Ribonuclease A homologues of the zebrafish: polymorphism, crystal structures of two representatives and their evolutionary implications

Paternal methotrexate exposure affects sperm small RNA content and causes craniofacial defects in the offspring

Folate is an essential vitamin for vertebrate embryo development. Methotrexate (MTX) is a folate antagonist that is widely prescribed for autoimmune diseases, blood and solid organ malignancies, and dermatologic diseases. Although it is highly contraindicated for pregnant women, because it is associated with an increased risk of multiple birth defects, the effect of paternal MTX exposure on their offspring has been largely unexplored. Here, we found MTX treatment of adult medaka male fish (Oryzias latipes) causes cranial cartilage defects in their offspring. Small non-coding RNA (sncRNAs) sequencing in the sperm of MTX treated males identify differential expression of a subset of tRNAs, with higher abundance for specific 5' tRNA halves. Sperm RNA methylation analysis on MTX treated males shows that m5C is the most abundant and differential modification found in RNAs ranging in size from 50 to 90 nucleotides, predominantly tRNAs, and that it correlates with greater testicular Dnmt2 methyltransferase expression. Injection of sperm small RNA fractions from MTX-treated males into normal fertilized eggs generated cranial cartilage defects in the offspring. Overall, our data suggest that paternal MTX exposure alters sperm sncRNAs expression and modifications that may contribute to developmental defects in their offspring.

Emerging biological functions of ribonuclease 1 and angiogenin

Pancreatic-type ribonucleases (ptRNases) are a large family of vertebrate-specific secretory endoribonucleases. These enzymes catalyze the degradation of many RNA substrates and thereby mediate a variety of biological functions. Though the homology of ptRNases has informed biochemical characterization and evolutionary analyses, the understanding of their biological roles is incomplete. Here, we review the functions of two ptRNases: RNase 1 and angiogenin. RNase 1, which is an abundant ptRNase with high catalytic activity, has newly discovered roles in inflammation and blood coagulation. Angiogenin, which promotes neovascularization, is now known to play roles in the progression of cancer and amyotrophic lateral sclerosis, as well as in the cellular stress response. Ongoing work is illuminating the biology of these and other ptRNases.

The structural features of an ancient ribonuclease from Salmo salar reveal an intriguing case of auto-inhibition

The superfamily of vertebrate ribonucleases, a large group of evolutionarily related proteins, continues to provide interesting structural and functional information. In particular, the crystal structure of SS-RNase-2 from Salmo salar (SS2), here presented, has revealed a novel auto-inhibition mechanism that enriches the number of inhibition strategies observed in some members of the family. Within an essentially unmodified RNase folding, the SS2 active site cleft is in part obstructed by the collapse of an extra pentapeptide inserted in the C-terminal region. This unexpected intrusion alters the organization of the catalytic triad by pushing one catalytic histidine off the pocket. Possible mechanisms to remove the active site obstruction have also been studied through the production of two mutants that provide useful information on the functionality of this intriguing version of the ribonuclease superfamily.

An ancient evolutionary connection between Ribonuclease A and EndoU families

The ribonuclease A family of proteins is well studied from the biochemical and biophysical points of view, but its evolutionary origins are obscure, as no sequences homologous to this family have been reported outside of vertebrates. Recently, the spatial structure of the ribonuclease domain from a bacterial polymorphic toxin was shown to be closely similar to the structure of vertebrate ribonuclease A. The absence of sequence similarity between the two structures prompted a speculation of convergent evolution of bacterial and vertebrate ribonuclease A-like enzymes. We show that bacterial and homologous archaeal polymorphic toxin ribonucleases with a known or predicted ribonuclease A-like fold are distant homologs of the ribonucleases from the EndoU family, found in all domains of cellular life and in viruses. We also detected a homolog of vertebrate ribonucleases A in the transcriptome assembly of the sea urchin Mesocentrotus franciscanus These observations argue for the common ancestry of prokaryotic ribonuclease A-like and ubiquitous EndoU-like ribonucleases, and suggest a better-grounded scenario for the origin of animal ribonucleases A, which could have emerged in the deuterostome lineage, either by an extensive modification of a copy of an EndoU gene, or, more likely, by a horizontal acquisition of a prokaryotic immunity-mediating ribonuclease gene.

