Displaying publications 1 - 20 of 35 in total

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  1. See-Too WS, Ee R, Lim YL, Convey P, Pearce DA, Yin WF, et al.
    Sci Rep, 2017 02 22;7:42968.
    PMID: 28225085 DOI: 10.1038/srep42968
    Planococcus is a Gram-positive halotolerant bacterial genus in the phylum Firmicutes, commonly found in various habitats in Antarctica. Quorum quenching (QQ) is the disruption of bacterial cell-to-cell communication (known as quorum sensing), which has previously been described in mesophilic bacteria. This study demonstrated the QQ activity of a psychrotolerant strain, Planococcus versutus strain L10.15T, isolated from a soil sample obtained near an elephant seal wallow in Antarctica. Whole genome analysis of this bacterial strain revealed the presence of an N-acyl homoserine lactonase, an enzyme that hydrolyzes the ester bond of the homoserine lactone of N-acyl homoserine lactone (AHLs). Heterologous gene expression in E. coli confirmed its functions for hydrolysis of AHLs, and the gene was designated as aidP (autoinducer degrading gene from Planococcus sp.). The low temperature activity of this enzyme suggested that it is a novel and uncharacterized class of AHL lactonase. This study is the first report on QQ activity of bacteria isolated from the polar regions.
  2. Ee R, Madhaiyan M, Ji L, Lim YL, Nor NM, Tee KK, et al.
    Int J Syst Evol Microbiol, 2016 Jun;66(6):2297-2304.
    PMID: 26978486 DOI: 10.1099/ijsem.0.001025
    Phylogenetic and taxonomic characterization was performed for bacterium RB-25T, which was isolated from a soil sample collected in a former municipal landfill site in Puchong, Malaysia. Growth occurred at 20-37 °C at pH 5-8 but not in the presence of 9 % (w/v) NaCl or higher. The principal fatty acids were C16:0, C18:1ω7c and summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH). Ubiquinone-8 was the only isoprenoid quinone detected. Polar lipid analysis revealed the presence of phospholipid, phosphoaminolipid, phosphatidylethanolamine, phosphatidylglycerol and one unidentified aminolipid. DNA G+C content was 50.9 mol% phylogenetic analysis based on 16S rRNA gene sequence showed that strain RB-25T formed a distinct lineage within the family Enterobacteriaceae of the class Gammaproteobacteria. It exhibited a low level of 16S rRNA gene sequence similarity with its phylogenetic neighbours Pantoea rwandensis LMG 26275T (96.6 %), Rahnella aquatilis CIP 78.65T (96.5 %), Pectobacterium betavasculorum ATCC 43762T (96.4 %), Pantoea rodasii LMG 26273T (96.3 %), Gibbsiella dentisursi NUM 1720T (96.3 %) and Serratia glossinae C1T (96.2 %). Multilocus sequence analyses based on fusA, pyrG, rplB, rpoB and sucA sequences showed a clear distinction of strain RB-25T from the most closely related genera. Isolate RB-25T could also be distinguished from members of these genera by a combination of the DNA G+C content, respiratory quinone system, fatty acid profile, polar lipid composition and other phenotypic features. Strain RB-25T represents a novel species of a new genus, for which the name Chaniamultitudinisentens gen. nov., sp. nov. is proposed. The type strain is RB-25T (=DSM 28811T=LMG 28304T).
  3. Yaakop AS, Chan KG, Ee R, Lim YL, Lee SK, Manan FA, et al.
    Sci Rep, 2016 09 19;6:33660.
    PMID: 27641516 DOI: 10.1038/srep33660
    Jeotgalibacillus malaysiensis, a moderate halophilic bacterium isolated from a pelagic area, can endure higher concentrations of sodium chloride (NaCl) than other Jeotgalibacillus type strains. In this study, we therefore chose to sequence and assemble the entire J. malaysiensis genome. This is the first report to provide a detailed analysis of the genomic features of J. malaysiensis, and to perform genetic comparisons between this microorganism and other halophiles. J. malaysiensis encodes a native megaplasmid (pJeoMA), which is greater than 600 kilobases in size, that is absent from other sequenced species of Jeotgalibacillus. Subsequently, RNA-Seq-based transcriptome analysis was utilised to examine adaptations of J. malaysiensis to osmotic stress. Specifically, the eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) and KEGG (Kyoto Encyclopaedia of Genes and Genomes) databases were used to elucidate the overall effects of osmotic stress on the organism. Generally, saline stress significantly affected carbohydrate, energy, and amino acid metabolism, as well as fatty acid biosynthesis. Our findings also indicate that J. malaysiensis adopted a combination of approaches, including the uptake or synthesis of osmoprotectants, for surviving salt stress. Among these, proline synthesis appeared to be the preferred method for withstanding prolonged osmotic stress in J. malaysiensis.
  4. Lim YL, Roberts RJ, Ee R, Yin WF, Chan KG
    Genome Announc, 2016 Mar 03;4(2).
