Rapid thin layer chromatographic separation of para-phenylazophenyl thiohydantoins of amino acids

3 (p-phenylazophenyl) 2-thiohydantoins of amino acids were identified on silica gel plates in 30 mins using ascending thin layer chromatographic technique. Recovery percentages of these amino acid derivatives were calculated and observed that the method of preparation needed modification.     

Of proteins and RNA: The RNase P/MRP family

Nuclear ribonuclease (RNase) P is a ubiquitous essential ribonucleoprotein complex, one of only two known RNA-based enzymes found in all three domains of life. The RNA component is the catalytic moiety of RNases P across all phylogenetic domains; it contains a well-conserved core, whereas peripheral structural elements are diverse. RNA components of eukaryotic RNases P tend to be less complex than their bacterial counterparts, a simplification that is accompanied by a dramatic reduction of their catalytic ability in the absence of protein. The size and complexity of the protein moieties increase dramatically from bacterial to archaeal to eukaryotic enzymes, apparently reflecting the delegation of some structural functions from RNA to proteins and, perhaps, in response to the increased complexity of the cellular environment in the more evolutionarily advanced organisms; the reasons for the increased dependence on proteins are not clear. We review current information on RNase P and the closely related universal eukaryotic enzyme RNase MRP, focusing on their functions and structural organization.     

Identification of S-RNase and peroxidase in petunia nectar

Previous SDS PAGE gel analysis of the floral nectars from petunia and tobacco plants revealed significant differences in the protein patterns. Petunia floral nectar was shown to contain a number of RNase activities by in gel RNase activity assay. To identify these proteins in more detail, the bands with RNase activity were excised from gel and subjected to trypsin digestion followed by LC-MS/MS analysis. This analysis revealed that S-RNases accumulate in nectar from Petunia hybrida, where they should carry out a biological function different from self-pollen rejection. In addition, other proteins were identified by the LC-MS/MS analysis. These proteins include a peroxidase, an endochitinase, and a putative fructokinase. Each of these proteins contained a secretory signal sequence that marked them as potential nectar proteins. We developed RT-PCR assays for each of these five proteins and demonstrated that each of these proteins was expressed in the petunia floral nectary. A discussion of the role of these proteins in antimicrobial activity in nectar is presented.     

Ribonuclease II preserves chloroplast RNA homeostasis by increasing mRNA decay rates,and cooperates with polynucleotide phosphorylase in 3′ end maturation

Ribonuclease R (RNR1) and polynucleotide phosphorylase (cpPNPase) are the two known 3′→5′ exoribonucleases in Arabidopsis chloroplasts, and are involved in several aspects of rRNA and mRNA metabolism. In this work, we show that mutants lacking both RNR1 and cpPNPase exhibit embryo lethality, akin to the non‐viability of the analogous double mutant in Escherichia coli. We were successful, however, in combining an rnr1 null mutation with weak pnp mutant alleles, and show that the resulting chlorotic plants display a global reduction in RNA abundance. Such a counterintuitive outcome following the loss of RNA degradation activity suggests a major importance of RNA maturation as a determinant of RNA stability. Detailed analysis of the double mutant demonstrates that the enzymes catalyze a two‐step maturation of mRNA 3′ ends, with RNR1 polishing 3′ termini created by cpPNPase. The bulky quaternary structure of cpPNPase compared with RNR1 could explain this activity split between the two enzymes. In contrast to the double mutants, the rnr1 single mutant overaccumulates most mRNA species when compared with the wild type. The excess mRNAs in rnr1 are often present in non‐polysomal fractions, and half‐life measurements demonstrate a substantial increase in the stability of most mRNA species tested. Together, our data reveal the cooperative activity of two 3′→5′ exoribonucleases in chloroplast mRNA 3′ end maturation, and support the hypothesis that RNR1 plays a significant role in the destabilization of mRNAs unprotected by ribosomes.     

The evolutionarily conserved subunits Rrp4 and Csl4 confer different substrate specificities to the archaeal exosome

We studied the substrate specificity of the exosome of Sulfolobus solfataricus using the catalytically active Rrp41-Rrp42-hexamer and complexes containing the RNA-binding subunits Rrp4 or Csl4. The conservation of both Rrp4 and Csl4 in archaeal and eukaryotic exosomes suggests specific functions for each of them. We found that they confer different specificities to the exosome: RNA with an A-poor 3′-end is degraded with higher efficiency by the Csl4-exosome, while the Rrp4-exosome strongly prefers poly(A)-RNA. High C-content and polyuridylation negatively influence RNA processing by all complexes, and, in contrast to the hexamer, the Rrp4-exosome prefers longer substrates.     