Probing Protein Interaction Networks by Combining MS-Based Proteomics and Structural Data Integration

Protein-protein interactions play a major role in the molecular machinery of life, and various techniques such as AP-MS are dedicated to their identification. However, those techniques return lists of proteins devoid of organizational structure, not detailing which proteins interact with which others. Proposing a hierarchical view of the interactions between the members of the flat list becomes highly tedious for large data sets when done by hand. To help hierarchize this data, we introduce a new bioinformatics protocol that integrates information of the multimeric protein 3D structures available in the Protein Data Bank using remote homology detection, as well as information related to Short Linear Motifs and interaction data from the BioGRID. We illustrate on two unrelated use-cases of different complexity how our approach can be useful to decipher the network of interactions hidden in the list of input proteins, and how it provides added value compared to state-of-the-art resources such as Interactome3D or STRING. Particularly, we show the added value of using homology detection to distinguish between orthologs and paralogs, and to distinguish between core obligate and more facultative interactions. We also demonstrate the potential of considering interactions occurring through Short Linear Motifs.

Evolutionary Trends in RNA Base Selectivity Within the RNase A Superfamily

There is a growing interest in the pharmaceutical industry to design novel tailored drugs for RNA targeting. The vertebrate-specific RNase A superfamily is nowadays one of the best characterized family of enzymes and comprises proteins involved in host defense with specific cytotoxic and immune-modulatory properties. We observe within the family a structural variability at the substrate-binding site associated to a diversification of biological properties. In this work, we have analyzed the enzyme specificity at the secondary base binding site. Towards this end, we have performed a kinetic characterization of the canonical RNase types together with a molecular dynamic simulation of selected representative family members. The RNases' catalytic activity and binding interactions have been compared using UpA, UpG and UpI dinucleotides. Our results highlight an evolutionary trend from lower to higher order vertebrates towards an enhanced discrimination power of selectivity for adenine respect to guanine at the secondary base binding site (B2). Interestingly, the shift from guanine to adenine preference is achieved in all the studied family members by equivalent residues through distinct interaction modes. We can identify specific polar and charged side chains that selectively interact with donor or acceptor purine groups. Overall, we observe selective bidentate polar and electrostatic interactions: Asn to N1/N6 and N6/N7 adenine groups in mammals versus Glu/Asp and Arg to N1/N2, N1/O6 and O6/N7 guanine groups in non-mammals. In addition, kinetic and molecular dynamics comparative results on UpG versus UpI emphasize the main contribution of Glu/Asp interactions to N1/N2 group for guanine selectivity in lower order vertebrates. A close inspection at the B2 binding pocket also highlights the principal contribution of the protein ß6 and L4 loop regions. Significant differences in the orientation and extension of the L4 loop could explain how the same residues can participate in alternative binding modes. The analysis suggests that within the RNase A superfamily an evolution pressure has taken place at the B2 secondary binding site to provide novel substrate-recognition patterns. We are confident that a better knowledge of the enzymes' nucleotide recognition pattern would contribute to identify their physiological substrate and eventually design applied therapies to modulate their biological functions.

The catalytic activity and secretion of zebrafish RNases are essential for their in vivo function in motor neurons and vasculature

Angiogenin (hANG), a member of the Ribonuclease A superfamily has angiogenic, neurotrophic and neuroprotective activities. Mutations in hANG have been found in patients with Amyotrophic lateral sclerosis (ALS). The zebrafish (Danio rerio) rnasel-1, 2 and 3 are orthologues of hANG and of these only Rnasel-1 and Rnasel-2 have been shown to be angiogenic. Herein we show that NCI-65828, a potent and specific small molecule inhibitor of hANG inhibits Rnasel-1 to a similar extent. Treatment of early zebrafish embryos with NCI-65828, or with terrein, a fungal metabolite which prevents the secretion of hANG, resulted in spinal neuron aberrations as well defects in trunk vasculature. Our detailed expression analysis and inhibitor studies suggest that Rnasel-1 plays important roles in neuronal migration and pathfinding as well as in angiogenesis in zebrafish. Our studies suggest the usefulness of the zebrafish as a model to dissect the molecular consequences of the ANG ALS variants.

