Whole genome co-expression analysis of soybean cytochrome P450 genes identifies nodulation-specific P450 monooxygenases

Background  

Cytochrome P450 monooxygenases (P450s) catalyze oxidation of various substrates using oxygen and NAD(P)H. Plant P450s are involved in the biosynthesis of primary and secondary metabolites performing diverse biological functions. The recent availability of the soybean genome sequence allows us to identify and analyze soybean putative P450s at a genome scale. Co-expression analysis using an available soybean microarray and Illumina sequencing data provides clues for functional annotation of these enzymes. This approach is based on the assumption that genes that have similar expression patterns across a set of conditions may have a functional relationship.     

Synthetic studies in butenonyl C-glycosides: Preparation of polyfunctional alkanonyl glycosides and their enzyme inhibitory activity

A simple synthesis of phenyl butenoyl C-glycosides has been achieved by Aldol condensation of peracetylated glycosyl acetones with aromatic aldehydes followed by deacetylation with methanolic NaOMe. The selected butenoyl C-glycosides on conjugate addition of diethyl malonate resulted in polyfunctional alkanonyl glycosides in good yields. The butenoyl C- and alkanoyl C-glycosides were evaluated for their α-glucosidase, glucose-6-phosphatse and glycogen phosphorylase enzyme inhibitory activities in vitro. Three of the synthesized (3, 5 and 9) showed potent enzyme inhibitory activities as compared to standard drugs. Compounds 3, 5 and 9 were evaluated in vivo too displaying significant activity as compared to standard drugs acarbose and metformin.     

Genome organization and polyploid evolution in the genus Eleusine (Poaceae)

 Eleusine (Poaceae) includes six diploid and three polyploid species and has three basic chromosome numbers, x=8, 9 and 10. The species are annual as well as perennial and all are wild except E. coracana, which is cultivated for grain and fodder in Africa and the Indian subcontinent. Eleusine coracana and E. africana have the same genome and chromosome number (2n=36). Eleusine indica and E. floccifolia are identified as two genome donors to these polyploid species. Eleusine kigeziensis is the third polyploid species of the genus with 2n=38. Its genome may have come from E. jaegeri and from one of the species with x=9, most probably from E. indica. Eleusine indica, E. tristachya, E. floccifolia and E. intermedia with x=9 and two polyploid species, E. coracana and E. africana, are closely related and there is free genetic flow between them. Eleusine multiflora with x=8 is significantly different in morphology and at genomic level from other species. Eleusine jaegeri with x=10 is morphologically similar to E. indica, however, more information is needed to ascertain its position in the genus. Eleusine coracana, which is commonly called finger millet, is a potential and nutritious crop for the increasing population of the world, particularly in arid and semi-arid regions. It can also serve as a gene pool for various important characters and disease resistant genes. Received February 11, 2002; accepted May 27, 2002 Published online: October 14, 2002 Addresses of the authors: Madho Singh Bisht and Yasuhiko Mukai (e-mail: ymukai@cc.osaka-kyoiku.ac.jp), Laboratory of Plant Molecular Genetics, Division of Natural Science, Osaka Kyoiku University, 4-698-1 Asahigaoka, Kashiwara, Osaka 582-8582, Japan.     

<Emphasis Type="Italic">Pseudomonas lurida</Emphasis> M2RH3 (MTCC 9245), a psychrotolerant bacterium from the Uttarakhand Himalayas,solubilizes phosphate and promotes wheat seedling growth

Pseudomonas lurida strain M2RH3 (MTCC 9245) is a Gram negative, non spore forming, fluorescent bacterium isolated from a high altitude rhizospheric soil from the Uttarakhand Himalayas. The identity of the bacterium was arrived by sequencing of the 16S rRNA gene and subsequent phylogenetic analysis. It grew and exhibited plant growth promoting traits at 4, 15 and 30°C, under in vitro conditions. The expression of plant growth promoting (PGP) traits by the bacterium was highest at 30°C, with a proportionate reduction in PGP activity at lower temperatures. Determination of phosphate solubilization by the bacterium at three incubation temperatures revealed a steady increase in the soluble P levels across the incubation temperatures, coupled with a concomitant drop in the pH levels of the culture supernatant, till the 14th day of incubation. Seed bacterization with the isolate positively influenced the growth and nutrient uptake parameters of wheat seedlings cv. VL 804 in pot culture conditions at controlled cold growing temperature. This is an early report on the phosphate solubilization and plant growth promotion by Pseudomonas lurida, which is a relatively new species of the genus Pseudomonas and opens up a hitherto unknown facet of this bacterium.     

