Wan K

References (8)

Title : Loop of Streptomyces Feruloyl Esterase Plays an Important Role in the Enzyme's Catalyzing the Release of Ferulic Acid from Biomass - Uraji_2018_Appl.Environ.Microbiol_84_
Author(s) : Uraji M , Tamura H , Mizohata E , Arima J , Wan K , Ogawa K , Inoue T , Hatanaka T
Ref : Applied Environmental Microbiology , 84 : , 2018
Abstract : Feruloyl esterases (FAEs) are key enzymes required for the production of ferulic acid from agricultural biomass. Previously, we identified and characterized R18, an FAE from Streptomyces cinnamoneus NBRC 12852, which showed no sequence similarity to the known FAEs. To determine the region involved in its catalytic activity, we constructed chimeric enzymes using R18 and its homolog (TH2-18) from S. cinnamoneus strain TH-2. Although R18 and TH2-18 showed 74% identity in their primary sequences, the recombinant proteins of these two FAEs (recombinant R18 [rR18] and rTH2-18) showed very different specific activities toward ethyl ferulate. By comparing the catalytic activities of the chimeras, a domain comprised of residues 140 to 154 was found to be crucial for the catalytic activity of R18. Furthermore, we analyzed the crystal structure of rR18 at a resolution of 1.5 A to elucidate the relationship between its activity and its structure. rR18 possessed a typical catalytic triad, consisting of Ser-191, Asp-214, and His-268, which was characteristic of the serine esterase family. By structural analysis, the above-described domain was found to be present in a loop-like structure (the R18 loop), which possessed a disulfide bond conserved in the genus Streptomyces Moreover, compared to rTH2-18 of its parental strain, the TH2-18 mutant, in which Pro and Gly residues were inserted into the domain responsible for forming the R18 loop, showed markedly high kcat values using artificial substrates. We also showed that the FAE activity of TH2-18 toward corn bran, a natural substrate, was improved by the insertion of the Gly and Pro residues.IMPORTANCEStreptomyces species are widely distributed bacteria that are predominantly present in soil and function as decomposers in natural environments. They produce various enzymes, such as carbohydrate hydrolases, esterases, and peptidases, which decompose agricultural biomass. In this study, based on the genetic information on two Streptomyces cinnamoneus strains, we identified novel feruloyl esterases (FAEs) capable of producing ferulic acid from biomass. These two FAEs shared high similarity in their amino acid sequences but did not resemblance any known FAEs. By comparing chimeric proteins and performing crystal structure analysis, we confirmed that a flexible loop was important for the catalytic activity of Streptomyces FAEs. Furthermore, we determined that the catalytic activity of one FAE was improved drastically by inserting only 2 amino acids into its loop-forming domain. Thus, differences in the amino acid sequence of the loop resulted in different catalytic activities. In conclusion, our findings provide a foundation for the development of novel enzymes for industrial use.
ESTHER : Uraji_2018_Appl.Environ.Microbiol_84_
PubMedSearch : Uraji_2018_Appl.Environ.Microbiol_84_
PubMedID: 29150515
Gene_locus related to this paper: strcj-estA

Title : Whole-genome sequences of four Mycobacterium bovis BCG vaccine strains - Pan_2011_J.Bacteriol_193_3152
Author(s) : Pan Y , Yang X , Duan J , Lu N , Leung AS , Tran V , Hu Y , Wu N , Liu D , Wang Z , Yu X , Chen C , Zhang Y , Wan K , Liu J , Zhu B
Ref : Journal of Bacteriology , 193 :3152 , 2011
Abstract : Mycobacterium bovis Bacille Calmette-Guerin (BCG) is the only vaccine available against tuberculosis (TB). A number of BCG strains are in use, and they exhibit biochemical and genetic differences. We report the genome sequences of four BCG strains representing different lineages, which will help to design more effective TB vaccines.
ESTHER : Pan_2011_J.Bacteriol_193_3152
PubMedSearch : Pan_2011_J.Bacteriol_193_3152
PubMedID: 21478353
Gene_locus related to this paper: myctu-RV1215C

