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At least 937 records · Page 52Linked to original sources
PubMed2002

Genome-wide identification of nodule-specific transcripts in the model legume Medicago truncatula.

The Medicago truncatula expressed sequence tag (EST) database (Gene Index) contains over 140,000 sequences from 30 cDNA libraries. This resource offers the possibility of identifying previously uncharacterized genes and assessing the frequency and tissue specificity of their expression in silico. Because M. truncatula forms symbiotic root nodules, unlike Arabidopsis, this is a particularly important approach in investigating genes specific to nodule development and function in legumes. Our analyses have revealed 340 putative gene products, or tentative consensus sequences (TCs), expressed solely in root nodules. These TCs were represented by two to 379 ESTs. Of these TCs, 3% appear to encode novel proteins, 57% encode proteins with a weak similarity to the GenBank accessions, and 40% encode proteins with strong similarity to the known proteins. Nodule-specific TCs were grouped into nine categories based on the predicted function of their protein products. Besides previously characterized nodulins, other examples of highly abundant nodule-specific transcripts include plantacyanin, agglutinin, embryo-specific protein, and purine permease. Six nodule-specific TCs encode calmodulin-like proteins that possess a unique cleavable transit sequence potentially targeting the protein into the peribacteroid space. Surprisingly, 114 nodule-specific TCs encode small Cys cluster proteins with a cleavable transit peptide. To determine the validity of the in silico analysis, expression of 91 putative nodule-specific TCs was analyzed by macroarray and RNA-blot hybridizations. Nodule-enhanced expression was confirmed experimentally for the TCs composed of five or more ESTs, whereas the results for those TCs containing fewer ESTs were variable.

Agglutinins↗
PubMed2003

Insect attack and wounding induce traumatic resin duct development and gene expression of (-)-pinene synthase in Sitka spruce.

Conifers possess inducible terpenoid defense systems. These systems are associated with the formation of traumatic resin ducts (TRD) and are underpinned by enhanced gene expression and activity of terpene synthases (TPS), enzymes responsible for oleoresin formation. We first determined that Sitka spruce (Picea sitchensis [Bong.] Carriere) had the capacity for TRD formation by mechanically wounding representative trees. We then proceeded to investigate whether the white pine weevil (Pissodes strobi Peck.), a stem-boring insect, can influence the expression of genes encoding monoterpene synthases (mono-tps) in Sitka spruce. We went on to compare this response with the effects of a simulated insect attack by drill wounding. A significant increase in mono-tps transcript level was observed in the leaders of lateral branches of weevil-attacked and mechanically wounded trees. In this study, weevils induced a more rapid enhancement of mono-tps gene expression. A full-length Sitka spruce mono-tps cDNA (PsTPS2) was isolated, expressed in Escherichia coli, and functionally identified as (-)-pinene synthase. The recombinant (-)-pinene synthase catalyzes the formation of (-)-alpha-pinene and (-)-beta-pinene, both of which are known constituents of stem oleoresin in Sitka spruce and increase in abundance after weevil attack. These data suggest that increased (-)-pinene synthase gene expression is an important element of the direct defense system deployed in Sitka spruce after insect attack.

Amino Acid Sequence↗
PubMed2000

AINTEGUMENTA promotes petal identity and acts as a negative regulator of AGAMOUS.

The Arabidopsis AINTEGUMENTA (ANT) gene has been shown previously to be involved in ovule development and in the initiation and growth of floral organs. Here, we show that ANT acts in additional processes during flower development, including repression of AGAMOUS (AG) in second whorl cells, promotion of petal epidermal cell identity, and gynoecium development. Analyses of ap2-1 ant-6 double mutants reveal that ANT acts redundantly with AP2 to repress AG in second whorl cells. The abaxial surface of ant petals contains features such as stomata and elongated, interdigitated cells that are not present on wild-type petals. The loss of petal identity in these second whorl cells does not result from ectopic AG expression, suggesting that ANT acts in a pathway promoting petal cell identity that is independent of its role in repression of AG. These data suggest that ANT may function as a class A gene.

AGAMOUS Protein, Arabidopsis↗
PubMed2001

Farnesyl hydroxybenzoic acid derivatives from Ferula kuhistanica.

Four new farnesyl hydroxybenzoic acid derivatives, kuhistanols E-H (1-4), were isolated from the roots of the Uzbekistan medicinal plant Ferula kuhistanica. The structures of the new compounds were elucidated based on spectroscopic and chemical evidence.

Apiaceae↗
PubMedDate not supplied

Barbeyol: a new phenolic indane type component from Barbeya oleoides.