Differential Expression of Six Rnase2 and Three Rnase3 Paralogs Identified in Blunt Snout Bream in Response to Aeromonas hydrophila Infection

Ribonucleases (Rnases)2 and Rnase3 belong to the ribonuclease A (RnaseA) superfamily. Apart from their role in molecular evolutionary and functional biological studies, these genes have also been studied in the context of defense against pathogen infection in mammals. However, expression patterns, structures and response to bacterial infection of the two genes in blunt snout bream (Megalobrama amblycephala) remain unknown. In this study, we identified multiple copies of Rnase2 (six) and Rnase3 (three) in the M. amblycephala genome. The nine genes all possess characteristics typical of the RnaseA superfamily. No expression was detected in the early developmental stages, while a weak expression was observed at 120 and 140 h post-fertilization (hpf) for Rnase2b, Rnase2c, Rnase2e and Rnase3a, suggesting that only three copies of Rnase2 and one of Rnase3 are expressed. Interestingly, only Rnase2e was up-regulated in the kidney of M. amblycephala after Aeromonas hydrophila infection, while Rnase3a was significantly up-regulated in liver, gut and blood after the infection. We conclude that the paralogs of Rnase3 are more susceptible to A. hydrophila infection than Rnase2. These results indicate that different Rnase2 and Rnase3 paralogs suggest a role in the innate immune response of M. amblycephala to bacterial infection.

Expression Patterns and Functional Novelty of Ribonuclease 1 in Herbivorous Megalobrama amblycephala

Ribonuclease 1 (RNase1) is an important digestive enzyme that has been used to study the molecular evolutionary and plant-feeding adaptation of mammals. However, the expression patterns and potential biological function of RNase1 in herbivorous fish is not known. Here, we identified RNase1 from five fish species and illuminated the functional diversification and expression of RNase1 in herbivorous Megalobrama amblycephala. The five identified fish RNase1 genes all have the signature motifs of the RNase A superfamily. No expression of Ma-RNase1 was detected in early developmental stages but a weak expression was detected at 120 and 144 hours post-fertilization (hpf). Ma-RNase1 was only expressed in the liver and heart of one-year-old fish but strongly expressed in the liver, spleen, gut, kidney and testis of two-year-old fish. Moreover, the immunostaining localized RNase1 production to multiple tissues of two-year-old fish. A biological functional analysis of the recombinant protein demonstrated that M. amblycephala RNase1 had a relatively strong ribonuclease activity at its optimal pH 6.1, which is consistent with the pH of its intestinal microenvironment. Collectively, these results clearly show that Ma-RNase1 protein has ribonuclease activity and the expression patterns of Ma-RNase1 are dramatically different in one year and two-year-old fish, suggesting the functional differentiation during fish growing.

Computational studies on receptor-ligand interactions between novel buffalo (Bubalus bubalis) nucleotide-binding oligomerization domain-containing protein 2 (NOD2) variants and muramyl dipeptide (MDP)

Nucleotide binding and oligomerization domain 2 (NOD2), a member of intracellular NOD-like receptors (NLRs) family, recognizes the bacterial peptidoglycan, muramyl dipeptide (MDP) and initiates host immune response. The precise ligand recognition mechanism of NOD2 has remained elusive, although studies have suggested leucine rich repeat (LRR) region of NOD2 as the possible binding site of MDP. In this study, we identified multiple transcripts of NOD2 gene in buffalo (buNOD2) and at least five LRR variants (buNOD2-LRRW (wild type), buNOD2-LRRV1-V4) were found to be expressed in buffalo peripheral blood mononuclear cells. The newly identified buNOD2 transcripts were shorter in lengths as a result of exon-skipping and frame-shift mutations. Among the variants, buNOD2-LRRW, V1, and V3 were expressed more frequently in the animals studied. A comparative receptor-ligand interaction study through modeling of variants, docking, and molecular dynamics simulation revealed that the binding affinity of buNOD2-LRRW towards MDP was greater than that of the shorter variants. The absence of a LRR segment in the buNOD2 variants had probably affected their affinity toward MDP. Notwithstanding a high homology among the variants, the amino acid residues that interact with MDP were located on different LRR motifs. The binding free energy calculation revealed that the amino acids Arg850(LRR4) and Glu932(LRR7) of buNOD2-LRRW, Lys810(LRR3) of buNOD2-LRRV1, and Lys830(LRR3) of buNOD2-LRRV3 largely contributed towards MDP recognition. The knowledge of MDP recognition and binding modes on buNOD2 variants could be useful to understand the regulation of NOD-mediated immune response as well as to develop next generation anti-inflammatory compounds.

Ribonuclease like 5 regulates zebrafish yolk extension by suppressing a p53-dependent DNA damage response pathway

Ribonuclease like 5 (Rnasel5) is a novel member of the zebrafish ribonuclease A family and its expression is increased during early embryogenesis. However, the in vivo biological function of Rnasel5 remains to be elucidated. Here, we report that knockdown of Rnasel5 by morhpolinos caused shrunken yolk extension as well as increased DNA damage at yolk syncytial layer and external tissue layers via the activation of p53 pathway. In addition, the morphological defects caused by Rnasel5 knockdown can be partially rescued by mRNA injection. Our findings provide the first functional characterization of Rnasel5 in zebrafish development and reveal its critical role in yolk extension by modulation of the p53 pathway.

