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PubMed2000

Structural and expression analysis of uricase mRNA from Lotus japonicus.

Uricase (nodulin-35) cDNA, LjUr, was isolated from nodules of a model legume, Lotus japonicus. LjUr expression was most abundant in nodules, although it was detected in nonsymbiotic tissues as well, particularly in roots. Expression in nodules was detected in uninfected cells, nodule parenchyma, and, more intensely, in vascular bundles. Phylogenetic analysis of uricase sequences from various legumes indicated that uricases of amide- and ureide-transporting legumes form two distinct clades. LjUr is in the cluster of amide-transport legumes even though L. japonicus bears determinate nodules.

Amino Acid Sequence↗
PubMed1995

Native bovine selenocysteine tRNA(Sec) secondary structure as probed by two plant single-strand-specific nucleases.

Two single-strand-specific nucleases, discovered in plants, have been used to investigate the secondary and tertiary structures of the native bovine liver selenocysteine tRNA(Sec). To check the possible influence of nucleotide modifications on these structures, we compared the results obtained with the fully modified tRNA to the unmodified transcript prepared by in vitro T7 transcription of the Xenopus laevis tRNA(Sec) gene. We found that the structures in solution of the native tRNA(Sec) and the transcript are very similar despite some differences in accessibility to the enzymatic probes. Indeed, the modified anticodon-loop of native bovine tRNA(Sec), containing 5-methylcarboxymethyluridine (mcm5U34) and N6-isopentenyladenosine (i6A37), is less accessible to Rn nuclease than that of the transcript: the intensity of bands representing cuts at A36 and A38 is much lower as compared to those of the transcript, whereas no cuts were found at the level of i6A37 in the anticodon loop of the native molecule. Surprisingly, the variable arm of the native molecule has been found to be more susceptible to single-strand-specific nuclease action, suggesting a looser structure of the variable arm in native bovine tRNA(Sec) than in the transcript.

Animals↗
PubMed2004

The primary structure of a novel goose-type lysozyme from rhea egg white.

G-type lysozyme is a hydrolytic enzyme sharing a similar tertiary structure with plant chitinase. To discover the relation of function and structure, we analyzed the primary structure of new G-type lysozyme. The complete 185 amino acid residues of lysozyme from rhea egg white were sequenced using the peptides hydrolyzed by trypsin, V8 protease, and cyanogen bromide. Rhea lysozyme had sequence similarity to ostrich, cassowary, goose, and black swan, with 93%, 90%, 83%, and 82%, respectively. The six substituted positions were newly found at positions 3 (Asn), 9 (Ser), 43 (Arg), 114 (Ile), 127 (Met), and 129 (Arg) when compared with ostrich, cassowary, goose, and black swan lysozymes. The amino acid substitutions of rhea lysozyme at subsite B were the same as ostrich and cassowary lysozymes (Ser122 and Met123). This study was also constructed in a phylogenetic tree of G-type lysozyme that can be classified into at least three groups of this enzyme, namely, group 1; rhea, ostrich, and cassowary, group 2; goose, black swan, and chicken, and group 3; Japanese flounder. The amino acid sequences in assembled three alpha-helices found in this enzyme group (Thammasirirak, S., Torikata, T., Takami, K., Murata, K., and Araki, T., Biosci. Biotechnol. Biochem., 66, 147-156 (2002)) were also highly conserved, so that they were considered to be important for the formation of the hydrophobic core structure of the catalytic site and for maintaining a similar three-dimensional structure in this enzyme group.

Amino Acid Sequence↗
PubMed1991

Comparative calorimetric studies on the dynamic conformation of plant 5S rRNA: II. Structural interpretation of the thermal unfolding patterns for lupin seeds and wheat germ.

Thermal unfolding of 5S rRNA from wheat germ (WG) and lupin seeds (LS) was studied in solution. Experimental curves of differential scanning calorimetry (DSC) were resolved into particular components according to the thermodynamic model of two-state transitions. The DSC temperature profiles for WG and LS differ significantly in spite of very high similarities in the sequence of both molecules. Those results are interpreted according to a model of the secondary and tertiary molecular structure of 5S rRNA. A comparison of the 'nearest neighbour' model of interaction with the experimental thermodynamic results enables a complete interpretation of the process of the melting of its structures. In light of our observations, the crucial differences between both DSC melting profiles are mainly an outcome of different thermodynamic properties of the first helical fragment 'A' made up of 9 complementary base pairs. It contains 6 differences in the nucleotide sequence of both types of molecules, which still retain 9-meric double helixes. The temperature stability of his helix in WG is much lower than of the LS one. Moreover, the results supply evidence for a strong specific tertiary interaction between the two hairpin loops 'c' and 'e' in both 5S rRNA molecules, modulated by small differences in the thermodynamic properties of both 5S rRNA.