The structures of RNase A complexed with 3'-CMP and d(CpA): active site conformation and conserved water molecules.

The interactions of RNase A with cytidine 3'-monophosphate (3'-CMP) and deoxycytidyl-3',5'-deoxyadenosine (d(CpA)) were analyzed by X-ray crystallography. The 3'-CMP complex and the native structure were determined from trigonal crystals, and the d(CpA) complex from monoclinic crystals. The differences between the overall structures are concentrated in loop regions and are relatively small. The protein-inhibitor contacts are interpreted in terms of the catalytic mechanism. The general base His 12 interacts with the 2' oxygen, as does the electrostatic catalyst Lys 41. The general acid His 119 has 2 conformations (A and B) in the native structure and is found in, respectively, the A and the B conformation in the d(CpA) and the 3'-CMP complex. From the present structures and from a comparison with RNase T1, we propose that His 119 is active in the A conformation. The structure of the d(CpA) complex permits a detailed analysis of the downstream binding site, which includes His 119 and Asn 71. The comparison of the present RNase A structures with an inhibitor complex of RNase T1 shows that there are important similarities in the active sites of these 2 enzymes, despite the absence of any sequence homology. The water molecules were analyzed in order to identify conserved water sites. Seventeen water sites were found to be conserved in RNase A structures from 5 different space groups. It is proposed that 7 of those water molecules play a role in the binding of the N-terminal helix to the rest of the protein and in the stabilization of the active site.     

Two neutral variants segregating at the gametophytic self‐incompatibility locus of European pear (Pyrus communis L.) (Rosaceae,Pyrinae)

Extensive survey of the S‐locus diversity of plant species with RNase‐based gametophytic self‐incompatibility has failed to identify neutral variation segregating within S‐allele specificities. Although this is the expected result according to population genetics theory, it conflicts with recent models of S‐allele evolution, which suggest that new specificities might arise by a continuous process of subtle changes that individually do not alter the specificity of the S‐genes, but whose cumulative effects result in new S‐allele functions. Genomic analysis of S‐RNase sequences associated with the S₁₀₄ (=S₄, =S_b) allele of European pear (Pyrus communis L.) cultivars yielded two distinct variants (named herein S_104‐1 and S_104‐2) that differed at five nucleotide positions within the open reading frame, two of which resulted in changes in the predicted protein sequence. Test‐cross experiments indicated that the S‐alleles associated with the S_104‐1 and S_104‐2RNases exhibit the same pollen and pistil functions, suggesting that they are two neutral variants segregating within the S₁₀₄ haplotype of European pear. These allelic forms might represent transitional states in the process of generating new specificities in the species, in accordance with models that predict S‐function transition through neutral intermediates. This possibility was further evaluated through the pattern of molecular evolution of functionally distinct European pear S‐RNases, which indicated that most recent S‐allele diversification in this species proceeded in the absence of adaptive selective pressure.     

Aspartic acid-121 functions at the active site of bovine pancreatic ribonuclease

6-Phosphofructo-2-kinase (PFK2) is activated by a cAMP-dependent protein kinase, and inactivated by phosphatase, indicating the interconversion of PFK2. Inorganic phosphate also activates PFK2, and the optimum pH for the PFK2 activity varies with the concentration of phosphate. Phosphate also enhances the inactivation of PFK2 by citrate, suggesting that phosphate acts as a regulator of PFK2.     

Leucine 145 of the ribotoxin alpha-sarcin plays a key role for determining the specificity of the ribosome-inactivating activity of the protein

Secreted fungal RNases, represented by RNase T1, constitute a family of structurally related proteins that includes ribotoxins such as alpha-sarcin. The active site residues of RNase T1 are conserved in all fungal RNases, except for Phe 100 that is not present in the ribotoxins, in which Leu 145 occupies the equivalent position. The mutant Leu145Phe of alpha-sarcin has been recombinantly produced and characterized by spectroscopic methods (circular dichroism, fluorescence spectroscopy, and NMR). These analyses have revealed that the mutant protein retained the overall conformation of the wild-type alpha-sarcin. According to the analyses performed, Leu 145 was shown to be essential to preserve the electrostatic environment of the active site that is required to maintain the anomalous low pKa value reported for the catalytic His 137 of alpha-sarcin. Enzymatic characterization of the mutant protein has revealed that Leu 145 is crucial for the specific activity of alpha-sarcin on ribosomes.     