    PMID: 26941143 DOI: 10.1128/genomeA.00060-16
    In this report, we announce the complete genome sequence of Aeromonas hydrophila strain YL17. Single-molecule real-time (SMRT) DNA sequencing was used to generate the complete genome sequence and the genome-wide DNA methylation profile of this environmental isolate. A total of five unique DNA methyltransferase recognition motifs were reported here.
  5. Chan KG, Yin WF, Lim YL
    Genome Announc, 2014;2(2).
    PMID: 24699957 DOI: 10.1128/genomeA.00246-14
    Here, we report the complete genome sequence of Pseudomonas aeruginosa strain YL84, which was isolated from compost. This strain was found to be a chitinase-producing quorum-sensing bacterium.
  6. See-Too WS, Ee R, Lim YL, Convey P, Pearce DA, Mohidin TBM, et al.
    Stand Genomic Sci, 2017;12:52.
    PMID: 28904741 DOI: 10.1186/s40793-017-0264-0
    Arthrobacter alpinus R3.8 is a psychrotolerant bacterial strain isolated from a soil sample obtained at Rothera Point, Adelaide Island, close to the Antarctic Peninsula. Strain R3.8 was sequenced in order to help discover potential cold active enzymes with biotechnological applications. Genome analysis identified various cold adaptation genes including some coding for anti-freeze proteins and cold-shock proteins, genes involved in bioremediation of xenobiotic compounds including naphthalene, and genes with chitinolytic and N-acetylglucosamine utilization properties and also plant-growth-influencing properties. In this genome report, we present a complete genome sequence of A. alpinus strain R3.8 and its annotation data, which will facilitate exploitation of potential novel cold-active enzymes.
  7. Lim YL, Ee R, Yong D, Tee KK, Yin WF, Chan KG
    J Biotechnol, 2015 Nov 20;214:83-4.
    PMID: 26393955 DOI: 10.1016/j.jbiotec.2015.09.018
    Pandoraea pnomenusa RB-38 is a bacterium isolated from a former sanitary landfill site. Here, we present the complete genome of P. pnomenusa RB38 in which an oxalate utilization pathway was identified. The genome analysis suggested the potential of this strain as an effective biocontrol agent against oxalate-producing phytopathogens.
  8. See-Too WS, Convey P, Pearce DA, Lim YL, Ee R, Yin WF, et al.
    J Biotechnol, 2016 Mar 10;221:114-5.
    PMID: 26808870 DOI: 10.1016/j.jbiotec.2016.01.026
    Planococcus rifietoensis M8(T) (=DSM 15069(T)=ATCC BAA-790(T)) is a halotolerant bacterium with potential plant growth promoting properties isolated from an algal mat collected from a sulfurous spring in Campania (Italy). This paper presents the first complete genome of P. rifietoensis M8(T). Genes coding for various potentially plant growth promoting properties were identified within its genome.
  9. See-Too WS, Lim YL, Ee R, Convey P, Pearce DA, Yin WF, et al.
    J Biotechnol, 2016 Mar 20;222:84-5.
    PMID: 26876481 DOI: 10.1016/j.jbiotec.2016.02.017
    Pseudomonas sp. strain L10.10 (=DSM 101070) is a psychrotolerant bacterium which was isolated from Lagoon Island, Antarctica. Analysis of its complete genome sequence indicates its possible role as a plant-growth promoting bacterium, including nitrogen-fixing ability and indole acetic acid (IAA)-producing trait, with additional suggestion of plant disease prevention attributes via hydrogen cyanide production.
  10. Lim YL, Chan KG, Ee R, Belduz AO, Canakci S, Kahar UM, et al.
    J Biotechnol, 2015 Oct 20;212:65-6.
    PMID: 26297905 DOI: 10.1016/j.jbiotec.2015.08.007
    Anoxybacillus gonensis type strain G2(T) (=NCIMB 13,933(T) =NCCB 100040(T)) has been isolated from the Gönen hot springs in Turkey. This strain produces a number of well-studied, biotechnologically important enzymes, including xylose isomerase, carboxylesterase, and fructose-1,6-bisphosphate aldolase. In addition, this strain is an excellent candidate for the bioremediation of areas with heavy metal pollution. Here, we present a high-quality, annotated, complete genome of A. gonensis G2(T). Furthermore, this report provides insights into several novel enzymes of strain G2(T) and their potential industrial applications.
  11. Chan KG, Yong D, Ee R, Lim YL, Yu CY, Tee KK, et al.
    J Biotechnol, 2016 Feb 10;219:124-5.
    PMID: 26742625 DOI: 10.1016/j.jbiotec.2015.12.037
    Pandoraea oxalativorans DSM 23570(T) is an oxalate-degrading bacterium that was originally isolated from soil litter near to oxalate-producing plant of the genus Oxalis. Here, we report the first complete genome of P. oxalativorans DSM 23570(T) which would allow its potential biotechnological applications to be unravelled.
  12. Yong D, Ee R, Lim YL, Yu CY, Ang GY, How KY, et al.
    J Biotechnol, 2016 Jan 10;217:51-2.