Adhesion mechanisms in European whitefish Coregonus lavaretus eggs: is this a survival mechanism for high-energy spawning grounds?

This study examined the potential biochemical and mechanical structures that may contribute to egg adhesion in European whitefish Coregonus lavaretus. Experiments showed that eggs from a population of C. lavaretus from Loch Eck remained non-adhesive in a solution chemically similar to ovarian fluid but became adhesive seconds after contact with water. Examination of the ultrastructure of the chorion showed that the morphology changed significantly after contact with water, with nodule-like protuberances attached to connective filaments on the surface present in water-hardened but not non-water hardened eggs. Biochemical analysis showed the presence of Chain A, RNase ZF-3e proteins in the chorion of water-hardened but not non-water hardened eggs. Histochemical staining of the chorion of C. lavaretus eggs showed that the externa, but not the interna, stained positively for the presence of glycoproteins. From these results, it was concluded that C. lavaretus from Loch Eck possess both anatomical and biochemical adhesive mechanisms that have been undocumented in this species so far.

Functional and structural analyses of N-acylsulfonamide-linked dinucleoside inhibitors of RNase A

Molecular probes are useful for both studying and controlling the functions of enzymes and other proteins. The most useful probes have high affinity for their target, along with small size and resistance to degradation. Here, we report on new surrogates for nucleic acids that fulfill these criteria. Isosteres in which phosphoryl [R–O–P(O₂⁻)–O–R′] groups are replaced with N-acylsulfonamidyl [R–C(O)–N⁻–S(O₂)–R′] or sulfonimidyl [R–S(O₂)–N⁻–S(O₂)–R′] groups increase the number of nonbridging oxygens from two (phosphoryl) to three (N-acylsulfonamidyl) or four (sulfonimidyl). Six such isosteres were found to be more potent inhibitors of catalysis by bovine pancreatic RNase A than are parent compounds containing phosphoryl groups. The atomic structures of two RNase A·N-acylsulfonamide complexes were determined at high resolution by X-ray crystallography. The N-acylsulfonamidyl groups were observed to form more hydrogen bonds with active site residues than did the phosphoryl groups in analogous complexes. These data encourage the further development and use of N-acylsulfonamides and sulfonimides as antagonists of nucleic acid-binding proteins.

A new RNase sheds light on the RNase/angiogenin subfamily from zebrafish

Recently, extracellular RNases of the RNase A superfamily, with the characteristic CKxxNTF sequence signature, have been identified in fish. This has led to the recognition that these RNases are present in the whole vertebrate subphylum. In fact, they comprise the only enzyme family unique to vertebrates. Four RNases from zebrafish (Danio rerio) have been previously reported and have a very low RNase activity; some of these are endowed, like human angiogenin, with powerful angiogenic and bactericidal activities. In the present paper, we report the three-dimensional structure, the thermodynamic behaviour and the biological properties of a novel zebrafish RNase, ZF-RNase-5. The investigation of its structural and functional properties, extended to all other subfamily members, provides an inclusive description of the whole zebrafish RNase subfamily.

The bactericidal action on Escherichia coli of ZF-RNase-3 is triggered by the suicidal action of the bacterium OmpT protease

ZF-RNase-3 is one of the RNases from zebrafish (Danio rerio) with special (i.e. noncatalytic) properties. These include angiogenic and bactericidal activities. Given the interest of fish RNases as host-defense effectors, we studied the mechanism of the bactericidal action of ZF-RNase-3 on Escherichia coli as a model Gram-negative bacterium. The results obtained indicate that the bactericidal activity of ZF-RNase-3 is not lost when its catalytic RNase activity is obliterated. On the other hand, fully denatured ZF-RNase-3 conserves its bactericidal activity. When ZF-RNase-3 is added to E. coli cultures, it is cleaved at a specific Arg-Arg peptide bond, thus engendering two peptide fragments. The larger fragment (residues 31-124), produced by proteolysis and reduction of a disulfide, is recognized as the actual bactericidal agent. The protease responsible for the proteolytic attack has been identified with OmpT, an outer membrane E. coli omptin protease. However, the most remarkable result obtained in the present study is the finding that the microbicidal action of ZF-RNase-3 can be achieved only with the suicidal cooperation of the bacterium itself.