The aerial parts of Barbeya oleoides Schweinf (Family: Barbeyaceae) has afforded a new phenolic indane type component, which has been characterized as (6R, 4aR, 5aR)-5, 4a, 5a-trihydroindeno- (1, 2-a) indane-2, 4, 9-triol-6-O-beta-acetate (1) on the basis of spectral analysis and has been designated as barbeyol.

Indans↗
PubMedDate not supplied

[Biosynthesis of poppy isoquinoline alkaloids in nature and in vitro culture. 2. Bracteum poppy (Papaver bracteatum Lindl.)].

Literature data and the data of the author's investigations on production of isoquinoline alkaloids by Papaver bracteatum Lindl. have been analyzed. Information on the methods of regulation and cell localization of morphine and sanguinarine biosynthesis is presented. The works studying differentiation processes in tissue cultures of bracteum poppy and relationship thereof with thebaine biosynthesis have been analyzed. Possible mechanism determining the induction of somatic embryos development and thebaine biosynthesis in the culture in vitro are proposed.

Alkaloids↗
PubMed2003

Structurally homologous binding of plant calmodulin isoforms to the calmodulin-binding domain of vacuolar calcium-ATPase.

The discovery that plants contain multiple calmodulin (CaM) isoforms having variable sequence identity to mammalian CaM has sparked a flurry of new questions regarding the intracellular role of Ca(2+) regulation in plants. To date, the majority of research in this field has focused on the differential enzymatic regulation of various mammalian CaM-dependent enzymes by the different plant CaM isoforms. However, there is comparatively little information on the structural recognition of target enzymes found exclusively in plant cells. Here we have used a variety of spectroscopic techniques, including nuclear magnetic resonance, circular dichroism, and fluorescence spectroscopy, to study the interactions of the most conserved and most divergent CaM isoforms from soybean, SCaM-1, and SCaM-4, respectively, with a synthetic peptide derived from the CaM-binding domain of cauliflower vacuolar calcium-ATPase. Despite their sequence divergence, both SCaM-1 and SCaM-4 interact with the calcium-ATPase peptide in a similar calcium-dependent, stoichiometric manner, adopting an antiparallel binding orientation with an alpha-helical peptide. The single Trp residue is bound in a solvent-inaccessible hydrophobic pocket on the C-terminal domain of either protein. Thermodynamic analysis of these interactions using isothermal titration calorimetry demonstrates that the formation of each calcium-SCaM-calcium-ATPase peptide complex is driven by favorable binding enthalpy and is very similar to the binding of mammalian CaM to the CaM-binding domains of myosin light chain kinases and calmodulin-dependent protein kinase I.

Amino Acid Sequence↗
PubMed2004

Impact of lime, nitrogen and plant species on bacterial community structure in grassland microcosms.

A microcosm-based approach was used to study impacts of plant and chemical factors on the bacterial community structure of an upland acidic grassland soil. Seven perennial plant species typical of both natural, unimproved (Nardus stricta, Agrostis capillaris, Festuca ovina and F. rubra) and fertilized, improved (Holcus lanatus, Lolium perenne and Trifolium repens) grasslands were either left unamended or treated with lime, nitrogen, or lime plus nitrogen in a 75-day glasshouse experiment. Lime and nitrogen amendment were shown to have a greater effect on microbial activity, biomass and bacterial ribotype number than plant species. Liming increased soil pH, microbial activity and biomass, while decreasing ribotype number. Nitrogen addition decreased soil pH, microbial activity and ribotype number. Addition of lime plus nitrogen had intermediate effects, which appeared to be driven more by lime than nitrogen. Terminal restriction fragment length polymorphism (TRFLP) analysis revealed that lime and nitrogen addition altered soil bacterial community structure, while plant species had little effect. These results were further confirmed by multivariate redundancy analysis, and suggest that soil lime and nitrogen status are more important controllers of bacterial community structure than plant rhizosphere effects.

Analysis of Variance↗
PubMed2003

A device and standard variables to describe microhabitat structure of small mammals based on plant cover.

Studies quantifying habitat structure generally use several instruments. This paper aims to propose a new and efficient device to characterize microhabitat structure of small mammals. Seven measurements were taken: plant cover, litter cover, rock cover, canopy cover, and vegetative obstruction at three heights. The device is a 0.25 m2 square wooden frame (0.50 m x 0.50 m) divided in to 100 open squares by wire mesh. Average time spent to measure each trapping station was six minutes. This new device is efficient, i.e., quick, practical, simple, and reliable. It can be used in any kind of forest. We propose this method as a standard method to describe habitat structure.