Base Sequence↗
PubMed2006

Cross-reactive and species-specific immunoglobulin E epitopes of plant profilins: an experimental and structure-based analysis.

BACKGROUND: Profilins are cross-reactive plant allergens responsible for multiple pollen sensitization and pollen-associated food allergy. While it is assumed that profilins from different species are immunologically equivalent, some studies suggest partial or even lacking IgE cross-reactivity between certain profilins. OBJECTIVE: We aimed to obtain a semi-quantitative assessment of the contributions of conserved and species-specific epitopes to IgE binding of plant profilins. METHODS: We compared model structures of profilins from timothy, mugwort, celery and bell pepper with crystal structures of birch and latex profilins. We predicted potential conformational epitopes that consisted of contiguous patches of at least 20% surface-exposed residues. Celery and timothy profilins were purified from their natural sources, and profilins from birch, mugwort, bell pepper and latex were expressed in Escherichia coli. The structural integrity of all purified proteins was confirmed by circular dichroism spectroscopy. IgE ELISAs and ELISA inhibitions using sera from 22 profilin-sensitized allergic patients were carried out. RESULTS: Peptide backbone conformations of all six profilins were highly similar. Nine variable epitopes and two containing high proportions of conserved residues were predicted. IgE from all sera bound to all tested profilins and the amounts were highly correlated. However, IgE inhibition experiments revealed that up to 60% of total IgE binding was mediated by species-specific epitopes. The extent of cross-reactivity among profilins from timothy, birch, latex and celery was greater than cross-reactivity to mugwort and bell pepper profilins. This pattern was mirrored by sequence similarities among one of the predicted variable epitopes. Patients with IgE to cross-reactive epitopes displayed allergic reactions to a greater number of plant foods than patients having IgE directed to species-specific epitopes. CONCLUSION: The large extent of cross-reactivity among plant profilins justifies using a single profilin for diagnosis. However, the fine specificity of IgE directed to variable epitopes may influence the clinical manifestation of profilin sensitization.

Amino Acid Sequence↗
PubMed1999

Secondary xylem-specific expression of caffeoyl-coenzyme A 3-O-methyltransferase plays an important role in the methylation pathway associated with lignin biosynthesis in loblolly pine.

Two types of structurally distinct O-methyltransferases mediate the methylation of hydroxylated monomeric lignin precursors in angiosperms. Caffeate 3-O-methyltransferase (COMT; EC 2.1.1.68) methylates the free acids and caffeoyl CoA 3-O-methyltransferase (CCoAOMT; EC 2.1.1.104) methylates coenzyme A esters. Recently, we reported a novel hydroxycinnamic acid/hydroxycinnamoyl CoA ester O-methyltransferase (AEOMT) from loblolly pine differentiating xylem that was capable of methylating both acid and ester precursors with similar efficiency. In order to determine the possible existence and role of CCoAOMT in lignin biosynthesis in gymnosperms, a 1.3 kb CCoAOMT cDNA was isolated from loblolly pine that showed 79-82% amino acid sequence identity with many angiosperm CCoAOMTs. The recombinant CCoAOMT expressed in Escherichia coli exhibited a significant methylating activity with hydroxycinnamoyl CoA esters whereas activity with hydroxycinnamic acids was insignificant. Moreover, 3.2 times higher catalytic efficiency for methylating caffeoyl CoA over 5-hydroxyferuloyl CoA was observed which could serve as a driving force towards synthesis of guaiacyl lignin. The secondary xylem-specific expression of CCoAOMT was demonstrated using RNA blot analysis, western blot analysis, and O-methyltransferase enzyme assays. In addition, Southern blot analysis indicated that CCoAOMT may exist as a single-copy gene in loblolly pine genome. The transgenic tobacco plants carrying loblolly pine CCoAOMT promoter-GUS fusion localized the site of GUS activity at the secondary xylem tissues. These data suggest that CCoAOMT, in addition to AEOMT, plays an important role in the methylation pathway associated with lignin biosynthesis in loblolly pine.

Amino Acid Sequence↗
PubMed2000

Bordered pit structure and vessel wall surface properties. Implications for embolism repair.

