Evolution of ribonuclease inhibitor by exon duplication

Ribonuclease inhibitor and angiogenin system regulates cell type-specific global translation

Translation of mRNAs is a fundamental process that occurs in all cell types of multicellular organisms. Conventionally, it has been considered a default step in gene expression, lacking specific regulation. However, recent studies have documented that certain mRNAs exhibit cell type-specific translation. Despite this, it remains unclear whether global translation is controlled in a cell type-specific manner. By using human cell lines and mouse models, we found that deletion of the ribosome-associated protein ribonuclease inhibitor 1 (RNH1) decreases global translation selectively in hematopoietic-origin cells but not in the non-hematopoietic-origin cells. RNH1-mediated cell type-specific translation is mechanistically linked to angiogenin-induced ribosomal biogenesis. Collectively, this study unravels the existence of cell type-specific global translation regulators and highlights the complex translation regulation in vertebrates.

A STRP-ed definition of Structured Tandem Repeats in Proteins

Tandem Repeat Proteins (TRPs) are a class of proteins with repetitive amino acid sequences that have been studied extensively for over two decades. Different features at the level of sequence, structure, function and evolution have been attributed to them by various authors. And yet many of its salient features appear only when looking at specific subclasses of protein tandem repeats. Here, we attempt to rationalize the existing knowledge on Tandem Repeat Proteins (TRPs) by pointing out several dichotomies. The emerging picture is more nuanced than generally assumed and allows us to draw some boundaries of what is not a "proper" TRP. We conclude with an operational definition of a specific subset, which we have denominated STRPs (Structural Tandem Repeat Proteins), which separates a subclass of tandem repeats with distinctive features from several other less well-defined types of repeats. We believe that this definition will help researchers in the field to better characterize the biological meaning of this large yet largely understudied group of proteins.

LRR-protein RNH1 dampens the inflammasome activation and is associated with COVID-19 severity

RNH1 prevents inflammation by inhibiting inflammasome activation through controlling caspase-1 protein levels. In COVID-19 patients, RNH1 expression levels were negatively associated with disease severity and inflammation, suggesting a role for RNH1 in SARS-CoV-2–mediated inflammation and pathology.

Inflammasomes are cytosolic innate immune sensors of pathogen infection and cellular damage that induce caspase-1–mediated inflammation upon activation. Although inflammation is protective, uncontrolled excessive inflammation can cause inflammatory diseases and can be detrimental, such as in coronavirus disease (COVID-19). However, the underlying mechanisms that control inflammasome activation are incompletely understood. Here we report that the leucine-rich repeat (LRR) protein ribonuclease inhibitor (RNH1), which shares homology with LRRs of NLRP (nucleotide-binding oligomerization domain, leucine-rich repeat, and pyrin domain containing) proteins, attenuates inflammasome activation. Deletion of RNH1 in macrophages increases interleukin (IL)-1β production and caspase-1 activation in response to inflammasome stimulation. Mechanistically, RNH1 decreases pro-IL-1β expression and induces proteasome-mediated caspase-1 degradation. Corroborating this, mouse models of monosodium urate (MSU)-induced peritonitis and lipopolysaccharide (LPS)-induced endotoxemia, which are dependent on caspase-1, respectively, show increased neutrophil infiltration and lethality in Rnh1^−/− mice compared with wild-type mice. Furthermore, RNH1 protein levels were negatively related with disease severity and inflammation in hospitalized COVID-19 patients. We propose that RNH1 is a new inflammasome regulator with relevance to COVID-19 severity.