In Vitro Efficacy of Lipid Conjugated Peptidomimetics Against Mycobacterium smegmatis

International Journal of Peptide Research and Therapeutics - Tuberculosis has become a cause of worldwide concern; emergence of resistance in various mycobacterial strains has led to an urgent...     

Alleviation of cold stress in inoculated wheat (<Emphasis Type="Italic">Triticum aestivum L</Emphasis>.) seedlings with psychrotolerant Pseudomonads from NW Himalayas

Twelve psychrotolerant Pseudomonad strains were selected on the basis of various plant growth-promoting (PGP) activities at cold temperature (4°C). The effect of inoculation with Pseudomonad strains on cold alleviation and growth of wheat seedling at cold temperature (8°C) was investigated under greenhouse condition. Inoculation with Pseudomonad strains significantly enhanced root/shoot biomass and nutrients uptake as compared to non-bacterized control at 60 days of plant growth. Bacterization significantly improved the level of cellular metabolites like chlorophyll, anthocyanin, free proline, total phenolics, starch content, physiologically available iron, proteins, and amino acids that are sign of alleviation of cold stress in wheat plants. Increased relative water content, reduced membrane injury (electrolyte leakage), and Na⁺/K⁺ ratio were also recorded in bacterized wheat plants. Electrolyte leakage and Na⁺/K⁺ were found inversely proportional to plant growth at cold temperature. Statistical analysis of twenty-three measured parameters revealed that uninoculated control was under cold stress while eight bacterial strains were positively alleviating cold stress in wheat plants. Thus, the psychrotrophic Pseudomonad strains could effectively provide a promising solution to overcome cold stress, which is major factor hindering wheat productivity under cold climatic condition.     

Crystal structures of open and closed forms of d-serine deaminase from Salmonella typhimurium - implications on substrate specificity and catalysis

Metabolism of D-amino acids is of considerable interest due to their key importance in cell structure and function. Salmonella typhimuriumd-serine deaminase (StDSD) is a pyridoxal 5' phosphate (PLP) dependent enzyme that catalyses degradation of D-Ser to pyruvate and ammonia. The first crystal structure of d-serine deaminase described here reveals a typical Foldtype II or tryptophan synthase β subunit fold of PLP-dependent enzymes. Although holoenzyme was used for crystallization of both wild-type StDSD (WtDSD) and selenomethionine labelled StDSD (SeMetDSD), significant electron density was not observed for the cofactor, indicating that the enzyme has a low affinity for the cofactor under crystallization conditions. Interestingly, unexpected conformational differences were observed between the two structures. The WtDSD was in an open conformation while SeMetDSD, crystallized in the presence of isoserine, was in a closed conformation suggesting that the enzyme is likely to undergo conformational changes upon binding of substrate as observed in other Foldtype II PLP-dependent enzymes. Electron density corresponding to a plausible sodium ion was found near the active site of the closed but not in the open state of the enzyme. Examination of the active site and substrate modelling suggests that Thr166 may be involved in abstraction of proton from the Cα atom of the substrate. Apart from the physiological reaction, StDSD catalyses α, β elimination of D-Thr, D-Allothr and L-Ser to the corresponding α-keto acids and ammonia. The structure of StDSD provides a molecular framework necessary for understanding differences in the rate of reaction with these substrates.     

Identification and validation of sex-linked SCAR markers in dioecious Hippophae rhamnoides L. (Elaeagnaceae)

The actinorhizal plant seabuckthorn (Hippophae rhamnoides L., Elaeagnaceae) is a wind pollinated dioecious crop. To distinguish male genotypes from female genotypes early in the vegetative growth phase, we have developed robust PCR-based marker(s). DNA bulk samples from 20 male and 20 female plants each were screened with 60 RAPD primers. Two primers, OPA-04 and OPT-06 consistently amplified female-specific (FS) polymorphic fragments of 1,164 and 868 bp, respectively, that were absent in the male samples. DNA sequence of the two markers did not exhibit significant similarity to previously characterized sequences. A sequence-characterized amplified region marker HrX1 (JQ284019) and HrX2 (JQ284020) designed for the two fragments, continued to amplify the FS allele in 120 female plants but not in 100 male plants tested in the current study. Thus, HrX1 and HrX2 are FS markers that can determine the sex of seabuckthorn plants in an early stage and expedite cultivations for industrial applications.