The idea that embolized xylem vessels can be refilled while adjacent vessels remain under tension is difficult to accept if the cavitated vessels remain hydraulically connected to vessels under tension. A mechanism by which embolized conduits could be hydraulically isolated from adjacent conduits requires the existence of a non-zero contact angle and a flared opening into the bordered pit chamber such that a convex air-water interface forms at the entrance into the pit chamber. We measured the contact angle and pit chamber geometry for six species. The contact angle measured in the vessel lumen ranged between 42 degrees to 55 degrees, whereas the opening into the pit chamber ranged between 144 degrees and 157 degrees. If the surface properties within the pit chamber are similar to those in the lumen, a convex meniscus will form at the flared opening into the pit chamber. The maximum pressure difference between water in the lumen and gas in the pit chamber that could be stabilized by this interface was calculated to be within the range of 0.07 to 0.30 MPa.

Biological Transport↗
PubMed2005

Plant pigments (antioxidants) of medicinal plants Malva silvestris L. and Malva moschata L. (Malvaceae).

Qualitative-quantitative structure of plant pigments in wild plants Malva silvestrs L. and Malva moschata L. (Malvaceae), which were collected in 20 locations in Sarajevo area and surroundings, was tested during spring and summer in 2003. Acetone extracts of both categories were made and rising paper-chromatography done for the purpose of qualitative analysis. Quantitative analysis was done by spectrophotometry. Chlorophyll a, chlorophyll b and xanthophylls presence was confirmed by separation of pigments from acetone extract of these plant species. Spectrophotometric analysis of acetone extracts showed these results (given in mg/L): chlorophyll a 2,386, chlorophyll b 0,332 and carrotenoides 1,037. Data given in mg/g dry substance are: chlorophyll a 1,193x10(-2), chlorophyll b 1,66x10(-3), and carrotenoides 5,185x10(-3). Pigments structure (in mg/L) in species Malva moschata is 1,6 for chlorophyll; 1,419 for chlorophyll b; and 0,364 for carrotenoides. Data given in mg/g are: chlorophyll a 8x10(-3), chlorophyll b 7,09x10(-3), and carrotenoides 1,82x10(-3). Considering that species Malva moschata L. grows on ecologically clear soils as opposed to well-known medicinal species Malva sylvestris L., and considering the production of phytomass, phytochemical structure and pharmacological influence it can be considered very medical and be given advantage over this wider spread category.

Antioxidants↗
PubMed2004

Identification of naturally occurring spirostenols preventing beta-amyloid-induced neurotoxicity.

22R-Hydroxycholesterol is an intermediate in the steroid biosynthesis pathway shown to exhibit a neuroprotective property against beta-amyloid (1-42) (Abeta) toxicity in rat PCl2 and human NT2N neuronal cells by binding and inactivating Abeta. In search of potent 22R-hydroxycholesterol derivatives, we assessed the ability of a series of naturally occurring entities containing the 22R-hydroxycholesterol structure to protect PC12 cells against Abeta-induced neurotoxicity, determined by measuring changes in membrane potential, mitochondrial diaphorase activity, ATP levels and trypan blue uptake. 22R-Hydroxycholesterol derivatives sharing a common spirost-5-en-3-ol or a furost-5-en-3-ol structure were tested. Although some of these compounds were neuroprotective against 0.1 microM Abeta, only three protected against the 1-10 microM Abeta-induced toxicity and, in contrast to 22R-hydroxycholesterol, all were devoid of steroidogenic activity. These entities shared a common structural feature, a long chain ester in position 3 and common stereochemistry. The neuroprotective property of these compounds was coupled to their ability to displace radiolabeled 22R-hydroxycholesterol from Abeta, suggesting that the Abeta-22R-hydroxycholesterol physicochemical interaction contributes to their beneficial effect. In addition, a 22R-hydroxycholesterol derivative inhibited the formation of neurotoxic amyloid-derived diffusible ligands. Computational docking simulations of 22R-hydroxycholesterol and its derivatives on Abeta identified two binding sites. Chemical entities, as 22R-hydroxycholesterol, seem to bind preferentially only to one site. In contrast, the presence of the ester chain seems to confer the ability to bind to both sites on Abeta, leading to neuroprotection against high concentrations of Abeta. In conclusion, these results suggest that spirost-5-en-3-ol naturally occurring derivatives of 22R-hydroxycholesterol might offer a new approach for Alzheimer's disease therapy.

Amyloid beta-Peptides↗
PubMed2001

Structure-activity relationships of phenylcyclohexene and biphenyl antitubulin compounds against plant and mammalian cells.

Phenylcyclohexenes (PCHs) [e.g., trans-4-nitro-5-(2,3,4-trimethoxyphenyl)cyclohexene, 2d] were found to bind weakly to the colchicine site of bovine tubulin, but are the first mimics of colchicine found to have high activity towards plant cells. Structure-activity relationships for PCHs and biphenyl AC-ring analogues of colchicine (e.g., 2,3,4,4'-tetramethoxy-2'-methyl-1,1'-biphenyl, 3e) are discussed.