    PMID: 26603120 DOI: 10.1016/j.jbiotec.2015.11.009
    Pandoraea thiooxydans DSM 25325(T) is a thiosulfate-oxidizing bacterium isolated from rhizosphere soils of a sesame plant. Here, we present the first complete genome of P. thiooxydans DSM 25325(T). Several genes involved in thiosulfate oxidation and biodegradation of aromatic compounds were identified.
  13. See-Too WS, Chua KO, Lim YL, Chen JW, Convey P, Mohd Mohidin TB, et al.
    J Biotechnol, 2017 Jun 20;252:11-14.
    PMID: 28483443 DOI: 10.1016/j.jbiotec.2017.05.005
    The type strain Planococcus donghaensis JH1Tis a psychrotolerant and halotolerant bacterium with starch-degrading ability. Here, we determine the carbon utilization profile of P. donghaensis JH1Tand report the first complete genome of the strain. This study revealed the strain's ability to utilize pectin and d-galacturonic acid, and identified genes responsible for degradation of the polysaccharides. The genomic information provided may serve as a fundamental resource for full exploration of the biotechnological potential of P. donghaensis JH1T.
  14. Lim YL, Yong D, Ee R, Krishnan T, Tee KK, Yin WF, et al.
    J Biotechnol, 2015 Nov 20;214:43-4.
    PMID: 26376471 DOI: 10.1016/j.jbiotec.2015.09.005
    Here, we present the first complete genome sequence of Serratia fonticola DSM 4576(T), a potential plant growth promoting (PGP) bacterium which confers solubilization of inorganic phosphate, indole-3-acetic acid production, hydrogen cyanideproduction, siderophore production and assimilation of ammonia through the glutamate synthase (GS/GOGAT) pathway. This genome sequence is valuable for functional genomics and ecological studies which are related to PGP and biocontrol activities.
  15. Lim YL, Yong D, Ee R, Tee KK, Yin WF, Chan KG
    J Biotechnol, 2015 Aug 10;207:32-3.
    PMID: 25975625 DOI: 10.1016/j.jbiotec.2015.04.027
    Serratia multitudinisentens RB-25(T) (=DSM 28811(T) =LMG 28304(T)) is a newly proposed type strain in the genus of Serratia isolated from a municipal landfill site. Here, we present the complete genome of S. multitudinisentens RB-25(T) which contains a complete chitinase operon and other chitin and N-acetylglucosamine utilisation enzymes. To our knowledge, this is the first report of the complete genome sequence of this novel isolate and its chitinase gene discovery.
  16. Ee R, Yong D, Lim YL, Yin WF, Chan KG
    J Biotechnol, 2015 Jun 20;204:5-6.
    PMID: 25848988 DOI: 10.1016/j.jbiotec.2015.03.020
    Pandoraea vervacti DSM 23571(T) is an oxalate metabolizing bacterium isolated from an uncultivated field soil in Mugla, Turkey. Here, we present the first complete genome sequence of P. vervacti DSM 23571(T). A complete pathway for degradation of oxalate was revealed from the genome analysis. These data are important to path new opportunities for genetic engineering in the field of biotechnology.
  17. Lim YL, Ee R, How KY, Lee SK, Yong D, Tee KK, et al.
    PeerJ, 2015;3:e1225.
    PMID: 26336650 DOI: 10.7717/peerj.1225
    In this study, we sequenced the genome of Pandoraea pnomenusa RB38 using Pacific Biosciences RSII (PacBio) Single Molecule Real Time (SMRT) sequencing technology. A pair of cognate luxI/R homologs was identified where the luxI homolog, ppnI, was found adjacent to a luxR homolog, ppnR1. An additional orphan luxR homolog, ppnR2, was also discovered. Multiple sequence alignment and phylogenetic analysis revealed that ppnI is an N-acyl homoserine lactone (AHL) synthase gene that is distinct from those of the nearest phylogenetic neighbor viz. Burkholderia spp. High resolution tandem mass spectrometry (LC-MS/MS) analysis showed that Escherichia coli BL21 harboring ppnI produced a similar AHL profile (N-octanoylhomoserine lactone, C8-HSL) as P. pnomenusa RB38, the wild-type donor strain, confirming that PpnI directed the synthesis of AHL in P. pnomenusa RB38. To our knowledge, this is the first documentation of the luxI/R homologs of the genus Pandoraea.
  18. Ee R, Lim YL, Yin WF, Chan KG
    Genome Announc, 2014;2(2).
    PMID: 24699956 DOI: 10.1128/genomeA.00245-14
    We report the first complete genome sequence of Pandoraea sp. strain RB-44, which was found to possess quorum-sensing properties. To the best of our knowledge, this is the first documentation of both a complete genome sequence and quorum-sensing properties of a Pandoraea species.
  19. See-Too WS, Tan JY, Ee R, Lim YL, Convey P, Pearce DA, et al.
    Mar Genomics, 2016 Apr 22.
    PMID: 27117861 DOI: 10.1016/j.margen.2016.04.007
    Planococcus kocurii ATCC 43650(T) is a halotolerant and psychrotolerant bacterium isolated from the skin of a North sea cod. Here, we present the first complete genome and annotation of P. kocurii ATCC 43650(T), identifying its potential as a plant growth promoting bacterium and its capability in the biosynthesis of butanol.
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