A novel approach to investigate the evolution of structured tandem repeat protein families by exon duplication

Tandem Repeat Proteins (TRPs) are ubiquitous in cells and are enriched in eukaryotes. They contributed to the evolution of organism complexity, specializing for functions that require quick adaptability such as immunity-related functions. To investigate the hypothesis of repeat protein evolution through exon duplication and rearrangement, we designed a tool to analyze the relationships between exon/intron patterns and structural symmetries. The tool allows comparison of the structure fragments as defined by exon/intron boundaries from Ensembl against the structural element repetitions from RepeatsDB. The all-against-all pairwise structural alignment between fragments and comparison of the two definitions (structural units and exons) are visualized in a single matrix, the "repeat/exon plot". An analysis of different repeat protein families, including the solenoids Leucine-Rich, Ankyrin, Pumilio, HEAT repeats and the β propellers Kelch-like, WD40 and RCC1, shows different behaviors, illustrated here through examples. For each example, the analysis of the exon mapping in homologous proteins supports the conservation of their exon patterns. We propose that when a clear-cut relationship between exon and structural boundaries can be identified, it is possible to infer a specific "evolutionary pattern" which may improve TRPs detection and classification.

Ribonuclease inhibitor 1 regulates erythropoiesis by controlling GATA1 translation

Ribosomal proteins (RP) regulate specific gene expression by selectively translating subsets of mRNAs. Indeed, in Diamond-Blackfan anemia and 5q- syndrome, mutations in RP genes lead to a specific defect in erythroid gene translation and cause anemia. Little is known about the molecular mechanisms of selective mRNA translation and involvement of ribosomal-associated factors in this process. Ribonuclease inhibitor 1 (RNH1) is a ubiquitously expressed protein that binds to and inhibits pancreatic-type ribonucleases. Here, we report that RNH1 binds to ribosomes and regulates erythropoiesis by controlling translation of the erythroid transcription factor GATA1. Rnh1-deficient mice die between embryonic days E8.5 and E10 due to impaired production of mature erythroid cells from progenitor cells. In Rnh1-deficient embryos, mRNA levels of Gata1 are normal, but GATA1 protein levels are decreased. At the molecular level, we found that RNH1 binds to the 40S subunit of ribosomes and facilitates polysome formation on Gata1 mRNA to confer transcript-specific translation. Further, RNH1 knockdown in human CD34+ progenitor cells decreased erythroid differentiation without affecting myelopoiesis. Our results reveal an unsuspected role for RNH1 in the control of GATA1 mRNA translation and erythropoiesis.

Spontaneous self-assembly of engineered armadillo repeat protein fragments into a folded structure

Repeat proteins are built of modules, each of which constitutes a structural motif. We have investigated whether fragments of a designed consensus armadillo repeat protein (ArmRP) recognize each other. We examined a split ArmRP consisting of an N-capping repeat (denoted Y), three internal repeats (M), and a C-capping repeat (A). We demonstrate that the C-terminal MA fragment adopts a fold similar to the corresponding part of the entire protein. In contrast, the N-terminal YM2 fragment constitutes a molten globule. The two fragments form a 1:1 YM2:MA complex with a nanomolar dissociation constant essentially identical to the crystal structure of the continuous YM3A protein. Molecular dynamics simulations show that the complex is structurally stable over a 1 μs timescale and reveal the importance of hydrophobic contacts across the interface. We propose that the existence of a stable complex recapitulates possible intermediates in the early evolution of these repeat proteins.

Detecting repetitions and periodicities in proteins by tiling the structural space

The notion of energy landscapes provides conceptual tools for understanding the complexities of protein folding and function. Energy landscape theory indicates that it is much easier to find sequences that satisfy the “Principle of Minimal Frustration” when the folded structure is symmetric (Wolynes, P. G. Symmetry and the Energy Landscapes of Biomolecules. Proc. Natl. Acad. Sci. U.S.A.1996, 93, 14249–14255). Similarly, repeats and structural mosaics may be fundamentally related to landscapes with multiple embedded funnels. Here we present analytical tools to detect and compare structural repetitions in protein molecules. By an exhaustive analysis of the distribution of structural repeats using a robust metric, we define those portions of a protein molecule that best describe the overall structure as a tessellation of basic units. The patterns produced by such tessellations provide intuitive representations of the repeating regions and their association toward higher order arrangements. We find that some protein architectures can be described as nearly periodic, while in others clear separations between repetitions exist. Since the method is independent of amino acid sequence information, we can identify structural units that can be encoded by a variety of distinct amino acid sequences.

