Specific features of T-DNA insertion regions in transgenic plants

Experimental data from analysis of exogenous DNA (T-DNA) insertion sites in transgenic plants are summarized. Arguments are considered in favor and against the existence of genome DNA regions preferred for transgene integration that are determined by distinctive features characterizing the organization and nucleotide composition of the plant genome and the structure and conformational state of the chromatin. The main stages of T-DNA integration into a plant chromosome and possible molecular mechanisms of this process are discussed.     

Specific features of vector sequences insertion in the genome of transgenic plants

Upon processing of T-DNA, both borders may be recognized incorrectly. A number of transgenic plants containing, apart from a fragment of vector DNA adjacent to the left border of T-DNA, a vector fragment inserted irrespective of it were identified. Sequence analysis confirmed that genes located beyond the boundaries of T-DNA are transferred and inserted in the genome of transgenic plants. Recombination of vector DNA was discovered among plants of the first generation after self-pollination of the original transformants.     

Specific features of vector sequences insertion in the genome of transgenic plants

Upon processing of T-DNA, both borders may be recognized incorrectly. A number of transgenic plants containing, apart from a fragment of vector DNA adjacent to the left border of T-DNA, a vector fragment inserted irrespective of it were identified. Sequence analysis confirmed that genes located beyond the boundaries of T-DNA are transferred and inserted in the genome of transgenic plants. Recombination of vector DNA was discovered among plants of the first generation after self-pollination of the original transformants.     

Analysis of the features and source gene composition of the AluYg6 subfamily of human retrotransposons

Background  

Alu elements are a family of SINE retrotransposons in primates. They are classified into subfamilies according to specific diagnostic mutations from the general Alu consensus. It is now believed that there may be several retrotranspositionally-competent source genes within an Alu subfamily. To investigate the evolution of young Alu elements it is critical to have access to complete subfamilies, which, following the release of the final human genome assembly, can now be obtained using in silico methods.     

Specific herbivore-induced volatiles defend plants and determine insect community composition in the field

In response to insect attack, plants release complex blends of volatile compounds. These volatiles serve as foraging cues for herbivores, predators and parasitoids, leading to plant-mediated interactions within and between trophic levels. Hence, plant volatiles may be important determinants of insect community composition. To test this, we created rice lines that are impaired in the emission of two major signals, S-linalool and (E)-β-caryophyllene. We found that inducible S-linalool attracted predators and parasitoids as well as chewing herbivores, but repelled the rice brown planthopper Nilaparvata lugens, a major pest. The constitutively produced (E)-β-caryophyllene on the other hand attracted both parasitoids and planthoppers, resulting in an increased herbivore load. Thus, silencing either signal resulted in specific insect assemblages in the field, highlighting the importance of plant volatiles in determining insect community structures. Moreover, the results imply that the manipulation of volatile emissions in crops has great potential for the control of pest populations.     

Specific features of photorespiration in photosynthetically active organs of C3 plants

Photorespiration of photosynthetically active organs of C₃ plants (leaf, ear, stem, and leaf sheath) and C₄ plants (leaf, tassel, stem, leaf sheath, ear husk) grown under greenhouse and field conditions was studied. Photorespiration was measured using a PTM-48A high-technology monitor of photosynthesis (Bioinstruments S.R.L., Moldova). It is shown that photorespiration (CO₂ ejection after light turning off — apparent photorespiration) in C₃ plants is characteristic only for their leaves. In other photosynthesizing organs, photorespiration was absent, like in the photosynthesizing organs of C₄ plants. The absence of such after-light CO₂ outburst was observed for 31 genotypes: 18 cereal species belonging to four species (Triticum aestivum L., T. durum Desf., Secale cereale L., and Triticale); 6 grain legumes belonging to 2 species (Pisum sativum L. and Glycine max L.); 7 species of wild and rarely cultivated genotypes (T. boeoticum Boiss., T. dicoccoides Koern., T. dicoccum Schuebl., T. spelta L., T. compactum Host., T. monococcum L., and T. sphaerococcum Persiv.), and 2 genotypes of C₄ plants (Zea mays L. and Sorgum vulgaris L.). In all tested photosynthetically active genotypes, except of the C₃ plant leaves, apparent photorespiration was absent, but rather active glycolate cycle operated. The activity of this cycle was determined from the activity of the key enzyme of this cycle — glycolate oxidase. It was supposed that C₃ plants have two mechanisms of CO₂ assimilation: the first one — the mechanism of C₃ type localized in the leaves and the second one localized in other photosynthesizing organs, similar or with some elements of C₄ mechanism of CO₂ assimilation, limiting after-light CO₂ ejection during the metabolism of glycolate.     