Animals↗
PubMed1997

Homology modelling of an antimicrobial protein, Ace-AMP1, from lipid transfer protein structures.

BACKGROUND: Plant nonspecific lipid transfer proteins (ns-LTPs) are small basic proteins that facilitate lipid shuttling between membranes in vitro. The function of ns-LTPs in vivo is still unknown. It has been suggested, in relation to their lipid binding ability, that they may be involved in cutin formation. Alternatively, they may act in the plant defence system against pathogenic agents. Ace-AMP1 is an antimicrobial protein extracted from onion seed that shows sequence homology with ns-LTPs but that is unable to transfer lipids. We have recently determined the three-dimensional structure of wheat and maize ns-LTPs. In order to compare the structural features of Ace-AMP1 and ns-LTPs, we have used the comparative modelling software MODELLER to predict the structure of Ace-AMP1. RESULTS: The global fold of Ace-AMP1 is very similar to those of ns-LTPs, involving four helices and a C-terminal tail without secondary structure elements. The structure of maize and wheat ns-LTP is characterized by the existence of a tunnel-like hydrophobic cavity in which a lipid molecule can be inserted. In the Ace-AMP1 structure, this cavity is blocked by a number of bulky residues. Similarly, the electrostatic potential contours of ns-LTPs show some common features that were not observed in Ace-AMP1. CONCLUSIONS: Although Ace-AMP1 displays a similar global fold to ns-LTPs, it does not present a hydrophobic cavity, which may explain why Ace-AMP1 cannot shuttle lipids between membranes in vitro. The large differences in the electrostatic properties of Ace-AMP1 and ns-LTPs suggest a different mode of interaction with membranes.

Amino Acid Sequence↗
PubMed2005

Impact of lime, nitrogen and plant species on fungal community structure in grassland microcosms.

A microcosm-based approach was used to study impacts of plant and chemical factors on the fungal community structure of an upland acidic grassland soil. Seven plant species typical of both unimproved and fertilized grasslands were either left unamended or treated with lime, nitrogen or lime plus nitrogen. Fungal community structure was assessed by a molecular approach, fungal automated ribosomal intergenic spacer analysis (FARISA), while fungal biomass was estimated by measuring soil ergosterol content. Addition of nitrogen (with or without lime) had the largest effect, decreasing soil pH, fungal biomass and fungal ribotype number, but there was little corresponding change in fungal community structure. Although different plant species were associated with some changes in fungal biomass, this did not result in significant differences in fungal community structure between plant species. Addition of lime alone caused no changes in fungal biomass, ribotype number or community structure. Overall, fungal community structure appeared to be more significantly affected through interactions between plant species and chemical treatments, as opposed to being directly affected by changes in individual improvement factors. These results were in contrast to those found for the bacterial communities of the same soils, which changed substantially in response to chemical (lime and nitrogen) additions.

Calcium Compounds↗
PubMed2002

Psychotropic substance-seeking: evolutionary pathology or adaptation?

According to a conventional evolutionary perspective, the human propensity for substance use is the product of a 'mismatch' between emotional mechanisms that evolved in a past without pure drugs or direct routes of drug administration, and the occurrence of these phenomena in the contemporary environment. The primary purpose of this review is to assert that, contrary to the conventional view, humans have shared a coevolutionary relationship with psychotropic plant substances that is millions of years old. We argue that this 'deep time' relationship is self-evident both in the extant chemical-ecological adaptations that have evolved in mammals to metabolize psychotropic plant substances and in the structure of plant defensive chemicals that have evolved to mimic the structure, and interfere with the function, of mammalian neurotransmitters. Given this evidence, we question how emotional mechanisms easily triggered by plant toxins can have evolved. Our argument is also supported with archeological and historical evidence of substance use in antiquity suggesting that, for people in the past, psychotropic plant substances were as much a mundane everyday item as they are for many people today. Our second, and more speculative objective is to suggest provisional hypotheses of human substance-using phenomena that can incorporate the evolutionary implications of a deep time relationship between psychotropic substances and people. We discuss hypotheses of selective benefits of substance use, including the idea that neurotransmitter-analog plant chemicals were exploited as substitutes for costly, nutritionally constrained endogenous neurotransmitters. However, even if substance seeking was adaptive in the environment of our hominid ancestors, it may not still be so in the contemporary environment. Thus, the implications of our argument are not that the mismatch concept does not apply to human substance-using phenomena, but that it must be reconsidered and extended to incorporate the implications of a substance-rich, rather than substance-free, evolutionary past.

Adaptation, Physiological↗
PubMed1990

Tertiary structure and computer modeling of plant 5S ribosomal RNA.

