J. Barciszewski

Higher plant 5S rRNAs share common secondary and tertiary structure. A new three domains model.

A new model of secondary and tertiary structure of higher plant 5S RNA is proposed. It consists of three helical domains: domain alpha includes stem I; domain beta contains stems II and III and loops B and C; domain gamma consists of stems IV and V and loops D and E. Except for, presumably, a canonical RNA-A like domain alpha, the two remaining domains apparently adopt a perturbed RNA-A structure due to irregularities within internal loops B and E and three bulges occurring in the model. Bending of RNA could bring loops B and E and/or C and D closer making tertiary interactions likely. The model differs from that suggested for eukaryotic 5S rRNA, by organization of domain gamma. Our model is based on the results of partial digestion obtained with single- and double-strand RNA specific nucleases. The proposed secondary structure is strongly supported by the observation that crude plant 5S rRNA contains abundant RNA, identified as domain gamma of 5S rRNA. Presumably it is excised from the 5S rRNA molecule by a specific nuclease present in lupin seeds. Experimental results were confirmed by computer-aided secondary structure prediction analysis of all higher plant 5S rRNAs. Differences observed between earlier proposed models and our proposition are discussed.

Effect of elastase on elongation factor 1 from wheat germ

Abstract Elongation factor 1, species A, B and C, were isolated from wheat germ and purified to homogeneity by the following steps: supernatant 100 000 xg, precipitation with ammonium sulphate and column chromatography: Sephadex G-150, DEAE-Sephadex A-50 and hydroxylapatite. On the second column the activity was divided into three peaks: EF1 A, B and C. The pure proteins EF1A, B and C (molecular weight 61 000, 48 000 and 12 500 D, respectively) were treated with elastase. Two products of EF1A digestion, polypeptides b and c, were isolated. The molecular weights of polypeptides b and c were similar to molecular weight of species B and C of EF1. Both digestion products were active in binary complex formation with GDP and in binding of Phe-tRNA to ribosomes. EF1B was converted to polypeptide c or similar and EF1C was rather resistant to elastase treatment.

Structure of γ-conglutin: insight into the quaternary structure of 7S basic globulins from legumes

γ-Conglutin from lupin seeds is an unusual 7S basic globulin protein. It is capable of reducing glycaemia in mammals, but the structural basis of this activity is not known. γ-Conglutin shares a high level of structural homology with glycoside hydrolase inhibitor proteins, although it lacks any kind of inhibitory activity against plant cell-wall degradation enzymes. In addition, γ-conglutin displays a less pronounced structural similarity to pepsin-like aspartic proteases, but it is proteolytically dysfunctional. Only one structural study of a legume 7S basic globulin, that isolated from soybean, has been reported to date. The quaternary assembly of soybean 7S basic globulin (Bg7S) is arranged as a cruciform-shaped tetramer comprised of two superposed dimers. Here, the crystal structure of γ-conglutin isolated from Lupinus angustifolius seeds (LangC) is presented. The polypeptide chain of LangC is post-translationally cleaved into α and β subunits but retains its covalent integrity owing to a disulfide bridge. The protomers of LangC undergo an intricate quaternary assembly, resulting in a ring-like hexamer with noncrystallographic D3 symmetry. The twofold-related dimers are similar to those in Bg7S but their assembly is different as a consequence of mutations in a β-strand that is involved in intermolecular β-sheet formation in γ-conglutin. Structural elucidation of γ-conglutin will help to explain its physiological role, especially in the evolutionary context, and will guide further research into the hypoglycaemic activity of this protein in humans, with potential consequences for novel antidiabetic therapies.

Application of a nuclease from rye nucleus for structural studies of plant ribonucleic acids

A new nuclease (Rn) isolated from rye nucleus was applied for the structural studies of methionine initiator transfer ribonucleic acid and ribosomal 5S rRNA from yellow lupin seeds. The enzyme shows high specificity for some regions of both RNAs. The dihydrouridine and ribothymidine loops which are supposed to be involved in the tertiary interactions of the methionine initiator tRNA were hydrolysed. The anticodon loop is not digested at all. 5S rRNA was digested in single stranded regions (loops). The cleavage pattern of the tRNA and 5S rRNA obtained with Rn enzyme, suggests not only the high specificity toward single stranded regions, but also some dependence on their tertiary structure.

T-to-R switch of muscle fructose-1,6-bisphosphatase involves fundamental changes of secondary and quaternary structure.

When crystallized in the absence of the allosteric inhibitor AMP, human muscle fructose-1,6-bisphosphatase has a totally unexpected quaternary structure of its active R form, with the two dimers of the homotetrameric molecule in a perpendicular orientation, in stark contrast to the coplanar arrangement of the closely related liver isozyme. The T-to-R switch of the muscle enzyme also involves a highly unusual α→β refolding of the N-terminus.

