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Cloning and molecular characterization of plant aldehyde oxidase.

Primary structural information of a plant aldehyde oxidase (AO), which was purified from maize coleoptiles using indole-3-acetaldehyde as a substrate, was obtained by sequencing a series of cleavage peptides, permitting the cloning of the corresponding cDNA (zmAO-1). The complete nucleotide sequence was determined; the deduced amino acid sequence encodes a protein of 1358 amino acid residues of Mr 146,681, which is consistent with the size of the AO monomeric subunit. There is a significant similarity with AO from mammals and xanthine dehydrogenases from various sources. The maize AO polypeptide contains consensus sequences for iron-sulfur centers and a putative molybdopterin cofactor-binding domain. In addition, another cDNA (zmAO-2), highly homologous to zmAO-1 at both the nucleotide and amino acid sequence levels, was cloned. zmAO-2 would encode a protein of 1349 amino acid residues of Mr 145,173 and has molecular characteristics similar to those of zmAO-1. zmAO-1 was expressed at a high level in roots, which was closely correlated with immunoblotting results using antiserum raised against the purified maize AO protein, whereas zmAO-2 was expressed at a higher level in coleoptiles than in roots. We propose each zmAO may have a unique function during plant development.

Aldehyde Oxidase↗

Planting stress, water status and non-structural carbohydrate concentrations in Corsican pine seedlings.

Two-year-old Corsican pine (Pinus nigra ssp. laricio var. Corsicana) seedlings were either well watered or subjected to a moderate drought for one month before being lifted from the nursery bed on October 9 and transplanted. Well-watered, non-transplanted seedlings served as controls. Needle predawn water potential (Psi(wp)), non-structural carbohydrate concentrations and plant development (survival, bud break, shoot elongation) were assessed before and during the first growing season after transplanting. On April 16, just before bud break, Psi(wp) was lower for the well-watered + transplanted and drought-conditioned + transplanted seedlings (Psi(wp) = -1.45 and -1.83 MPa, respectively) than for the controls (Psi(wp) = -0.56). There was a close relationship between the Psi(wp) measured on April 16 and bud break, shoot elongation and plant survival during the following growing period. Above a Psi(wp) of -1.1 MPa, all plants developed normally. Between -1.1 MPa and -1.6 MPa, bud break, and thus shoot elongation, did not occur in all plants. Between -1.6 MPa and -2.1 MPa, the plants were characterized by the absence of shoot growth, but mortality was zero. Below -2.1 MPa, there was a large increase in plant mortality. On April 16, starch concentrations were markedly lower in the roots of transplanted seedlings than in the controls. There was a positive correlation between Psi(wp) and root starch concentration. The Psi(wp) (-2.3 MPa) at which complete starch depletion was observed in the roots corresponded to the Psi(wp) below which plants did not survive. These results suggest that mechanisms specifically linked to altered water status and metabolic processes associated with altered carbohydrate status are involved in transplanting stress; however, it was not possible to disentangle the two effects. Drought conditioning did not lead to a marked increase in soluble carbohydrate concentrations, as reported for other species, and did not increase plant tolerance to transplanting stress.

Journal Article↗

Crystal structure of papaya glutaminyl cyclase, an archetype for plant and bacterial glutaminyl cyclases.

Glutaminyl cyclases (QCs) (EC 2.3.2.5) catalyze the intramolecular cyclization of protein N-terminal glutamine residues into pyroglutamic acid with the concomitant liberation of ammonia. QCs may be classified in two groups containing, respectively, the mammalian enzymes, and the enzymes from plants, bacteria, and parasites. The crystal structure of the QC from the latex of Carica papaya (PQC) has been determined at 1.7A resolution. The structure was solved by the single wavelength anomalous diffraction technique using sulfur and zinc as anomalous scatterers. The enzyme folds into a five-bladed beta-propeller, with two additional alpha-helices and one beta hairpin. The propeller closure is achieved via an original molecular velcro, which links the last two blades into a large eight stranded beta-sheet. The zinc ion present in the PQC is bound via an octahedral coordination into an elongated cavity located along the pseudo 5-fold axis of the beta-propeller fold. This zinc ion presumably plays a structural role and may contribute to the exceptional stability of PQC, along with an extended hydrophobic packing, the absence of long loops, the three-joint molecular velcro and the overall folding itself. Multiple sequence alignments combined with structural analyses have allowed us to tentatively locate the active site, which is filled in the crystal structure either by a Tris molecule or an acetate ion. These analyses are further supported by the experimental evidence that Tris is a competitive inhibitor of PQC. The active site is located at the C-terminal entrance of the PQC central tunnel. W83, W110, W169, Q24, E69, N155, K225, F22 and F67 are highly conserved residues in the C-terminal entrance, and their putative role in catalysis is discussed. The PQC structure is representative of the plants, bacterial and parasite enzymes and contrasts with that of mammalian enzymes, that may possibly share a conserved scaffold of the bacterial aminopeptidase.