A new model of secondary and tertiary structure of higher plant 5S rRNA is proposed. It consists of three domains. Domain alpha includes stem I and loop A; 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. We propose that the domains beta and gamma adopt RNA-A like structure due to irregularities caused by the different in size internal loops B and E and the bulges occurring in the model. A suggested bending of RNA could bring single stranded fragments of domains beta and gamma close enough to each other to allow tertiary interactions. The new model of plant 5S rRNA differs from those suggested previously for eukaryotic 5S rRNA, by arrangement of the domains beta and gamma and the base pairing scheme of domain gamma. The model is based on our results of partial digestion obtained with single and double strand specific nucleases. The experimental results were confirmed by computer aided secondary structure prediction analysis of all higher plant 5S rRNAs and computer modeling using energy minimalization approach. Further support of our model have been provided by experiments including alpha sarcin, ribonuclease H and chemical modifications.

Base Sequence↗
PubMed1997

A 28-kilodalton pod storage protein of French bean plants. Purification, characterization, and primary structure.

When French bean (Phaseolus vulgaris) plants were depodded in the early stages of fruit development, relative levels of a specific protein with a relative molecular weight of 28,000 were enhanced in the young pods that formed later. The protein, designated pod storage protein (PSP), was purified from extracts of newly formed pods from plants that had been previously depodded four times at intervals of 2 weeks. Two-dimensional polyacrylamide gel electrophoresis showed the presence of three forms (designated A, B, and C) of PSP with identical electrophoretic mobilities but different charges. The molecular mass of native PSP was estimated by gel filtration to be 67 kD; therefore, the protein was most likely present as a dimer. The antisera raised against forms A and C were crossreactive with each other. Form B lacked the N-terminal alanine of forms A and C. An expression library from French bean pods was screened using the antiserum against form A, and a full-length cDNA clone was isolated. The cDNA insert included 765 bp potentially encoding a polypeptide with 255 amino acid residues (and a calculated molecular mass of 28,854 D). The amino acid sequence deduced from the PSP cDNA had 65 to 71% identity with soybean (Glycine max) vegetative storage protein sequences (P.E. Staswick [1988] Plant Physiol 87: 250-254; and Correction [1989] Plant Physiol 89: 717). Genomic Southern blot analysis suggested that PSP is derived from a single-copy gene.

Amino Acid Sequence↗
PubMed1979

[Relationship between anatomical structure and metabolism of plant tissues. I. Differences between the qualitative and quantitative composition of phenolic substances of apple explants and that of callus and cells produced by the culture].

Relationship between anatomical structure and metabolism of plant tissues. I. Differences between the qualitative and quantitative composition of phenolic substances of apple-fruit explants and that of calli and cells cultured from these explants. Phenolic compounds of intact apple-fruits (CV. Golden delicious), fruit fragments cultured on agar medium, newly formed calli and cell suspensions prepared from these calli, were studied quantitatively and qualitatively. The phenol content of the tissues decreased during the first days of culture, then recovered practically the initial level just before the initiating calli became visible. This content is very low in the calli and in the cultured cells. But the most remarkable result is that the qualitative compositions of the phenols extracted from the fruit tissues, the calli and the cells were different : p-coumaryglucose, which is abundant in the fruit, disappeared almost completely in the calli, in which three compounds were formed de novo, X1 which was tentatively identified as ferulylquinic acid, X2, a glycoside of p-coumaric acid different from p-coumarylglucose, and X3 not yet identified; the cells synthesized also X1 and X3 but not X2, and contained no p-coumaryglucose while feruylquinic acid was abundant. The study on the processes of induction or regulation of the enzymes implied in these metabolic modifications is under way.

Agar↗
PubMed2005

RNA silencing suppressor p21 of Beet yellows virus forms an RNA binding octameric ring structure.

Many plant viruses encode proteins that suppress the antiviral RNA silencing response mounted by the host. The suppressors p19 from tombusvirus and p21 from Beet yellows virus appear to block silencing by directly binding siRNA, a critical mediator in the process. Here, we report the crystal structure of p21, which reveals an octameric ring architecture with a large central cavity of approximately 90 A diameter. The all alpha-helical p21 monomer consists of N- and C-terminal domains that associate with their neighboring counterparts through symmetric head-to-head and tail-to-tail interactions. A putative RNA binding surface is identified in the conserved, positive-charged inner surface of the ring. In contrast to the specific p19-siRNA duplex interaction, p21 is a general nucleic acid binding protein, interacting with 21 nt or longer single- and double-stranded RNAs in vitro. This study reveals an RNA binding structure adopted by the p21 silencing suppressor.

Amino Acid Sequence↗