Leucine-Rich Repeat (LRR) Domains Containing Intervening Motifs in Plants

LRRs (leucine rich repeats) are present in over 14,000 proteins. Non-LRR, island regions (IRs) interrupting LRRs are widely distributed. The present article reviews 19 families of LRR proteins having non-LRR IRs (LRR@IR proteins) from various plant species. The LRR@IR proteins are LRR-containing receptor-like kinases (LRR-RLKs), LRR-containing receptor-like proteins (LRR-RLPs), TONSOKU/BRUSHY1, and MJK13.7; the LRR-RLKs are homologs of TMK1/Rhg4, BRI1, PSKR, PSYR1, Arabidopsis At1g74360, and RPK2, while the LRR-RLPs are those of Cf-9/Cf-4, Cf-2/Cf-5, Ve, HcrVf, RPP27, EIX1, clavata 2, fascinated ear2, RLP2, rice Os10g0479700, and putative soybean disease resistance protein. The LRRs are intersected by single, non-LRR IRs; only the RPK2 homologs have two IRs. In most of the LRR-RLKs and LRR-RLPs, the number of repeat units in the preceding LRR block (N₁) is greater than the number of the following block (N₂); N₁ » N₂ in which N₁ is variable in the homologs of individual families, while N₂ is highly conserved. The five families of the LRR-RLKs except for the RPK2 family show N₁ = 8 − 18 and N₂ = 3 − 5. The nine families of the LRR-RLPs show N₁ = 12 − 33 and N₂ = 4; while N₁ = 6 and N₂ = 4 for the rice Os10g0479700 family and the N₁ = 4 − 28 and N₂ = 4 for the soybean protein family. The rule of N₁ » N₂ might play a common, significant role in ligand interaction, dimerization, and/or signal transduction of the LRR-RLKs and the LRR-RLPs. The structure and evolution of the LRR domains with non-LRR IRs and their proteins are also discussed.

Polygalacturonase-inhibiting proteins--leucine-rich repeat proteins in plant defence

Plant polygalacturonase-inhibiting proteins (PGIPs) belong to the leucine-rich repeat (LRR) family and are known to prevent pathogen invasion by inhibiting the plant cell wall degrading enzyme, polygalacturonase. Our study reveals that these multigene-encoded defence proteins found in flowering plants only exhibit identical domain architecture with 10 tandemly-arranged LRRs. This implies that variations of PGIP inhibitory properties are not associated with the number of the repeats but with subtle changes in the sequence content of the repeats. The first and eighth repeat contain more mutations compared to the strict conservation of the plant-specific LRRs or any repeat at other positions. Each of these repeats forms a separate cluster in the phylogenetic tree, both within and across plant families, thus suggesting uniqueness with respect to their position. A study of the genes encoding PGIPs, shows the existence of two categories (i) single exon and hence no intron; and (ii) two exons with an intron in between. Analyses of the intron phase and correlation of the exon-intron structure with the compact structural modules in PGIPs support insertion of introns in the pre-existing single exon genes and thus the intron late model. Lack of conservation of phase across families and formation of individual clusters for each family in the phylogenetic tree drawn with the intron sequences illustrate the event of insertion that took place separately in each of these families.

Site-specific folate conjugation to a cytotoxic protein

Conjugation to folic acid is known to enhance the uptake of molecules by human cells that over-produce folate receptors. Variants of bovine pancreatic ribonuclease (RNase A) that have attenuated affinity for the endogenous ribonuclease inhibitor protein (RI) are toxic to mammalian cells. Here, the random acylation of amino groups in wild-type RNase A with folic acid is shown to decrease its catalytic activity dramatically, presumably because of the alteration to a key active-site residue, Lys41. To effect site-specific coupling, N(δ)-bromoacetyl-N(α)-pteroyl-l-ornithine, which is a folate analogue with an electrophilic bromoacetamido group, was synthesized and used to S-alkylate Cys88 of the G88C variant of RNase A. The pendant folate moiety does not decrease enzymatic activity, enables RI-evasion, and endows toxicity for cancer cells that over-produce the folate receptor. These data reveal a propitious means for targeting proteins and other molecules to cancer cells.