Title : Complete genome sequences of Mycobacterium tuberculosis strains CCDC5079 and CCDC5080, which belong to the Beijing family - Zhang_2011_J.Bacteriol_193_5591
Author(s) : Zhang Y , Chen C , Liu J , Deng H , Pan A , Zhang L , Zhao X , Huang M , Lu B , Dong H , Du P , Chen W , Wan K
Ref : Journal of Bacteriology , 193 :5591 , 2011
Abstract : Mycobacterium tuberculosis is one of most prevalent pathogens in the world. Drug-resistant strains of this pathogen caused by the excessive use of antibiotics have long posed serious threats to public health worldwide. A broader picture of drug resistance mechanisms at the genomic level can be obtained only with large-scale comparative genomic methodology. Two closely related Beijing family isolates, one resistant to four first-line drugs (CCDC5180) and one sensitive to them (CCDC5079), were completely sequenced. These sequences will serve as valuable references for further drug resistance site identification studies and could be of great importance for developing drugs targeting these sites.
ESTHER : Zhang_2011_J.Bacteriol_193_5591
PubMedSearch : Zhang_2011_J.Bacteriol_193_5591
PubMedID: 21914894
Gene_locus related to this paper: myctu-cut3 , myctu-cutas1 , myctu-cutas2 , myctu-Rv0160c , myctu-Rv1069c , myctu-RV1215C , myctu-Rv2045c , myctu-RV3452 , myctu-RV3724 , myctu-Rv3802c , myctu-y0571

Title : A Drosophila full-length cDNA resource - Stapleton_2002_Genome.Biol_3_RESEARCH0080
Author(s) : Stapleton M , Carlson J , Brokstein P , Yu C , Champe M , George R , Guarin H , Kronmiller B , Pacleb J , Park S , Wan K , Rubin GM , Celniker SE
Ref : Genome Biol , 3 :RESEARCH0080 , 2002
Abstract : BACKGROUND: A collection of sequenced full-length cDNAs is an important resource both for functional genomics studies and for the determination of the intron-exon structure of genes. Providing this resource to the Drosophila melanogaster research community has been a long-term goal of the Berkeley Drosophila Genome Project. We have previously described the Drosophila Gene Collection (DGC), a set of putative full-length cDNAs that was produced by generating and analyzing over 250,000 expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages.
RESULTS: We have generated high-quality full-insert sequence for 8,921 clones in the DGC. We compared the sequence of these clones to the annotated Release 3 genomic sequence, and identified more than 5,300 cDNAs that contain a complete and accurate protein-coding sequence. This corresponds to at least one splice form for 40% of the predicted D. melanogaster genes. We also identified potential new cases of RNA editing.
CONCLUSIONS: We show that comparison of cDNA sequences to a high-quality annotated genomic sequence is an effective approach to identifying and eliminating defective clones from a cDNA collection and ensure its utility for experimentation. Clones were eliminated either because they carry single nucleotide discrepancies, which most probably result from reverse transcriptase errors, or because they are truncated and contain only part of the protein-coding sequence.
ESTHER : Stapleton_2002_Genome.Biol_3_RESEARCH0080
PubMedSearch : Stapleton_2002_Genome.Biol_3_RESEARCH0080
PubMedID: 12537569
Gene_locus related to this paper: drome-KRAKEN