Effects of biocontrol agents on lipid and protein composition of Indian mustard seeds from plants infected with Alternaria species

Field experiments were carried out with Indian mustard (Brassica juncea L. Cv RLM 1359) to investigate the influence of biocontrol agents on seeds from plants infected with Alternaria blight. The biocontrol agents viz, Trichoderma harzianum, Pseudomonas fluorescens and Bacillus subtilis were applied as seed treatment/seed treatment coupled with spray on 30 and 60 days after sowing of seeds in experimental fields. The plants treated with different biocontrol agents were more developed than non-treated plants throughout the experiment. Biochemical analysis revealed that application of biocontrol agents resulted in increase in lipid and protein content in seeds from treated plants. The proportion of various lipidic fractions i.e. phospholipids, glycolipids and sterol content in seeds increased with a corresponding decrease in total glycerides. The proportion of 18:3, 20:1 and 22:1 fatty acids increased while that of 18:1 and 18:2 fatty acids decreased in seeds with application of biocontrol agents. There were both qualitative and quantitative differences in the banding patterns of albumin and globulin proteins after application of biocontrol agents. The data suggested that biochemical alterations in the host induced by treatment with biocontrol agents could be associated with defence mechanisms and enhanced growth of the plant.     

Specific features of plants at early stages of the colonization of loose volcanic matter

Plant morphology and seed germination have been studied in several species joining monodominant beds of pioneer plant species on loose volcanic matter on the Kamchatka Peninsula and Kuril Islands. The competition of these species is discussed.     

Embryogenetic features of the serum protein composition of chicken blood

Protein composition of the blood serum in chick embryos of two breeds and in their hybrids has been investigated by polyacrylamide gel electrophoresis. Significant changes in the proportion of protein components of pre-albumin, albumin and post-albumin zones during prenatal development of chicks were observed. These changes are alleviated in hybrid embryos. The decrease in protein content of post-albumin zone, which contains foetoproteins, takes place to the end of incubation. This decrease is less significant in hybrid chicks as compared to that in the original hen breeds.     

The multidrug resistance-associated protein (MRP/ABCC) subfamily of ATP-binding cassette transporters in plants

In many different plant species, genes belonging to the multidrug resistance-associated protein (MRP, ABCC) subfamily of ABC transporters have been identified. Following the discovery of vacuolar transport systems for xenobiotic or plant-produced conjugated organic anions, plant MRPs were originally proposed to be primarily involved in the vacuolar sequestration of potentially toxic metabolites. Indeed, heterologous expression of different Arabidopsis MRPs in yeast demonstrates their activity as ATP-driven pumps for structurally diverse substrates. Recent analysis of protein-protein interactions and the characterization of knockout mutants in Arabidopsis suggests that apart from transport functions plant MRPs play additional roles including the control of plant transpiration through the stomata. Here, we review and discuss the diverse functions of plant MRP-type ABC transporters and present an organ-related and developmental analysis of the expression of Arabidopsis MRPs using the publicly available full-genome chip data.     

A new subfamily of major intrinsic proteins in plants

The major intrinsic proteins (MIPs) form a large protein family of ancient origin and are found in bacteria, fungi, animals, and plants. MIPs act as channels in membranes to facilitate passive transport across the membrane. Some MIPs allow small polar molecules like glycerol or urea to pass through the membrane. However, the majority of MIPs are thought to be aquaporins (AQPs), i.e., they are specific for water transport. Plant MIPs can be subdivided into the plasma membrane intrinsic protein, tonoplast intrinsic protein, and NOD26-like intrinsic protein subfamilies. By database mining and phylogenetic analyses, we have identified a new subfamily in plants, the Small basic Intrinsic Proteins (SIPs). Comparisons of sequences from the new subfamily with conserved amino acid residues in other MIPs reveal characteristic features of SIPs. Possible functional consequences of these features are discussed in relation to the recently solved structures of AQP1 and GlpF. We suggest that substitutions at conserved and structurally important positions imply a different substrate specificity for the new subfamily.     