Antimicrobial peptide-like genes in Nasonia vitripennis: a genomic perspective

BACKGROUND

Antimicrobial peptides (AMPs) are an essential component of innate immunity which can rapidly respond to diverse microbial pathogens. Insects, as a rich source of AMPs, attract great attention of scientists in both understanding of the basic biology of the immune system and searching molecular templates for anti-infective drug design. Despite a large number of AMPs have been identified from different insect species, little information in terms of these peptides is available from parasitic insects.

RESULTS

By using integrated computational approaches to systemically mining the Hymenopteran parasitic wasp Nasonia vitripennis genome, we establish the first AMP repertoire whose members exhibit extensive sequence and structural diversity and can be distinguished into multiple molecular types, including insect and fungal defensin-like peptides (DLPs) with the cysteine-stabilized alpha-helical and beta-sheet (CSalphabeta) fold; Pro- or Gly-rich abaecins and hymenoptaecins; horseshoe crab tachystatin-type AMPs with the inhibitor cystine knot (ICK) fold; and a linear alpha-helical peptide. Inducible expression pattern of seven N. vitripennis AMP genes were verified, and two representative peptides were synthesized and functionally identified to be antibacterial. In comparison with Apis mellifera (Hymenoptera) and several non-Hymenopteran model insects, N. vitripennis has evolved a complex antimicrobial immune system with more genes and larger protein precursors. Three classical strategies that are likely responsible for the complexity increase have been recognized: 1) Gene duplication; 2) Exon duplication; and 3) Exon-shuffling.

CONCLUSION

The present study established the N. vitripennis peptidome associated with antimicrobial immunity by using a combined computational and experimental strategy. As the first AMP repertoire of a parasitic wasp, our results offer a basic platform for further studying the immunological and evolutionary significances of these newly discovered AMP-like genes in this class of insects.

Perspectives on fish gonadotropins and their receptors

Teleosts lack a hypophyseal portal system and hence neurohormones are carried by nerve fibers from the preoptic region to the pituitary. The various cell types in the teleost pituitary are organized in discrete domains. Fish possess two gonadotropins (GtH) similar to FSH and LH in other vertebrates; they are heterodimeric hormones that consist of a common alpha subunit non-covalently associated with a hormone-specific beta subunit. In recent years the availability of molecular cloning techniques allowed the isolation of the genes coding for the GtH subunits in 56 fish species representing at least 14 teleost orders. Advanced molecular engineering provides the technology to produce recombinant GtHs from isolated cDNAs. Various expression systems have been used for the production of recombinant proteins. Recombinant fish GtHs were produced for carp, seabream, channel and African catfish, goldfish, eel, tilapia, zebrafish, Manchurian trout and Orange-spotted grouper. The hypothalamus in fishes exerts its regulation on the release of the GtHs via several neurohormones such as GnRH, dopamine, GABA, PACAP, IGF-I, norepinephrine, NPY, kisspeptin, leptin and ghrelin. In addition, gonadal steroids and peptides exert their effects on the gonadotropins either directly or via the hypothalamus. All these are discussed in detail in this review. In mammals, the biological activities of FSH and LH are directed to different gonadal target cells through the cell-specific expression of the FSH receptor (FSHR) and LH receptor (LHR), respectively, and the interaction between each gonadotropin-receptor couple is highly selective. In contrast, the bioactivity of fish gonadotropins seems to be less specific as a result of promiscuous hormone-receptor interactions, while FSHR expression in Leydig cells explains the strong steroidogenic activity of FSH in certain fish species.

Analyses of non-leucine-rich repeat (non-LRR) regions intervening between LRRs in proteins

BACKGROUND

Many proteins have LRR (leucine-rich repeat) units interrupted by non-LRRs which we call IR (non-LRR island region).