Amino Acid Sequence↗

The plant cytolytic protein enterolobin assumes a dimeric structure in solution.

Enterolobin is a plant cytolytic protein similar to the bacterial cytolysin aerolysin. Biochemical and biophysical techniques were used to verify if enterolobin, like aerolysin, adopts a dimeric structure in solution. SDS-PAGE showed bands corresponding to enterolobin monomer, dimer and oligomers, whilst gel filtration chromatography and electrospray mass spectrometry revealed preferred association of enterolobin as a dimer. Atomic force microscopy (AFM) of enterolobin showed images of a dimer assembly at a concentration as low as 10 microg/ml, similarly to aerolysin. The enterolobin in silico docked structure is coherent with AFM enterolobin dimer shapes.

Chromatography, Gel↗

Host species-dependent population structure of a pollen-borne plant virus, Cherry leaf roll virus.

Cherry leaf roll virus (CLRV) belongs to the Nepovirus genus within the family Comoviridae. It has a host range which includes a number of wild tree and shrub species. The serological and molecular diversity of CLRV was assessed using a collection of isolates and samples recovered from woody and herbaceous host plants from different geographical origins. Molecular diversity was assessed by sequencing a short (375-bp) region of the 3' noncoding region (NCR) of the genomic RNAs while serological diversity was assessed using a panel of seven monoclonal antibodies raised initially against a walnut isolate of CLRV. The genomic region analyzed was shown to exhibit a significant degree of molecular variability with an average pairwise divergence of 8.5% (nucleotide identity). Similarly, serological variability proved to be high, with no single monoclonal antibody being able to recognize all isolates analyzed. Serological and molecular phylogenetic reconstructions showed a strong correlation. Remarkably, the diversity of CLRV populations is to a large extent defined by the host plant from which the viral samples are originally obtained. There are relatively few reports of plant viruses for which the genetic diversity is structured by the host plant. In the case of CLRV, we hypothesize that this situation may reflect the exclusive mode of transmission in natural plant populations by pollen and by seeds. These modes of transmission are likely to impose barriers to host change by the virus, leading to rapid biological and genetic separation of CLRV variants coevolving with different plant host species.

3' Untranslated Regions↗

Structural genomics projects in Japan.

Two major structural genomics projects exist in Japan. The oldest, the RIKEN Structural Genomics Initiative, has two major goals: to determine bacterial, mammalian, and plant protein structures by X-ray crystallography and NMR spectroscopy and to perform functional analyses with the target proteins. The newest, the structural genomics project at the Biological Information Research Center, focuses on human membrane proteins.

Animals↗

Pinusolidic acid: a platelet-activating factor inhibitor from Biota orientalis.

The water extract of Biota orientalis showed a potent inhibitory effect on platelet activating factor (PAF) binding to rabbit platelets using [3H]PAF as a ligand in our previous screening studies for Korean medicinal antagonists by the activity-guided purification studies. Another active compound, compound 1 (IC50 = 2.3 x 10(-5) M, 7.48 +/- 2.11 micrograms/ml, n = 4) was isolated from the title plant. The chemical structure of compound 1 was elucidated as pinusolidic acid by chemical and spectrometric analyses.

Animals↗

How do plants regulate the function, community structure, and diversity of mycorrhizal fungi?

In many semi-natural and natural ecosystems, mycorrhizal fungi are the most abundant and functionally important group of soil micro-organisms. They are almost wholly dependent on their host plants to supply them with photosynthate in return for which they enable the plant to access greater quantities of nutrients. Thus, there is considerable potential for plant communities to regulate the structure and function of mycorrhizal communities. This paper reviews some of the key recent developments that have enabled the influence of plant species richness, composition, and age on mycorrhizal communities in boreal forests and temperate grassland to be determined. It discusses the emerging evidence that, in some situations, plant species richness is related to mycorrhizal species richness, in contrast to previous thinking. The paper also includes some preliminary data on the effect of host stand age on root-associated basidiomycete communities. It concludes by highlighting some of the new methodological advances that promise to unravel the linkages between mycorrhizal diversity and their function in situ.

Biodiversity↗

Assembly of protein tertiary structures from secondary structures using optimized potentials.

We present a simulated annealing-based method for the prediction of the tertiary structures of proteins given knowledge of the secondary structure associated with each amino acid in the sequence. The backbone is represented in a detailed fashion whereas the sidechains and pairwise interactions are modeled in a simplified way, following the LINUS model of Srinivasan and Rose. A perceptron-based technique is used to optimize the interaction potentials for a training set of three proteins. For these proteins, the procedure is able to reproduce the tertiary structures to below 3 A in root mean square deviation (rmsd) from the PDB targets. We present the results of tests on twelve other proteins. For half of these, the lowest energy decoy has a rmsd from the native state below 6 A and, in 9 out of 12 cases, we obtain decoys whose rmsd from the native states are also well below 5 A.