Selective inhibition of the growth of incompatible pollen tubes by S-protein in the Japanese pear

The S-allele-associated proteins (S-proteins) in the styles of the Japanese pear (Pyrus serotina Rehd. var. culta Rehd.) were purified by cation exchange chromatography. Their inhibitory action on the growth of incompatible pollen tubes (pollen tubes bearing the same S- allele as in the style from which the S-proteins were prepared) was characterized in vitro. Germination and tube growth of self-pollen (pollen from the same cultivar from which the S-proteins were prepared) decreased dose-dependently when the S-protein was added to the medium. Tube length was reduced to 10% that of compatible pollen tubes (pollen tubes bearing the S-allele different from that in the style from which the S-proteins were prepared) at 1.5 μg μl¹. S-proteins from Shinsui (S ₄ S ₅ ) also inhibited growth of cross-incompatible Kosui (S ₄ S ₅ ) pollen tubes, but not of compatible Chojuro (S ₂ S ₃ ) pollen tubes. After inactivation of RNase of the S- protein, the inhibitory action of the S-protein disappeared. These results indicate that the S-protein acts directly to inhibit growth of incompatible pollen tubes in Japanese pear styles, and that the RNase activity of the protein is essential for the biological function. However, small amounts of proteins that co-migrated with the S-protein may also play some roles in the inhibition. This is the first report on the selective inhibitory action of S-proteins in Rosaceae. Received: 11 April 2000 / Revision accepted: 28 September 2000     

乙型肝炎病毒靶向核糖核酸酶及其突变体的原核表达和活性分析

目的：研究原核表达的乙型肝炎病毒（HBV）靶向核糖核酸酶（RNase）及其突变体（点突变失去RNase活性）的活性。方法：将构建的靶向核糖核酸酶及其突变体基因克隆入原核表达载体pET32a（＋）,转化大肠杆菌BL21（DE3）,以IPTG诱导融合蛋白（HBV核心蛋白与人嗜酸性粒细胞来源的神经毒素的融合蛋白）的表达;表达产物经包涵体纯化、SDS-PAGE和Western印迹鉴定,将纯化的蛋白用透析方法复性;以酵母tRNA为作用底物,应用复性的蛋白进行RNase活性分析。结果：纯化和复性了HBV靶向核糖核酸酶及其突变体;复性的HBV靶向核糖核酸酶可以降解酵母tRNA且具有剂量依赖性,而复性后的突变的靶向核糖核酸酶体不具有RNase活性。结论：原核表达的HBV靶向核糖核酸酶具有较强的RNase活性,为探索HBV靶向核糖核酸酶抑制乙肝病毒复制的机理奠定了基础。     

Structural and functional relationships of natural and artificial dimeric bovine ribonucleases: New scaffolds for potential antitumor drugs

Protein aggregation via 3D domain swapping is a complex mechanism which can lead to the acquisition of new biological, benign or also malignant functions, such as amyloid deposits. In this context, RNase A represents a fascinating model system, since by dislocating different polypeptide chain regions, it forms many diverse oligomers. No other protein displays such a large number of different quaternary structures. Here we report a comparative structural analysis between natural and artificial RNase A dimers and bovine seminal ribonuclease, a natively dimeric RNase with antitumor activity, with the aim to design RNase A derivatives with improved pharmacological potential.     

Purification and properties of barley leaf ribonuclease

The principal ribonuclease from young barley plants was purified 29 200-fold by a six-step procedure. The enzyme showed a high specific activity (15 5OO ΔA₂₆₀ units/min/mg protein) and a molecular weight of about 25 000 was indicated by gel filtration and equilibrium sedimentation. Kinetic analysis of the cleavage of dinucleoside monophosphates and of yeast RNA indicated a base preference of Gua > Ade ≥ Ura ? Cyt, and was sensitive to the base located on either side of the phosphodiester bond. The enzyme resembles the Type I class of plant ribonucleases (E.C. 2.7.7.x).     

The Diversity of Self-Incompatibility Systems in Flowering Plants

Abstract: Flowering plants are the most successful group of land plants and dominate the earth's vegetation with around 300 000 species. This success is, in part, the consequence of a set of unique reproductive innovations that evolved with the flower. Most notable of these innovations were the closed carpel and double fertilization. Closed carpels permitted the evolution of effective mechanisms for pollen selection and discrimination, while double fertilization leading to endosperm formation allowed for more efficient utilization of resources because reserves are only allocated to the seed after fertilization. This review will focus on the most important and best understood mechanism of pollen discrimination, self-incompatibility (SI), a genetically determined pollen recognition system that prevents self-fertilization and fertilization by other individuals with the same incompatibility phenotype. In recent years much progress has been made towards elucidating the molecular mechanisms of SI operating in three distinct SI systems found in the Brassicaceae, Solanaceae and Papaveraceae, respectively. More recent molecular data obtained from the Poaceae, Convolvulaceae and Asteraceae, however, suggest that other molecular mechanisms of SI exist. A survey of classical genetic studies of SI predicts yet further potential molecular mechanisms of SI. We discuss the evolutionary implications of this apparent diversity in molecular pathways leading to SI and stress the need for more molecular studies of different SI systems.     