Animals↗
PubMed2006

Plant genotypic diversity predicts community structure and governs an ecosystem process.

Theory predicts, and recent empirical studies have shown, that the diversity of plant species determines the diversity of associated herbivores and mediates ecosystem processes, such as aboveground net primary productivity (ANPP). However, an often-overlooked component of plant diversity, namely population genotypic diversity, may also have wide-ranging effects on community structure and ecosystem processes. We showed experimentally that increasing population genotypic diversity in a dominant old-field plant species, Solidago altissima, determined arthropod diversity and community structure and increased ANPP. The effects of genotypic diversity on arthropod diversity and ANPP were comparable to the effects of plant species diversity measured in other studies.

Animals↗
PubMed1986

Evidence that the amino acid composition of the particle proteins of plant viruses is characteristic of the virus group. II. Discriminant analysis according to structural biological and classification properties of plant viruses.

The amino acid composition (AAC) of the coat proteins (CPs) of 126 plant viruses or strains were analyzed by stepwise discriminant analysis. The criteria chosen for discrimination were: the structure of virus particles (3 clusters); the mode of of transmission of the viruses (6 clusters); and the grouping of viruses according to the classification of the International Committee on Taxonomy of Viruses (23 groups). Statistically significant correlations were obtained with different groups of discriminant amino acids. The results confirm that the AAC of the CPs contains all the information needed for a quantitative classification of plant viruses. These results and possible explanations of these clustering patterns are discussed.

Amino Acids↗
PubMed2004

Structure and function of plant-type ferredoxins.

The plant-type ferredoxins (Fds) are the [2Fe-2S] proteins that function primarily in photosynthesis; they transfer electrons from photoreduced Photosystem I to ferredoxin NADP(+) reductase in which NADPH is produced for CO(2) assimilation. In addition, Fds partition electrons to various ferredoxin-dependent enzymes not only for assimilations of inorganic nitrogen and sulfur and N(2) fixation but also for regulation of CO(2) assimilation cycle. Although Fds are small iron-sulfur proteins with molecular weight of 11 KDa, they are expected to interact with surprisingly many enzymes. Several Fd isoforms were found in non-photosynthetic cells as well as Fds in photosynthetic cells, leading to the recognition that they have differentiated physiological roles. In a quarter of century, X-ray crystallography and NMR spectroscopy provided wealth of structural data, which shed light on the structure-function relationship of the plant-type Fds and gave structural basis for the biochemical and spectroscopic properties so far accumulated. Thus the structural studies of Fds have come to a new era in which different roles of Fds and interactions with various enzymes are clarified on the basis of the tertiary and quaternary structures, although they are premature at present. This article reviews briefly the structures of the plant-type Fds together with their functions, properties, and interactions with Fd related enzymes. Lastly the folding motif of Fd, that has grown to be a large family by including many functionally unrelated proteins, is noted.

Journal Article↗
PubMed1997

Characterization of the gene for pyruvate,orthophosphate dikinase from rice, a C3 plant, and a comparison of structure and expression between C3 and C4 genes for this protein.

To investigate the molecular changes that might have occurred in genes for pyruvate,orthophosphate dikinase (PPDK) during the evolution of C4 plants from C3 plants, we isolated a full-length cDNA and the corresponding gene for a C4-like PPDK from rice, a C3 gramineous plant and compared their structures and promoter activities to those of the corresponding gene from maize, a C4 gramineous plant. As in maize, there are at least two ppdk genes in rice and one of them was very similar to the maize C4-type ppdk. The deduced amino acid sequence of the rice PPDK was 88% homologous to the maize C4-type PPDK in the mature peptide region and 56% homologous in the transit peptide region. The C4-like ppdk in rice contained 21 exons, which were interrupted by twenty introns, and the positions of the introns were essentially the same as those in the gene from maize, with the except in that the gene from rice had two extra introns. Such extra introns were also found in the C4-type ppdk from a dicot, Flaveria, at the same positions. These results strongly suggest that the two introns were present in an ancestral gene before the divergence of monocot and dicot plants. The C4-like ppdk in rice contained two functionally independent promoters had generated a larger transcript with the transit peptide region and a smaller transcript without this region. The unusual dual-promoter system for transcription has been conserved in the C4-type ppdk gene from maize, indicating that the dual-promoter system is a common feature of ppdk genes in both C3 and C4 plants. The patterns of expression of the two transcripts in rice were different: the larger transcript was expressed exclusively in green leaves at a low level whereas the smaller transcript was expressed in some reproductive organs at a high level. Essentially the same patterns of expression were observed in maize, but the level of expression of the larger transcript in maize green leaves was much higher than that in green leaves of rice. The promoter activities of the rice and maize genes for PPDK were examined directly in a transient expression assay in maize mesophyll protoplasts after electroporation with promoter::beta-glucuronidase chimeric genes. The rice promoter for the smaller transcript was very active in the protoplasts but the rice promoter for the larger transcript had relatively low activity. By contrast, both promoters of the maize gene had high activity. Taken together, these results demonstrate that the rice C4-like ppdk is very similar to the maize C4-type ppdk, not only in terms of primary structure but also in terms of the regulation of expression, with the exception that the strength of the maize promoter for the larger transcript is higher. The results strongly suggest that the genetic alterations required to give rise to the C4-type ppdk gene were relatively limited.