Amino Acids↗

Floral transcription factor AGAMOUS interacts in vitro with a leucine-rich repeat and an acid phosphatase protein complex.

We are interested in identifying potential protein interactors of MADS domain transcription factors during Arabidopsis thaliana flower development. We based our biochemical search on a conserved motif in the MADS domain that includes putative phosphatase and phosphorylation sites that may mediate protein interactions. An affinity column with this motif and a few surrounding hypervariable amino acids derived from the AGAMOUS sequence was prepared and used to isolate potential interactors from floral crude extracts. Only two proteins were specifically bound to the affinity column. The first corresponds to a carpel specific storage protein, VSP1, that presents acid phosphatase activity, and the second is a novel leucine-rich repeat protein that we have named FLOR1. Coimmunoprecipitation, two-hybrid yeast, and affinity column assays show that the FLOR1-VSP1 complex interacts with AGAMOUS and that this transcription factor directly interacts with FLOR1. This is the first assay to show an interaction between plant MADS domain factors and non-MADS proteins.

AGAMOUS Protein, Arabidopsis↗

The three-dimensional solution structure by 1H NMR of a 6-kDa proteinase inhibitor isolated from the stigma of Nicotiana alata.

The three-dimensional structure and disulfide connectivities of a 6-kDa protein isolated from the stigma of the ornamental tobacco Nicotiana alata has been determined by 1H NMR spectroscopy combined with simulated annealing calculations. The protein, termed C1, is a chymotrypsin inhibitor and is one of five homologous proteinase inhibitors that are proteolytically cleaved from a 40.3-kDa precursor protein. The other four proteinase inhibitors (T1 to T4) contain reactive sites for trypsin. The three-dimensional structure of C1 is generally well defined and contains a triple stranded beta-sheet as the dominant secondary structural feature. Several turns and a short region of 3(10) helix are also present. The putative chymotrypsin reactive site is present on an exposed loop which is less defined than the rest of the protein. The overall shape of C1 is disc-like and the N and C termini are exposed, supporting the proposal that this protein results from post-translational processing of the 40.3-kDa precursor protein.

Amino Acid Sequence↗

X-ray structure of gelonin at 1.8 A resolution.

Gelonin is a single chain ribosome inactivating protein (RIP) with potential application in the treatment of cancer and AIDS. Diffraction quality crystals grown using PEG3350, belong to the space group P21, with a = 49.4 A, b = 44.9 A, c = 137.4 A and beta = 98.4 degrees, and contain two molecules in the asymmetric unit. Diffraction data collected to 1.8 A resolution has a Rm value of 7.3%. Structure of gelonin has been solved by the molecular replacement method, using ricin A chain as the search model. Crystallographic refinement using X-PLOR resulted in a model for which the r.m.s deviations from ideal bond lengths and bond angles are 0.012 A and 2.7 degrees, respectively. The final R-factor is 18.4% for 39,806 reflections for which I > 1.0 sigma (I). The C alpha atoms of the two molecules in the asymmetric unit superpose to within 0.38 A for 247 atom pairs. The overall fold of gelonin is similar to that of other RIPs such as ricin A chain and alpha-momorcharin, the r.m.s.d. for C alpha superpositions being 1.3 and 1.4 A, respectively. The catalytic residues (Glu166, Arg169 and Tyr113) in the active site form a hydrogen bond scheme similar to that observed in other RIPs. The conformation of Tyr74 in the active site, however, is significantly different from that in alpha-momorcharin. Three well defined water molecules are located in the active site cavity, and one of them, X319, superposes to within 0.2 A of a corresponding water molecule in the structure of alpha-momorcharin. Any of the three could be the substrate water molecule in the hydrolysis reaction catalysed by gelonin. Difference electron density for a N-linked sugar moiety has been observed near only one of the two potential glycosylation sites in the sequence. The amino acid at position 239 has been established as Lys by calculation of omit electron density maps. The two cysteine residues in the sequence, Cys44 and Cys50, form a disulphide bond, and are therefore not available for disulphide conjugation with antibodies. Based on the structure, the region of the molecule that is involved in intradimer interactions is suggested to be suitable for introducing a Cys residue for purposes of conjugation with an antibody to produce useful immunotoxins.

Binding Sites↗

Diterpenoids from Isodon eriocalyx var. laxiflora.

Three new, seco-ent-kaurane diterpenoids, laxiflorins A, B and C, together with four known diterpenoids eriocalyxin B, oriodonin, and maeocrystals A and B, were isolated from the leaves of Isodon eriocalyx var. laxiflora. Their structures were assigned by a combination of one- and two-dimensional NMR techniques and computer modeling calculations. Laxiflorin C displayed weak cytotoxic activity.