Analysis of the tertiary structure of bacterial RNase P RNA

The ubiquitous occurrence of ribonuclease P (RNase P) as a ribonucleoprotein and the catalytic properties of bacterial RNase P RNAs indicate that RNA fulfills an ancient and important role in the function of this enzyme. This review focuses on efforts to determine the structure of the bacterial RNase P RNA ribozyme. Phylogenetic comparative analysis of a library of bacterial RNase P RNA sequences has resulted in a well-developed secondary structure model and allowed identification of some elements of tertiary structure. The native structure has been redesigned by circular permutation to facilitate intra- and inter-molecular crosslinking experiments in order to gain further structural information. The crosslinking constraints, together with the constraints provided by comparative analyses, have been incorporated into a first-order model of the structure of the ribozyme-substrate complex. The developing structural perspective allows the design of self-cleaving pre-tRNA-RNase P RNA conjugates which are useful tools for additional structure-probing experiments.Abbreviations cpRNA circularly permuted RNA     

Binding of 8-bromoguanylic acid to ribonuclease T1 as studied by absorption and circular dichroism spectroscopy

8-Bromoguanosine 2'- and 3'-phosphates have been shown to bind to RNase T1 with the same affinity as the corresponding guanosine phosphates, inducing difference absorption and circular dichroism spectra similar to those induced by the guanosine phosphates. Since the brominated ligands have reduced electron density on N-7 of the guanine ring and syn-fixed conformation due to a bulky, electron-withdrawing Br substituent on C-8, the difference spectra are not attributable to the protonation on N-7 and to the restriction of the ligand to syn-conformation as proposed previously.     

Multiple bursts of pancreatic ribonuclease gene duplication in insect-eating bats

Pancreatic ribonuclease gene (RNASE1) was previously shown to have undergone duplication and adaptive evolution related to digestive efficiency in several mammalian groups that have evolved foregut fermentation, including ruminants and some primates. RNASE1 gene duplications thought to be linked to diet have also been recorded in some carnivores. Of all mammals, bats have evolved the most diverse dietary specializations, mainly including frugivory and insectivory. Here we cloned, sequenced and analyzed RNASE1 gene sequences from a range of bat species to determine whether their dietary adaptation is mirrored by molecular adaptation. We found that seven insect-eating members of the families Vespertilionidae and Molossidae possessed two or more duplicates, and we also detected three pseudogenes. Reconstructed RNASE1 gene trees based on both Bayesian and maximum likelihood methods supported independent duplication events in these two families. Selection tests revealed that RNASE1 gene duplicates have undergone episodes of positive selection indicative of functional modification, and lineage-specific tests revealed strong adaptive evolution in the Tadarida β clade. However, unlike the RNASE1 duplicates that function in digestion in some mammals, the bat RNASE1 sequences were found to be characterized by relatively high isoelectric points, a feature previously suggested to promote defense against viruses via the breakdown of double-stranded RNA. Taken together, our findings point to an adaptive diversification of RNASE1 in these two bat families, although we find no clear evidence that this was driven by diet. Future experimental assays are needed to resolve the functions of these enzymes in bats.     

Crystal structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis and implications for its quaternary structure and tRNA binding

RNase PH is a member of the family of phosphorolytic 3' --> 5' exoribonucleases that also includes polynucleotide phosphorylase (PNPase). RNase PH is involved in the maturation of tRNA precursors and especially important for removal of nucleotide residues near the CCA acceptor end of the mature tRNAs. Wild-type and triple mutant R68Q-R73Q-R76Q RNase PH from Bacillus subtilis have been crystallized and the structures determined by X-ray diffraction to medium resolution. Wild-type and triple mutant RNase PH crystallize as a hexamer and dimer, respectively. The structures contain a rare left-handed beta alpha beta-motif in the N-terminal portion of the protein. This motif has also been identified in other enzymes involved in RNA metabolism. The RNase PH structure and active site can, despite low sequence similarity, be overlayed with the N-terminal core of the structure and active site of Streptomyces antibioticus PNPase. The surface of the RNase PH dimer fit the shape of a tRNA molecule.