Specific features of the prion protein transmembrane domain regulate nascent chain orientation

The sequence of a transmembrane (TM) domain and the adjacent regions are important for recognition, orientation, and integration at the translocon during membrane protein biosynthesis. However, the sequences of individual TM domains vary considerably. Although some general effects of electrostatic and hydrophobic interactions have been observed, it is still not clear what features of diverse sequences influence TM domain orientation. Here we utilized the ability of the prion protein (PrP) to be synthesized in multiple topological forms to assay the effects of substitutions and mutations on TM domain orientation. Several of the TM domains we tested appear to contain no inherent information regulating orientation. In contrast, we found that the middle region of the PrP TM domain significantly reduces the ability of the chain to invert its orientation in the translocon. We also observed that the C-terminal region of the PrP TM domain influences orientation, and we characterized the orientation differences between two forms of a physiologically relevant polymorphism in this region. Specifically, we found that the identity of a single amino acid, that at position 129, can significantly alter PrP TM domain orientation. Because position 129 is the location of the disease-associated Met/Val polymorphism, we discuss both how this small change may affect TMD orientation and the larger biological implications of these results.     

Specific biological features of opportunistic bacteria determining dysbacteriosis in the composition of the large intestine normal microflora

Dysbiotic manifestations in the gastrointestinal tract are widely spread. They are characterized by a prolonged, persistent course with the tendency to transition to the chronic form and poorly respond to corrective treatment. The occurrence of high concentrations is 70% for Klebsiella oxytoca, while for K. pneumoniae--within the limit of 30%. The most topical problem is colonization of the intestinal mucosa in children aged up to 1 year by Klebsiella, the seeded bacteria retaining their capacity for growth for up to 2-3 years despite the use of probiotics. As shown in this study, the occurrence of Klebsiella and the level of the antilysozyme and "antiinterferon" activity of these bacteria, their resistance to antimicrobial preparations increase, correlating with the level of dysbiotic disturbances.     

Predicting protein subnuclear localization using GO-amino-acid composition features

The nucleus guides life processes of cells. Many of the nuclear proteins participating in the life processes tend to concentrate on subnuclear compartments. The subnuclear localization of nuclear proteins is hence important for deeply understanding the construction and functions of the nucleus. Recently, Gene Ontology (GO) annotation has been used for prediction of subnuclear localization. However, the effective use of GO terms in solving sequence-based prediction problems remains challenging, especially when query protein sequences have no accession number or annotated GO term. This study obtains homologies of query proteins with known accession numbers using BLAST to retrieve GO terms for sequence-based subnuclear localization prediction. A prediction method PGAC, which involves mining informative GO terms associated with amino acid composition features, is proposed to design a support vector machine-based classifier. PGAC yields 55 informative GO terms with training and test accuracies of 85.7% and 76.3%, respectively, using a data set SNL_35 (561 proteins in 9 localizations) with 35% sequence identity. Upon comparison with Nuc-PLoc, which combines amphiphilic pseudo amino acid composition of a protein with its position-specific scoring matrix, PGAC using the data set SNL_80 yields a leave-one-out cross-validation accuracy of 81.1%, which is better than that of Nuc-PLoc, 67.4%. Experimental results show that the set of informative GO terms are effective features for protein subnuclear localization. The prediction server based on PGAC has been implemented at http://iclab.life.nctu.edu.tw/prolocgac.     

菊科几种入侵和非入侵植物种子需光发芽特性差异

对入侵菊科植物(假苍耳、薇甘菊、紫茎泽兰、飞机草)以及非入侵菊科植物(扫帚梅、天人菊、金鸡菊、麦秆菊、翠菊、黑心菊)对比研究发现,入侵组种子往往是需光发芽,即有光条件下平均高出无光条件发芽率40%(P0.01),而非入侵组的需光发芽特性不明显,即有光和无光条件下种子发芽率差异不显著(P0.05)。以入侵植物假苍耳为例对其种子需光发芽的特性研究发现:红光有利于提高种子的萌发率(萌发率为62%),而蓝光起到相反的作用(萌发率37%);当以全光的25%照射种子时,最能够促进种子的萌发(萌发率59%),更高的光强抑制种子萌发(100%光强时,发芽率为21%)。适宜浓度水杨酸SA处理(0.01mmol/L)可以起到与光照类似的效果而促进种子萌发(提高30%发芽率),而PEG和低温处理对其不存在显著影响,说明这种需光发芽的机理可能与SA处理影响种子萌发存在一定的联系。研究证实了入侵和非入侵菊科植物之间确实存在需光发芽的差异,其生理生化差异及是否有利于入侵植物的快速入侵需深入研究。     

