining the core fold. We exemplify the growing importance of divergent dsRBDs in mRNA decay by discussing Dicer, Staufen (STAU)1 and 2, trans-activation responsive RNA-binding protein (TARBP)2, protein activator of protein kinase RNA-activated (PKR) (PACT), DiGeorge syndrome critical region (DGCR)8, DEAH box helicase proteins (DHX) 9 and 30, and dsRBD-like fold-containing proteins that have ribosome-related functions. We also elaborate on the computational limitations to discovering yet-to-be-identified divergent dsRBDs.