METHODS

We identified proteins containing LRR@IRs (LRRs having IR) by using a new method and then analyzed their natures and distributions.

RESULTS

LRR@IR proteins were found in over two hundred proteins from prokaryotes and from eukaryotes. These are divided into twenty-one different protein families. The IRs occur one to four times in LRR regions and range in length from 5 to 11,265 residues. The IR lengths in Fungi adenylate cyclases (acys) range from 5 to 116 residues; there are 22 LRR repeats. The IRs in Leishmania proteophosphoglycans (ppgs) vary from 105 to 11,265 residues. These results indicate that the IRs evolved rapidly. A group of LRR@IR proteins-LRRC17, chondroadherin-like protein, ppgs, and four Pseudomonas proteins-have a super motif consisting of an LRR block and its adjacent LRR@IR region. This indicates that the entire super motif experienced duplication. The sequence analysis of IRs offers functional similarity in some LRR@IR protein families.

GENERAL SIGNIFICANCE

This study suggests that various IRs and super motifs provide a great variety of structures and functions for LRRs.

Interaction of onconase with the human ribonuclease inhibitor protein

One of the tightest known protein-protein interactions in biology is that between members of the ribonuclease A superfamily and the ribonuclease inhibitor protein (RI). Some members of this superfamily are able to kill cancer cells, and the ability to evade RI is a major determinant of whether a ribonuclease will be cytotoxic. The archetypal cytotoxic ribonuclease, onconase (ONC), is in late-stage clinical trials for the treatment of malignant mesothelioma. We present here the first measurement of the inhibition of the ribonucleolytic activity of ONC by RI. This inhibition occurs with K(i)=0.15muM in a solution of low salt concentration.

Intraspecies regulation of ribonucleolytic activity

The evolutionary rate of proteins involved in obligate protein-protein interactions is slower and the degree of coevolution higher than that for nonobligate protein-protein interactions. The coevolution of the proteins involved in certain nonobligate interactions is, however, essential to cell survival. To gain insight into the coevolution of one such nonobligate protein pair, the cytosolic ribonuclease inhibitor (RI) proteins and secretory pancreatic-type ribonucleases from cow (Bos taurus) and human (Homo sapiens) were produced in Escherichia coli and purified, and their physicochemical properties were analyzed. The two intraspecies complexes were found to be extremely tight (bovine Kd = 0.69 fM; human Kd = 0.34 fM). Human RI binds to its cognate ribonuclease (RNase 1) with 100-fold greater affinity than to the bovine homologue (RNase A). In contrast, bovine RI binds to RNase 1 and RNase A with nearly equal affinity. This broader specificity is consistent with there being more pancreatic-type ribonucleases in cows (20) than humans (13). Human RI (32 cysteine residues) also has 4-fold less resistance to oxidation by hydrogen peroxide than does bovine RI (29 cysteine residues). This decreased oxidative stability of human RI, which is caused largely by Cys74, implies a larger role for human RI as an antioxidant. The conformational and oxidative stabilities of both RIs increase upon complex formation with ribonucleases. Thus, RI has evolved to maintain its inhibition of invading ribonucleases, even when confronted with extreme environmental stress. That role appears to take precedence over its role in mediating oxidative damage.

A ribonuclease zymogen activated by the NS3 protease of the hepatitis C virus

Translating proteases as inactive precursors, or zymogens, protects cells from the potentially lethal action of unregulated proteolytic activity. Here, we impose this strategy on bovine pancreatic ribonuclease (RNase A) by creating a zymogen in which quiescent ribonucleolytic activity is activated by the NS3 protease of the hepatitis C virus. Connecting the N-terminus and C-terminus of RNase A with a 14-residue linker was found to diminish its ribonucleolytic activity by both occluding an RNA substrate and dislocating active-site residues, which are devices used by natural zymogens. After cleavage of the linker by the NS3 protease, the ribonucleolytic activity of the RNase A zymogen increased 105-fold. Both before and after activation, the RNase A zymogen displayed high conformational stability and evasion of the endogenous ribonuclease inhibitor protein of the mammalian cytosol. Thus, the creation of ribonuclease zymogens provides a means to control ribonucleolytic activity and has the potential to provide a new class of antiviral chemotherapeutic agents.