Antineoplastic Agents↗

Binding of the bioactive component jatrorrhizine to human serum albumin.

The interaction between Jatrorrhizine with human serum albumin (HSA) were studied by fluorescence quenching technique, circular dichroism (CD) spectroscopy, and Fourier transform infrared (FT-IR) spectroscopy. Fluorescence data revealed the presence of a single class of binding site on HSA and its binding constants (K) are 7.278 x 10(4), 6.526 x 10(4), and 5.965 x 10(4) L.mol(-1) at 296, 303, and 310 K, respectively. The CD spectra and FT-IR spectra have proved that the protein secondary structure changed in the presence of Jatrorrhizine in aqueous solution. The effect of common ions on the binding constants was also investigated. In addition, the thermodynamic functions standard enthalpy (DeltaH(0)) and standard entropy (DeltaS(0)) for the reaction were calculated to be -10.891 kJ.mol(-1) and 56.267 J.mol(-1) K(-1), according to the van't Hoff equation. These data indicated that hydrophobic and electrostatic interactions played a major role in the binding of Jatrorrhizine to HSA. Furthermore, the displacement experiments indicated that Jatrorrhizine could bind to the site I of HSA, which was also in agreement with the result of the molecular modeling study.

Berberine↗

(+)-12alpha-Hydroxysophocarpine, a new quinolizidine alkaloid and related anti-HBV alkaloids from Sophora flavescens.

(+)-12alpha-Hydroxysophocarpine (8), a new quinolizidine alkaloid was isolated from the roots of Sophora flavescens, together with 10 known quinolizidine alkaloids, (+)-oxymatrine (1), (+)-matrine (2), (+)-9alpha-hydroxymatrine (3), (+)-allomatrine (4), (+)-oxysophocarpine (5), (-)-sophocarpine (6), (-)-9alpha-hydroxysophocarpine (7), (+)-lehmannine (9), (-)-13,14-dehydrosophoridine (10), and (-)-anagyrine (11). Their structures were elucidated by spectroscopic methods, and the stereochemistry of 8 was confirmed by X-ray analysis. These alkaloids were tested for anti-hepatitis B virus (HBV) activity in vitro, compounds 5, 6, 9, and 10 showed significant anti-HBV activity with inhibitory potency against HBsAg secretion at 48.3-79.3% and that against HBeAg secretion at 24.6-34.6%.

Alkaloids↗

Unveiling the mechanism of micro-and-nano plastic phytotoxicity on terrestrial plants: A comprehensive review of omics approaches.

Micro-and-nano plastics (MNPs) are pervasive in terrestrial ecosystems and represent an increasing threat to plant health; however, the mechanisms underlying their phytotoxicity remain inadequately understood. MNPs can infiltrate plants through roots or leaves, causing a range of toxic effects, including inhibiting water and nutrient uptake, reducing seed germination rates, and impeding photosynthesis, resulting in oxidative damage within the plant system. The effects of MNPs are complex and influenced by various factors including size, shape, functional groups, and concentration. Recent advancements in omics technologies such as proteomics, metabolomics, transcriptomics, and microbiomics, coupled with emerging technologies like 4D omics, phenomics, spatial transcriptomics, and single-cell omics, offer unprecedented insight into the physiological, molecular, and cellular responses of terrestrial plants to MNPs exposure. This literature review synthesizes current findings regarding MNPs-induced phytotoxicity, emphasizing alterations in gene expression, protein synthesis, metabolic pathways, and physiological disruptions as revealed through omics analyses. We summarize how MNPs interact with plant cellular structures, disrupt metabolic processes, and induce oxidative stress, ultimately affecting plant growth and productivity. Furthermore, we have identified critical knowledge gaps and proposed future research directions, highlighting the necessity for integrative omics studies to elucidate the complex pathways of MNPs toxicity in terrestrial plants. In conclusion, this review underscores the potential of omics approaches to elucidate the mechanisms of MNPs-phytotoxicity and to develop strategies for mitigating the environmental impact of MNPs on plant health.

Plants↗

p-coumaric acid esters from Tanacetum longifolium.

Two new long chain alkyl p-coumaric acid esters (2-3) along with eicosanyl trans-p-coumarate (1) were isolated from chloroform extract of the roots of Tanacetum longifolium. The structures of new compounds were assigned as 21'-hydroxyheneicosanyl-4-hydroxy-(cis and trans) p-coumarate (2a, 2b) and 27'-hydroxy heptacosanyl-cis-p-coumarate (3) by extensive chromatographic and spectroscopic analysis and by comparison with literature data of known compounds.

Coumaric Acids↗