Title : Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome - Bergman_2002_Genome.Biol_3_RESEARCH0086
Author(s) : Bergman CM , Pfeiffer BD , Rincon-Limas DE , Hoskins RA , Gnirke A , Mungall CJ , Wang AM , Kronmiller B , Pacleb J , Park S , Stapleton M , Wan K , George RA , de Jong PJ , Botas J , Rubin GM , Celniker SE
Ref : Genome Biol , 3 :RESEARCH0086 , 2002
Abstract : BACKGROUND: It is widely accepted that comparative sequence data can aid the functional annotation of genome sequences; however, the most informative species and features of genome evolution for comparison remain to be determined.
RESULTS: We analyzed conservation in eight genomic regions (apterous, even-skipped, fushi tarazu, twist, and Rhodopsins 1, 2, 3 and 4) from four Drosophila species (D. erecta, D. pseudoobscura, D. willistoni, and D. littoralis) covering more than 500 kb of the D. melanogaster genome. All D. melanogaster genes (and 78-82% of coding exons) identified in divergent species such as D. pseudoobscura show evidence of functional constraint. Addition of a third species can reveal functional constraint in otherwise non-significant pairwise exon comparisons. Microsynteny is largely conserved, with rearrangement breakpoints, novel transposable element insertions, and gene transpositions occurring in similar numbers. Rates of amino-acid substitution are higher in uncharacterized genes relative to genes that have previously been studied. Conserved non-coding sequences (CNCSs) tend to be spatially clustered with conserved spacing between CNCSs, and clusters of CNCSs can be used to predict enhancer sequences.
CONCLUSIONS: Our results provide the basis for choosing species whose genome sequences would be most useful in aiding the functional annotation of coding and cis-regulatory sequences in Drosophila. Furthermore, this work shows how decoding the spatial organization of conserved sequences, such as the clustering of CNCSs, can complement efforts to annotate eukaryotic genomes on the basis of sequence conservation alone.
ESTHER : Bergman_2002_Genome.Biol_3_RESEARCH0086
PubMedSearch : Bergman_2002_Genome.Biol_3_RESEARCH0086
PubMedID: 12537575
Gene_locus related to this paper: drops-CG4390 , drowi-b4ngb5 , droya-q71d76

Title : Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence - Celniker_2002_Genome.Biol_3_RESEARCH0079
Author(s) : Celniker SE , Wheeler DA , Kronmiller B , Carlson JW , Halpern A , Patel S , Adams M , Champe M , Dugan SP , Frise E , Hodgson A , George RA , Hoskins RA , Laverty T , Muzny DM , Nelson CR , Pacleb JM , Park S , Pfeiffer BD , Richards S , Sodergren EJ , Svirskas R , Tabor PE , Wan K , Stapleton M , Sutton GG , Venter C , Weinstock G , Scherer SE , Myers EW , Gibbs RA , Rubin GM
Ref : Genome Biol , 3 :RESEARCH0079 , 2002
Abstract : BACKGROUND: The Drosophila melanogaster genome was the first metazoan genome to have been sequenced by the whole-genome shotgun (WGS) method. Two issues relating to this achievement were widely debated in the genomics community: how correct is the sequence with respect to base-pair (bp) accuracy and frequency of assembly errors? And, how difficult is it to bring a WGS sequence to the accepted standard for finished sequence? We are now in a position to answer these questions.
RESULTS: Our finishing process was designed to close gaps, improve sequence quality and validate the assembly. Sequence traces derived from the WGS and draft sequencing of individual bacterial artificial chromosomes (BACs) were assembled into BAC-sized segments. These segments were brought to high quality, and then joined to constitute the sequence of each chromosome arm. Overall assembly was verified by comparison to a physical map of fingerprinted BAC clones. In the current version of the 116.9 Mb euchromatic genome, called Release 3, the six euchromatic chromosome arms are represented by 13 scaffolds with a total of 37 sequence gaps. We compared Release 3 to Release 2; in autosomal regions of unique sequence, the error rate of Release 2 was one in 20,000 bp.
CONCLUSIONS: The WGS strategy can efficiently produce a high-quality sequence of a metazoan genome while generating the reagents required for sequence finishing. However, the initial method of repeat assembly was flawed. The sequence we report here, Release 3, is a reliable resource for molecular genetic experimentation and computational analysis.
ESTHER : Celniker_2002_Genome.Biol_3_RESEARCH0079
PubMedSearch : Celniker_2002_Genome.Biol_3_RESEARCH0079
PubMedID: 12537568
Gene_locus related to this paper: drome-CG8058 , drome-CG9542 , drome-CG11309 , drome-CG11406 , drome-CG17097 , drome-CG17374 , drome-glita , drome-KRAKEN