Amino Acid Sequence↗
PubMed1991

Comparisons of Golgi structure and dynamics in plant and animal cells.

The Golgi apparatus of both higher plant and animal cells sorts and packages macromolecules which are in transit to and from the cell surface and to the lysosome (vacuole). It is also the site of oligosaccharide and polysaccharide synthesis and modification. The underlying similarity of function of plant and animal Golgi is reflected in similar morphological features, such as cisternal stacking. There are, however, several fundamental differences between the Golgi of plant and animal cells, reflecting, in large part, the fact that the extracellular matrices and lysosomal systems differ between these kingdoms. These include 1) the form and replication of the Golgi during cell division; 2) the disposition of the Golgi in the interphase cell; 3) the nature of "anchoring" the Golgi in the cytoplasm; 4) the genesis, extent, and nature of membranes at the trans side of the stack; 5) targeting signals to the lysosome (vacuole); and 6) physiological regulation of secretion events (constitutive vs. regulated secretion). The degree of participation of the Golgi in endocytosis and membrane recycling is becoming clear for animal cells, but has yet to be explored in detail for plant cells.

Animals↗
PubMed1978

Plant anticancer agents VII: Structural effects on cytotoxicity of bisindole alkaloids of voacamine type.

Structural effects on the cytotoxicity of bisindole alkaloids of the voacamine series were investigated with compounds isolated from various Tabernaemontana species and compounds synthesized specifically for this purpose. Activity is sensitive both to the position of attachment of the vobasane unit on the iboga moiety and to the presence of an N-methyl group on the vobasane unit.

Alkaloids↗
PubMed1994

An 1H NMR determination of the three-dimensional structures of mirror-image forms of a Leu-5 variant of the trypsin inhibitor from Ecballium elaterium (EETI-II).

The 3-dimensional structures of mirror-image forms of a Leu-5 variant of the trypsin inhibitor Ecballium elaterium (EETI-II) have been determined by 1H NMR spectroscopy and simulated annealing calculations incorporating NOE-derived distance constraints. Spectra were assigned using 2-dimensional NMR methods at 400 MHz, and internuclear distances were determined from NOESY experiments. Three-bond spin-spin couplings between C alpha H and amide protons, amide exchange rates, and the temperature dependence of amide chemical shifts were also measured. The structure consists largely of loops and turns, with a short region of beta-sheet. The Leu-5 substitution produces a substantial reduction in affinity for trypsin relative to native EETI-II, which contains an Ile at this position. The global structure of the Leu-5 analogue studied here is similar to that reported for native EETI-II (Heitz A, Chiche L, Le-Nguyen D, Castro B, 1989, Biochemistry 28:2392-2398) and to X-ray and NMR structures of the related proteinase inhibitor CMTI-I (Bode W et al., 1989, FEBS Lett 242:285-292; Holak TA et al., 1989a, J Mol Biol 210:649-654; Holak TA, Gondol D, Otlewski J, Wilusz T, 1989b, J Mol Biol 210:635-648; Holak TA, Habazettl J, Oschkinat H, Otlewski J, 1991, J Am Chem Soc 113:3196-3198). The region near the scissile bond is the most disordered part of the structure, based on geometric superimposition of 40 calculated structures. This disorder most likely reflects additional motion being present in this region relative to the rest of the protein. This motional disorder is increased in the Leu-5 analogue relative to the native form and may be responsible for its reduced trypsin binding. A second form of the protein synthesized with all (D) amino acids was also studied by NMR and found to have a spectrum identical with that of the (L) form. This is consistent with the (D) form being a mirror image of the (L) form and not distinguishable by NMR in an achiral solvent (i.e., H2O). The (D) form has no activity against trypsin, as would be expected for a mirror-image form.

Amino Acid Sequence↗