King G

References (2)

Title : Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea - Parkin_2014_Genome.Biol_15_R77
Author(s) : Parkin IA , Koh C , Tang H , Robinson SJ , Kagale S , Clarke WE , Town CD , Nixon J , Krishnakumar V , Bidwell SL , Denoeud F , Belcram H , Links MG , Just J , Clarke C , Bender T , Huebert T , Mason AS , Pires JC , Barker G , Moore J , Walley PG , Manoli S , Batley J , Edwards D , Nelson MN , Wang X , Paterson AH , King G , Bancroft I , Chalhoub B , Sharpe AG
Ref : Genome Biol , 15 :R77 , 2014
Abstract : BACKGROUND: Brassica oleracea is a valuable vegetable species that has contributed to human health and nutrition for hundreds of years and comprises multiple distinct cultivar groups with diverse morphological and phytochemical attributes. In addition to this phenotypic wealth, B. oleracea offers unique insights into polyploid evolution, as it results from multiple ancestral polyploidy events and a final Brassiceae-specific triplication event. Further, B. oleracea represents one of the diploid genomes that formed the economically important allopolyploid oilseed, Brassica napus. A deeper understanding of B. oleracea genome architecture provides a foundation for crop improvement strategies throughout the Brassica genus.
RESULTS: We generate an assembly representing 75% of the predicted B. oleracea genome using a hybrid Illumina/Roche 454 approach. Two dense genetic maps are generated to anchor almost 92% of the assembled scaffolds to nine pseudo-chromosomes. Over 50,000 genes are annotated and 40% of the genome predicted to be repetitive, thus contributing to the increased genome size of B. oleracea compared to its close relative B. rapa. A snapshot of both the leaf transcriptome and methylome allows comparisons to be made across the triplicated sub-genomes, which resulted from the most recent Brassiceae-specific polyploidy event.
CONCLUSIONS: Differential expression of the triplicated syntelogs and cytosine methylation levels across the sub-genomes suggest residual marks of the genome dominance that led to the current genome architecture. Although cytosine methylation does not correlate with individual gene dominance, the independent methylation patterns of triplicated copies suggest epigenetic mechanisms play a role in the functional diversification of duplicate genes.
ESTHER : Parkin_2014_Genome.Biol_15_R77
PubMedSearch : Parkin_2014_Genome.Biol_15_R77
PubMedID: 24916971
Gene_locus related to this paper: braol-a0a0d3dpb2 , braol-a0a0d3dx76 , brana-a0a078jxa8 , brana-a0a078i2k3 , braol-a0a0d3ef55 , braol-a0a0d3bur9 , braol-a0a0d3ck99 , braol-a0a0d3cns1 , braol-a0a0d3e654 , brana-a0a078i6d2 , braol-a0a0d3a922

Title : Altered acyl chain length specificity of Rhizopus delemar lipase through mutagenesis and molecular modeling - Klein_1997_Lipids_32_123
Author(s) : Klein RR , King G , Moreau RA , Haas MJ
Ref : Lipids , 32 :123 , 1997
Abstract : The acyl binding site of Rhizopus delemar prolipase and mature lipase was altered through site-directed mutagenesis to improve lipase specificity for short- or medium-chain length fatty acids. Computer-generated structural models of R. delemar lipase were used in mutant protein design and in the interpretation of the catalytic properties of the resulting recombinant enzymes. Molecular dynamics simulations of the double mutant, val209trp + phe112trp, predicted that the introduction of trp112 and trp209 in the acyl binding groove would sterically hinder the docking of fatty acids longer than butyric acid. Assayed against a mixture of triacylglycerol substrates, the val209trp + phe112trp mature lipase mutant showed an 80-fold increase in the hydrolysis of tributyrin relative to the hydrolysis of tricaprylin while no triolein hydrolysis was detected. By comparison, the val94Trp mutant, predicted to pose steric or geometric constraints for docking fatty acids longer than caprylic acid in the acyl binding groove, resulted in a modest 1.4-fold increase in tricaprylin hydrolysis relative to the hydrolysis of tributyrin. Molecular models of the double mutant phe95asp + phe214arg indicated the creation of a salt bridge between asp95 and arg214 across the distal end of the acyl binding groove. When challenged with a mixture of triacylglycerols, the phe95asp + phe214arg substitutions resulted in an enzyme with 3-fold enhanced relative activity for tricaprylin compared to triolein, suggesting that structural determinants for medium-chain length specificity may reside in the distal end of the acyl binding groove. Attempts to introduce a salt bridge within 8 A of the active site by the double mutation leu146lys + ser115asp destroyed catalytic activity entirely. Similarly, the substitution of polar Gln at the rim of the acyl binding groove for phe112 largely eliminated catalytic activity of the lipase.
ESTHER : Klein_1997_Lipids_32_123
PubMedSearch : Klein_1997_Lipids_32_123
PubMedID: 9075201