Title : Enzyme-octadecylamine Langmuir-Blodgett membranes for ENFET biosensors - Wan_2000_Talanta_52_663
Author(s) : Wan K , Chovelon JM , Jaffrezic-Renault N
Ref : Talanta , 52 :663 , 2000
Abstract : Langmuir-Blodgett (LB) films containing butyrylcholinesterase (BuChE) are fabricated to realise an enzymatic field effect transistor (ENFET) for the detection of organophosphorus pesticides in water. Trichlorfon as a common pesticide is examined in our work. The BuChE-immobilised LB films are formed by adsorbing the enzyme molecules onto a stearylamine monolayer using the electrostatic force. Enzyme/stearylamine mixed LB films are immobilized onto a pH-ISFET surface and treated by glutaraldehyde vapour to improve the LB film's stability. The ENFET thus obtained worked as a potentiometric biosensor for trichlorfon detection on the basis of enzyme inhibition. The detection limit for trichlorfon can reach 10(-7) M (26 ppb). The surface characteristics of BuChE/stearylamine LB films obtained under various conditions of the dipping surface pressures are analysed qualitatively by atomic force microscopy (AFM) and analysed quantitatively by FTIR spectroscopy.
ESTHER : Wan_2000_Talanta_52_663
PubMedSearch : Wan_2000_Talanta_52_663
PubMedID: 18968024

Title : An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster: the Adh region - Ashburner_1999_Genetics_153_179
Author(s) : Ashburner M , Misra S , Roote J , Lewis SE , Blazej R , Davis T , Doyle C , Galle R , George R , Harris N , Hartzell G , Harvey D , Hong L , Houston K , Hoskins R , Johnson G , Martin C , Moshrefi A , Palazzolo M , Reese MG , Spradling A , Tsang G , Wan K , Whitelaw K , Celniker S , Rubin GM
Ref : Genetics , 153 :179 , 1999
Abstract : A contiguous sequence of nearly 3 Mb from the genome of Drosophila melanogaster has been sequenced from a series of overlapping P1 and BAC clones. This region covers 69 chromosome polytene bands on chromosome arm 2L, including the genetically well-characterized "Adh region." A computational analysis of the sequence predicts 218 protein-coding genes, 11 tRNAs, and 17 transposable element sequences. At least 38 of the protein-coding genes are arranged in clusters of from 2 to 6 closely related genes, suggesting extensive tandem duplication. The gene density is one protein-coding gene every 13 kb; the transposable element density is one element every 171 kb. Of 73 genes in this region identified by genetic analysis, 49 have been located on the sequence; P-element insertions have been mapped to 43 genes. Ninety-five (44%) of the known and predicted genes match a Drosophila EST, and 144 (66%) have clear similarities to proteins in other organisms. Genes known to have mutant phenotypes are more likely to be represented in cDNA libraries, and far more likely to have products similar to proteins of other organisms, than are genes with no known mutant phenotype. Over 650 chromosome aberration breakpoints map to this chromosome region, and their nonrandom distribution on the genetic map reflects variation in gene spacing on the DNA. This is the first large-scale analysis of the genome of D. melanogaster at the sequence level. In addition to the direct results obtained, this analysis has allowed us to develop and test methods that will be needed to interpret the complete sequence of the genome of this species. Before beginning a Hunt, it is wise to ask someone what you are looking for before you begin looking for it. Milne 1926
ESTHER : Ashburner_1999_Genetics_153_179
PubMedSearch : Ashburner_1999_Genetics_153_179
PubMedID: 10471707