Dissecting the proteome of pea mature seeds reveals the phenotypic plasticity of seed protein composition

Pea (Pisum sativum L.) is the most cultivated European pulse crop and the pea seeds mainly serve as a protein source for monogastric animals. Because the seed protein composition impacts on seed nutritional value, we aimed at identifying the determinants of its variability. This paper presents the first pea mature seed proteome reference map, which includes 156 identified proteins (http://www.inra.fr/legumbase/peaseedmap/). This map provides a fine dissection of the pea seed storage protein composition revealing a large diversity of storage proteins resulting both from gene diversity and post‐translational processing. It gives new insights into the pea storage protein processing (especially 7S globulins) as a possible adaptation towards progressive mobilization of the proteins during germination. The nonstorage seed proteome revealed the presence of proteins involved in seed defense together with proteins preparing germination. The plasticity of the seed proteome was revealed for seeds produced in three successive years of cultivation, and 30% of the spots were affected by environmental variations. This work pinpoints seed proteins most affected by environment, highlighting new targets to stabilize storage protein composition that should be further analyzed.     

Lipid composition and content in the seeds of radish plants of different magnetic orientation grown in weak permanent magnetic field

The content and composition of lipids were studied in the seeds of radish plants (Raphanus sativus L. var. radicula D.C., cv. Rosovo-krashyi s belym konchikom) grown from “seed to seed” in 2008 and 2009 in the greenhouse of the Institute of Plant Physiology in a permanent horizontal magnetic field (PMF) of Helmholz coils with the strength of ～400 A/m, in soil culture, at natural day length, and a temperature changing during the day. PMF suppressed all stages of radish plant development, from the appearance of alternative leaves to the formation of pods and mature seeds. In plants of the North-South magnetically oriented type (NS MOT), PMF reduced the number and weight of seeds; in the West-East magnetically oriented type (WEMOT), the number of seeds was reduced but their weights increased. In the seeds of the first generation of NS MOT, the total lipid content was higher than in the seeds of WE MOT. The amount of polar lipids in the seeds of NS MOT increased, whereas in the seeds of WE MOT it decreased or remained unchanged as compared with control. The content of neutral lipids reduced in both plant types. The strongest changes in the fatty acid composition of lipids with the highest content of unsaturated fatty acids were observed in the seeds of WE MOT in 2008. The weak PMF-induced differences in the changes of lipid composition and content in the seeds of different MOTs were evidently determined by seed sensitivity to the direction of field action. It is suggested that the occurrence of different MOTs increases the tolerance of plant population to unfavorable environmental factors, thus affecting its survival.     

Specific protein synthesis in isolated epithelium of guinea-pig seminal vesicle. General features

Four intrinsic soluble proteins are synthesized and secreted by sexually mature guinea-pig seminal-vesicle mucosa, which comprises a monolayer of a homogeneous columnar epithelial cell. All four proteins can be extracted readily in 154mm-NaCl from the organ's luminal constituents in which they are present in high concentration. They are referred to as proteins 1, 2, 3 and 4 in order of their elution during DEAE-cellulose column chromatography. Specific primary antibodies were harvested from goats that had been inoculated with the purified vesicular proteins; secondary antibodies were obtained from a donkey inoculated with goat γ-globulins. Double-antibody-immunoprecipitation techniques were developed to precipitate the vesicular proteins. Thus proteins newly synthesized from ¹⁴C-labelled amino acids could be precipitated and the incorporated radioactivity assessed. Isolated seminal-vesicle mucosa, incubated in only a buffered salt solution containing glucose, readily synthesized the soluble secreted proteins from added [¹⁴C]lysine plus [¹⁴C]glycine, [¹⁴C]histidine plus [¹⁴C]glutamate, [¹⁴C]glutamine alone and [¹⁴C]arginine alone. The rates of incorporation (d.p.m./mg of total soluble protein) of labelled lysine and glycine and of labelled arginine were linear with time over 180min. With the other labelled precursors, rates diminished between 60 and 180min. Labelled protein could be detected after only 10–15min of incubation. Only 4–9% of the newly synthesized protein remained associated with the mucosa; the remainder was found in the cell-free incubation medium. The isolated seminal-vesicle mucosal preparation will provide a unique opportunity to study the synthesis and secretion of abundant cell-specific proteins by this androgen-dependent tissue.