Influence of naturally-occurring 5'-pyrophosphate-linked substituents on the binding of adenylic inhibitors to ribonuclease a: an X-ray crystallographic study

Ribonuclease A is the archetype of a functionally diverse superfamily of vertebrate-specific ribonucleases. Inhibitors of its action have potential use in the elucidation of the in vivo roles of these enzymes and in the treatment of pathologies associated therewith. Derivatives of adenosine 5'-pyrophosphate are the most potent nucleotide-based inhibitors known. Here, we use X-ray crystallography to visualize the binding of four naturally-occurring derivatives that contain 5'-pyrophosphate-linked extensions. 5'-ATP binds with the adenine occupying the B(2) subsite in the manner of an RNA substrate but with the gamma-phosphate at the P(1) subsite. Diadenosine triphosphate (Ap(3)A) binds with the adenine in syn conformation, the beta-phosphate as the principal P(1) subsite ligand and without order beyond the gamma-phosphate. NADPH and NADP(+) bind with the adenine stacked against an alternative rotamer of His119, the 2'-phosphate at the P(1) subsite, and without order beyond the 5'-alpha-phosphate. We also present the structure of the complex formed with pyrophosphate ion. The structural data enable existing kinetic data on the binding of these compounds to a variety of ribonucleases to be rationalized and suggest that as the complexity of the 5'-linked extension increases, the need to avoid unfavorable contacts places limitations on the number of possible binding modes.

Zebrafish RNase T2 genes and the evolution of secretory ribonucleases in animals

Background

Members of the Ribonuclease (RNase) T2 family are common models for enzymological studies, and their evolution has been well characterized in plants. This family of acidic RNases is widespread, with members in almost all organisms including plants, animals, fungi, bacteria and even some viruses. While several biological functions have been proposed for these enzymes in plants, their role in animals is unknown. Interestingly, in vertebrates most of the biological roles of plant RNase T2 proteins are carried out by members of a different family, RNase A. Still, RNase T2 proteins are conserved in these animals

Results

As a first step to shed light on the role of animal RNase T2 enzymes, and to understand the evolution of these proteins while co-existing with the RNase A family, we characterized RNase Dre1 and RNase Dre2, the two RNase T2 genes present in the zebrafish (Danio rerio) genome. These genes are expressed in most tissues examined, including high expression in all stages of embryonic development, and their expression corresponds well with the presence of acidic RNase activities in every tissue analyzed. Embryo expression seems to be a conserved characteristic of members of this family, as other plant and animal RNase T2 genes show similar high expression during embryo development. While plant RNase T2 proteins and the vertebrate RNase A family show evidences of radiation and gene sorting, vertebrate RNase T2 proteins form a monophyletic group, but there is also another monophyletic group defining a fish-specific RNase T2 clade.

Conclusion

Based on gene expression and phylogenetic analyses we propose that RNase T2 enzymes carry out a housekeeping function. This conserved biological role probably kept RNase T2 enzymes in animal genomes in spite of the presence of RNases A. A hypothetical role during embryo development is also discussed.

Characterization of the angiogenic activity of zebrafish ribonucleases

Ribonucleases identified from zebrafish possess angiogenic and bactericidal activities. Zebrafish RNases have three intramolecular disulfide bonds, a characteristic structural feature of angiogenin, different from the typical four disulfide bonds of the other members of the RNase A superfamily. They also have a higher degree of sequence homology to angiogenin than to RNase A. It has been proposed that all RNases evolved from these angiogenin-like progenitors. In the present study, we characterize, in detail, the function of zebrafish RNases in various steps in the process of angiogenesis. We report that zebrafish RNase-1, -2 and -3 bind to the cell surface specifically and are able to compete with human angiogenin. Similar to human angiogenin, all three zebrafish RNases are able to induce phosphorylation of extracellular signal-regulated kinase 1/2 mitogen-activated protein kinase. They also undergo nuclear translocation, accumulate in the nucleolus and stimulate rRNA transcription. However, zebrafish RNase-3 is defective in cleaving rRNA precursor, even though it has been reported to have an open active site and has higher enzymatic activity toward more classic RNase substrates such as yeast tRNA and synthetic oligonucleotides. Taken together with the findings that zebrafish RNase-3 is less angiogenic than zebrafish RNase-1 and -2 as well as human angiogenin, these results suggest that zebrafish RNase-1 is the ortholog of human angiogenin and that the ribonucleolytic activity of zebrafish RNases toward the rRNA precursor substrate is functionally important for their angiogenic activity.