Specific binding of gibberellic acid by Cytokinin‐Specific Binding Proteins: a new aspect of plant hormone‐binding proteins with the PR‐10 fold

Pathogenesis-related proteins of class 10 (PR-10) are a family of plant proteins with the same fold characterized by a large hydrophobic cavity that allows them to bind various ligands, such as phytohormones. A subfamily with only ~20% sequence identity but with a conserved canonical PR-10 fold have previously been recognized as Cytokinin-Specific Binding Proteins (CSBPs), although structurally the binding mode of trans-zeatin (a cytokinin phytohormone) was found to be quite diversified. Here, it is shown that two CSBP orthologues from Medicago truncatula and Vigna radiata bind gibberellic acid (GA3), which is an entirely different phytohormone, in a conserved and highly specific manner. In both cases a single GA3 molecule is found in the internal cavity of the protein. The structural data derived from high-resolution crystal structures are corroborated by isothermal titration calorimetry (ITC), which reveals a much stronger interaction with GA3 than with trans-zeatin and pH dependence of the binding profile. As a conclusion, it is postulated that the CSBP subfamily of plant PR-10 proteins should be more properly linked with general phytohormone-binding properties and termed phytohormone-binding proteins (PhBP).

The initiator transfer ribonucleic acid from yellow lupin seeds, correction of nucleotide sequence and crystallization

Abstract Two methionine specific tRNAs from yellow lupin seeds have been purified to homogeneity. Initiator tRNA (tRNA i Met ) but not tRNA m Met was charged with Escherichia coli methionyl-tRNA synthetase. The nucleotide composition, T i and pancreatic RNase digestion fingerprints and nucleotide sequence of lupin tRNA i Met showed its identity with wheat germ and bean initiator tRNAs. The differences in the primary structure of the lupin tRNA i Met observed by other authors have not been confirmed. We have defined the conditions under which single crystals of lupin tRNA i Met can be grown reproducibly.

Unfolding of the tertiary structure of specific tRNA and ribosomal 5S RNA from plants as studied with hydroxyl radicals

Ribosomal 5S RNA is present in all eubacterial and eukaryotic ribosomes. Despite a large amount of experimental data on the primary and secondary structures of these types of molecules, details of their tertiary structure and their precise function in protein biosynthesis are still not known. Recently we have proposed a new model for the tertiary structure of plant 5S rRNA. In this study we applied the Fe(II)-mediated cleavage reaction to test the model. The data presented here provide experimental evidence that in the 5S rRNA molecule only a few nucleotides are buried in the tertiary structure. Similar experiments performed with methionine initiator tRNA gave results which imply the difference in its structure when compared with the X-ray structure of yeast tRNAPhe.

Method for isolation of aminoacyl-tRNA synthetases from plants: purification and some properties of methionyl, phenylalanyl and arginyl tRNA synthetases from yellow lupin seeds

Abstract A method for the simultaneous purification of methionyl-, phenylalanyl- and arginyl-tRNA synthetases from yellow lupin seeds ( Lupinus luteus ) is described. The method uses ammonium sulphate fractionation, and DEAE-cellulose and DEAE-Sephadex A-50 column chromatography. Molecular weight and kinetic parameters of the pure enzymes are reported.

Cytochrome c(6B) of Synechococcus sp. WH 8102--crystal structure and basic properties of novel c(6)-like family representative.

Cytochromes c are soluble electron carriers of relatively low molecular weight, containing single heme moiety. In cyanobacteria cytochrome c6 participates in electron transfer from cytochrome b6f complex to photosystem I. Recent phylogenetic analysis revealed the existence of a few families of proteins homologous to the previously mentioned. Cytochrome c6A from Arabidopsis thaliana was identified as a protein responsible for disulfide bond formation in response to intracellular redox state changes and c550 is well known element of photosystem II. However, function of cytochromes marked as c6B, c6C and cM as well as the physiological process in which they take a part still remain unidentified. Here we present the first structural and biophysical analysis of cytochrome from the c6B family from mesophilic cyanobacteria Synechococcus sp. WH 8102. Purified protein was crystallized and its structure was refined at 1.4 Å resolution. Overall architecture of this polypeptide resembles typical I-class cytochromes c. The main features, that distinguish described protein from cytochrome c6, are slightly red-shifted α band of UV-Vis spectrum as well as relatively low midpoint potential (113.2±2.2 mV). Although, physiological function of cytochrome c6B has yet to be determined its properties probably exclude the participation of this protein in electron trafficking between b6f complex and photosystem I.