Nelson BA

References (2)

Title : Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species - Rey_2004_Genome.Biol_5_R77
Author(s) : Rey MW , Ramaiya P , Nelson BA , Brody-Karpin SD , Zaretsky EJ , Tang M , Lopez de Leon A , Xiang H , Gusti V , Clausen IG , Olsen PB , Rasmussen MD , Andersen JT , Jorgensen PL , Larsen TS , Sorokin A , Bolotin A , Lapidus A , Galleron N , Ehrlich SD , Berka RM
Ref : Genome Biol , 5 :R77 , 2004
Abstract : BACKGROUND: Bacillus licheniformis is a Gram-positive, spore-forming soil bacterium that is used in the biotechnology industry to manufacture enzymes, antibiotics, biochemicals and consumer products. This species is closely related to the well studied model organism Bacillus subtilis, and produces an assortment of extracellular enzymes that may contribute to nutrient cycling in nature.
RESULTS: We determined the complete nucleotide sequence of the B. licheniformis ATCC 14580 genome which comprises a circular chromosome of 4,222,336 base-pairs (bp) containing 4,208 predicted protein-coding genes with an average size of 873 bp, seven rRNA operons, and 72 tRNA genes. The B. licheniformis chromosome contains large regions that are colinear with the genomes of B. subtilis and Bacillus halodurans, and approximately 80% of the predicted B. licheniformis coding sequences have B. subtilis orthologs.
CONCLUSIONS: Despite the unmistakable organizational similarities between the B. licheniformis and B. subtilis genomes, there are notable differences in the numbers and locations of prophages, transposable elements and a number of extracellular enzymes and secondary metabolic pathway operons that distinguish these species. Differences include a region of more than 80 kilobases (kb) that comprises a cluster of polyketide synthase genes and a second operon of 38 kb encoding plipastatin synthase enzymes that are absent in the B. licheniformis genome. The availability of a completed genome sequence for B. licheniformis should facilitate the design and construction of improved industrial strains and allow for comparative genomics and evolutionary studies within this group of Bacillaceae.
ESTHER : Rey_2004_Genome.Biol_5_R77
PubMedSearch : Rey_2004_Genome.Biol_5_R77
PubMedID: 15461803
Gene_locus related to this paper: bacld-q62u01 , bacld-Q65L73 , bacld-q62yz9 , bacld-q65dz7 , bacld-q65e02 , bacld-q65eq1 , bacld-q65fc5 , bacld-q65fg2 , bacld-q65fg3 , bacld-q65fk9 , bacld-q65ft3 , bacld-q65fw3 , bacld-q65fy2 , bacld-q65gx2 , bacld-q65hn8 , bacld-q65hr4 , bacld-q65if8 , bacld-q65iy4 , bacld-q65j72 , bacld-q65le0 , bacld-q65ly2 , bacld-q65m29 , bacld-q65mg8 , bacld-q65my7 , bacld-q65n63 , bacld-q65nk2 , bacld-q65nm7 , bacli-LICC

Title : The catalytic cysteine and histidine in the plant acyl-acyl carrier protein thioesterases - Yuan_1996_J.Biol.Chem_271_3417
Author(s) : Yuan L , Nelson BA , Caryl G
Ref : Journal of Biological Chemistry , 271 :3417 , 1996
Abstract : The plant acyl-acyl carrier protein (acyl-ACP) thioesterases (TEs) play an essential role in chain termination during de novo fatty acid synthesis and are of biochemical interest because of their utilities in the genetic engineering of plant seed oils. Biochemical data have shown the possible involvement of an active-site cysteine and a histidine in catalysis, suggesting that these enzymes activate the hydrolysis of the thioester bond using the same basic catalytic machinery as those of proteases and lipases. To identify the cysteine and histidine residues that are critical in catalysis we substituted, in a 12:0 ACP TE (Uc FatB1), a conserved cysteine (Cys-320) to an Ala or a Ser, and three conserved histidines (His-140, His-285, and His-345) to an Ala or an Arg. Each Ala mutation caused a substantial loss of enzyme activity. However, only C320A and H285A completely inactivated the enzyme, indicating that these two residues are essential for catalysis. Considerable activity (>60%) still remained when Cys-320 was converted to a Ser, but this mutant (C320S) displayed a reversed sensitivity toward thiol or serine hydroxyl inhibitors compared with the wild-type enzyme. A pH optimal study demonstrates that while the wild-type enzyme has the highest activity between pH 8.5 and 9.5, the mutant H285A shows a shifted optimum to higher pH and a significant increase of activity around pH 12. This result suggests that Arg-285 (pKa 12) is deprotonated at high pH, thus partially mimicking the role of His-285 for proton abstraction in the wild-type enzyme. We conclude that the Cys-320 of the wild-type enzyme and Ser-320 of the mutant enzyme can attack the thioester bond of the substrate 12:0 ACP, assisted by His-285. Because plant TEs are highly conserved in length and sequence and the residues investigated here are completely conserved in all available TEs, it is reasonable to believe that homologues of Cys-320 and His-285 are present in the active sites of all plant acyl-ACP TEs.
ESTHER : Yuan_1996_J.Biol.Chem_271_3417
PubMedSearch : Yuan_1996_J.Biol.Chem_271_3417
PubMedID: 8631942