02468nas a2200265 4500008004100000022001400041245015900055210006900214260012000283300001000403490000700413520142200420653000901842653003001851653001901881653001201900653002601912653002201938100002101960700002501981700002502006700002102031700002402052856012602076 2013 eng d a0831-279600aGenome-wide identification and characterization of nucleotide binding site leucine-rich repeat genes in linseed reveal distinct patterns of gene structure0 aGenomewide identification and characterization of nucleotide bin a1200 MONTREAL ROAD, BUILDING M-55, OTTAWA, ON K1A 0R6, CANADAbCANADIAN SCIENCE PUBLISHING, NRC RESEARCH PRESScFEB a91-990 v563 a

Plants employ different disease-resistance genes to detect pathogens and to induce defense responses. The largest class of these genes encodes proteins with nucleotide binding site (NBS) and leucine-rich repeat (LRR) domains. To identify the putative NBS-LRR encoding genes from linseed, we analyzed the recently published linseed genome sequence and identified 147 NBS-LRR genes. The NBS domain was used for phylogeny construction and these genes were classified into two well-known families, non-TIR (CNL) and TIR related (TNL), and formed eight clades in the neighbor-joining bootstrap tree. Eight different gene structures were observed among these genes. An unusual domain arrangement was observed in the TNL family members, predominantly in the TNL-5 clade members belonging to class D. About 12% of the genes observed were linseed specific. The study indicated that the linseed genes probably have an ancient origin with few progenitor genes. Quantitative expression analysis of five genes showed inducible expression. The in silico expression evidence was obtained for a few of these genes, and the expression was not correlated with the presence of any particular regulatory element or with unusual domain arrangement in those genes. This study will help in understanding the evolution of these genes, the development of disease resistant varieties, and the mechanism of disease resistance in linseed.

10aFlax10ain silico gene expression10amotif analysis10aNBS-LRR10aPhylogenetic analysis10aPromoter analysis1 aKale, Sandip, M.1 aPardeshi, Varsha, C.1 aBarvkar, Vitthal, T.1 aGupta, Vidya, S.1 aKadoo, Narendra, Y. uhttps://library.ncl.res.in/content/genome-wide-identification-and-characterization-nucleotide-binding-site-leucine-rich-002188nas a2200241 4500008004100000022001400041245009900055210006900154260007300223300001200296490000700308520130000315653004101615653002401656653002601680653001401706100002101720700002701741700001701768700001601785700002701801856011801828 2015 eng d a0141-813000aBacopa monniera recombinant mevalonate diphosphate decarboxylase: biochemical characterization0 aBacopa monniera recombinant mevalonate diphosphate decarboxylase aPO BOX 211, 1000 AE AMSTERDAM, NETHERLANDSbELSEVIER SCIENCE BVcAUG a661-6680 v793 a

Mevalonate diphosphate decarboxylase (MDD; EC 4.1.1.33) is an important enzyme in the mevalonic acid pathway catalyzing the Mg2+-ATP dependant decarboxylation of mevalonate 5-diphosphate (MVAPP) to isopentenyl diphosphate (IPP). Bacopa monniera recombinant MDD (BmMDD) protein was overexpressed in Escherichia coli BL21 (DE3) strain and purified to apparent homogeneity. K-m and V-max for MVAPP were 144 mu M and 52 U mg(-1) respectively. The values of turnover (k(cat)) and k(cat)/K-m, for mevalonate 5-diphosphate were determined to be 40 s(-1) and 2.77 x 10(5) M-1 s(-1) and k(cat) and k(cat)/K-m values for ATP were found to be 30 s(-1) and 2.20 x 10(4) M-1 s(-1), respectively. pH activity profile indicated the involvement of carboxylate ion, lysine and arginine for the activity of enzyme. The apparent activation energy for the BmMDD catalyzed reaction was 12.7 kJ mol(-1). Optimum pH and temperature for the forward reaction was found to be 8.0 and 45 degrees C. The enzyme was most stable at pH 7 at 20 degrees C with the deactivation rate constant (K-d(*)) of 1.69 x 10(-4) and half life (t(1/2)) of 68 h. The cation studies suggested that BmMDD is a cation dependant enzyme and optimum activity was achieved in the presence of Mg2+. (C) 2015 Elsevier B.V. All rights reserved.

10aMevalonate diphosphate decarboxylase10apH activity profile10aPhylogenetic analysis10astability1 aAbbassi, Shakeel1 aVishwakarma, Rishi, K.1 aPatel, Parth1 aKumari, Uma1 aKhan, Bashir, Mohammad uhttps://library.ncl.res.in/content/bacopa-monniera-recombinant-mevalonate-diphosphate-decarboxylase-biochemical-102697nas a2200241 4500008004100000022001400041245015300055210006900208260008600277300001400363490000700377520171200384653002402096653002902120653003702149653002202186653002602208100002202234700002402256700001902280700002802299856012802327 2015 eng d a0739-110200aDistinct molecular features facilitating ice-binding mechanisms in hyperactive antifreeze proteins closely related to an Antarctic sea ice bacterium0 aDistinct molecular features facilitating icebinding mechanisms i a530 WALNUT STREET, STE 850, PHILADELPHIA, PA 19106 USAbTAYLOR & FRANCIS INCcJUL a1424-14410 v333 a

Antifreeze proteins or ice-binding proteins (IBPs) facilitate the survival of certain cellular organisms in freezing environment by inhibiting the growth of ice crystals in solution. Present study identifies orthologs of the IBP of Colwellia sp. SLW05, which were obtained from a wide range of taxa. Phylogenetic analysis on the basis of conserved regions (predicted as the `ice-binding domain' [IBD]) present in all the orthologs, separates the bacterial and archaeal orthologs from that of the eukaryotes'. Correspondence analysis pointed out that the bacterial and archaeal IBDs have relatively higher average hydrophobicity than the eukaryotic members. IBDs belonging to bacterial as well as archaeal AFPs contain comparatively more strands, and therefore are revealed to be under higher evolutionary selection pressure. Molecular docking studies prove that the ice crystals form more stable complex with the bacterial as well as archaeal proteins than the eukaryotic orthologs. Analysis of the docked structures have traced out the ice-binding sites (IBSs) in all the orthologs which continue to facilitate ice-binding activity even after getting mutated with respect to the well-studied IBSs of Typhula ishikariensis and notably, all these mutations performing ice-binding using `anchored clathrate mechanism' have been found to prefer polar and hydrophilic amino acids. Horizontal gene transfer studies point toward a strong selection pressure favoring independent evolution of the IBPs in some polar organisms including prokaryotes as well as eukaryotes because these proteins facilitate the polar organisms to acclimatize to the adversities in their niche, thus safeguarding their existence.

10aantifreeze proteins10ahorizontal gene transfer10aice-recrystallization inhibition10aMolecular docking10aPhylogenetic analysis1 aBanerjee, Rachana1 aChakraborti, Pratim1 aBhowmick, Rupa1 aMukhopadhyay, Subhasish uhttps://library.ncl.res.in/content/distinct-molecular-features-facilitating-ice-binding-mechanisms-hyperactive-antifreeze-1