Inflammatory caspases and inflammasomes: master switches of inflammation

Fifteen years have passed since the cloning and characterization of the interleukin-1beta-converting enzyme (ICE/caspase-1), the first identified member of a family of proteases currently known as caspases. Caspase-1 is the prototypical member of a subclass of caspases involved in cytokine maturation termed inflammatory caspases that also include caspase-4 caspase -5, caspase -11 and caspase -12. Efforts to elucidate the molecular mechanisms involved in the activation of these proteases have uncovered an important role for the NLR family members, NALPs, NAIP and IPAF. These proteins promote the assembly of multiprotein complexes termed inflammasomes, which are required for activation of inflammatory caspases. This article will review some evolutionary aspects, biochemical evidences and genetic studies, underlining the role of inflammasomes and inflammatory caspases in innate immunity against pathogens, autoinflammatory syndromes and in the biology of reproduction.

Ribonuclease inhibitor as an intracellular sentry

Onconase (ONC) is a homolog of RNase A that is in clinical trials as a cancer chemotherapeutic agent. The toxicity of ONC and RNase A variants relies on their ability to evade the cytosolic ribonuclease inhibitor protein (RI) and degrade cellular RNA. We find that these ribonucleases are more toxic for more rapidly growing cells. The enhanced cytotoxicity does not arise from variation in the endogenous level of RI, which is virtually constant. Overproduction of RI diminishes the potency of toxic RNase A variants, but has no effect on the cytotoxicity of ONC. Thus, RI constrains the cytotoxicity of RNase A. These data provide new insights for the development of an optimal ribonuclease-based cancer chemotherapy.

Genetic screen to dissect protein-protein interactions: ribonuclease inhibitor-ribonuclease A as a model system

Protein-protein interactions are critical for the function of biological systems. Here, we describe a means to dissect a protein-protein interaction. Our method is based on the in vivo interaction between a target protein and the peptide epitopes derived from its partner. This interaction is detected by using hybrid proteins in which the target protein and peptide epitopes are fused to the DNA-binding domain of the lambda repressor protein. An interaction prevents the transcription of a reporter gene. The efficacy of this approach is demonstrated with the ribonuclease inhibitor protein and ribonuclease A, which form a complex with an equilibrium dissociation constant in the femtomolar range. Our method can enable the identification of residues important in a designated protein-protein interaction and the development of antagonists for that interaction.

Fluorescence assay for the binding of ribonuclease A to the ribonuclease inhibitor protein

Ribonuclease A (RNase A) and the ribonuclease inhibitor protein (RI) form one of the tightest known protein-protein complexes. RNase A variants and homologues, such as G88R RNase A, that retain ribonucleolytic activity in the presence of RI are toxic to cancer cells. Herein, a new and facile assay is described for measuring the equilibrium dissociation constant (K(d)) and dissociation rate constant (k(d)) for complexes of RI and RNase A. This assay is based on the decrease in fluorescence intensity that occurs when a fluorescein-labeled RNase A binds to RI. To allow time for equilibration, the assay is most readily applied to those complexes with K(d) values in the nanomolar range or higher. Using this assay, the value of K(d) for the complex of RI with fluorescein-labeled G88R RNase A was determined to be 0.55 +/- 0.03 nM. In addition, the value of K(d) was determined for the complex of RI with unlabeled G88R RNase A to be 0.57 +/- 0.05 nM by using a competition assay with fluorescein-labeled G88R RNase A. Finally, the value of k(d) for the complex of RI with fluorescein-labeled G88R RNase A was determined to be (7.5 +/- 0.4) x 10(-3) s(-1) by monitoring the increase in fluorescence intensity upon dissociation. This assay can be used to characterize complexes of RI with a wide variety of RNase A variants and homologues, including those with cytotoxic activity.