MyMedR

Fulltext Unravelling the genome of long chain N-acylhomoserine lactone-producing Acinetobacter sp. strain GG2 and identification of its quorum sensing synthase gene

How KY, Hong KW, Sam CK, Koh CL, Yin WF, Chan KG

Front Microbiol, 2015;6:240.

PMID: 25926817 DOI: 10.3389/fmicb.2015.00240

Myriad proteobacteria use N-acyl homoserine lactone (AHL) molecules as quorum sensing (QS) signals to regulate different physiological functions, including virulence, antibiotic production, and biofilm formation. Many of these proteobacteria possess LuxI/LuxR system as the QS mechanism. Recently, we reported the 3.89 Mb genome of Acinetobacter sp. strain GG2. In this work, the genome of this long chain AHL-producing bacterium was unravelled which led to the molecular characterization of luxI homologue, designated as aciI. This 552 bp gene was cloned and overexpressed in Escherichia coli BL21(DE3). The purified protein was ∼20.5 kDa and is highly similar to several autoinducer proteins of LuxI family among Acinetobacter species. To verify the AHL synthesis activity of this protein, high-resolution liquid chromatography-mass spectrometry analysis revealed the production of 3-oxo-dodecanoyl-homoserine lactone and 3-hydroxy-dodecanoyl-homoserine lactone from induced E. coli harboring the recombinant AciI. Our data show for the first time, the cloning and characterization of the luxI homologue from Acinetobacter sp. strain GG2, and confirmation of its AHLs production. These data are of great significance as the annotated genome of strain GG2 has provided a valuable insight in the study of autoinducer molecules and its roles in QS mechanism of the bacterium.

Streptomyces gilvigriseus sp. nov., a novel actinobacterium isolated from mangrove forest soil

Ser HL, Zainal N, Palanisamy UD, Goh BH, Yin WF, Chan KG, et al.

Antonie Van Leeuwenhoek, 2015 Jun;107(6):1369-78.

PMID: 25863667 DOI: 10.1007/s10482-015-0431-5

A novel Streptomyces, strain MUSC 26(T), was isolated from mangrove soil at Tanjung Lumpur, Malaysia. The bacterium was observed to be Gram-positive and to form grayish yellow aerial and substrate mycelium on ISP 7 agar. A polyphasic approach was used to study the taxonomy of strain MUSC 26(T), which shows a range of phylogenetic and chemotaxonomic properties consistent with those of the members of the genus Streptomyces. The cell wall peptidoglycan was determined to contain LL-diaminopimelic acid. The predominant menaquinones were identified as MK-9 (H8) and MK-9(H6). The polar lipids detected were identified as diphosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylmethylethanolamine and hydroxyphosphatidylmethylethanolamine. The predominant cellular fatty acids (>10.0 %) were identified as anteiso-C15:0 (31.4 %), iso-C16:0 (16.3 %), iso-C15:0 (13.9 %) and anteiso-C17:0 (12.6 %). The cell wall sugars were found to be galactose, glucose, mannose, ribose and rhamnose. These results suggest that MUSC 26(T) should be placed within the genus Streptomyces. Phylogenetic analysis indicated that closely related strains include Streptomyces qinglanensis 172205(T) (96.5 % sequence similarity), S. sodiiphilus YIM 80305(T) (96.5 %) and S. rimosus subsp. rimosus ATCC 10970(T) (96.4 %). DNA-DNA relatedness values between MUSC 26(T) and closely related type strains ranged from 17.0 ± 2.2 to 33.2 ± 5.3 %. Comparison of BOX-PCR fingerprints indicated MUSC 26(T) presents a unique DNA profile. The DNA G+C content was determined to be 74.6 mol%. Based on this polyphasic study of MUSC 26(T), it is concluded that this strain represents a novel species, for which the name Streptomyces gilvigriseus sp. nov. is proposed. The type strain is MUSC 26(T) (=DSMZ 42173(T) = MCCC 1K00504(T)).

Fulltext Draft Genome Sequence of Lysinibacillus sp. Strain A1, Isolated from Malaysian Tropical Soil

Chan KG, Chen JW, Chang CY, Yin WF, Chan XY

Genome Announc, 2015;3(2).

PMID: 25814592 DOI: 10.1128/genomeA.00095-15

In this work, we describe the genome of Lysinibacillus sp. strain A1, which was isolated from tropical soil. Analysis of its genome sequence shows the presence of a gene encoding for a putative peptidase responsible for nitrogen compounds.

Fulltext Analysis of Pectate Lyase Genes in Dickeya chrysanthemi Strain L11, Isolated from a Recreational Lake in Malaysia: a Draft Genome Sequence Perspective

Chan KG, Kher HL, Chang CY, Yin WF, Tan KH

Genome Announc, 2015;3(2).

PMID: 25792063 DOI: 10.1128/genomeA.00145-15

Dickeya chrysanthemi is well known as a plant pathogen that caused major blackleg in the European potato industry in the 1990s. D. chrysanthemi strain L11 was discovered in a recreational lake in Malaysia. Here, we present its draft genome sequence.

Fulltext Microbial diversity of thermophiles with biomass deconstruction potential in a foliage-rich hot spring

Lee LS, Goh KM, Chan CS, Annie Tan GY, Yin WF, Chong CS, et al.

Microbiologyopen, 2018 12;7(6):e00615.

PMID: 29602271 DOI: 10.1002/mbo3.615

The ability of thermophilic microorganisms and their enzymes to decompose biomass have attracted attention due to their quick reaction time, thermostability, and decreased risk of contamination. Exploitation of efficient thermostable glycoside hydrolases (GHs) could accelerate the industrialization of biofuels and biochemicals. However, the full spectrum of thermophiles and their enzymes that are important for biomass degradation at high temperatures have not yet been thoroughly studied. We examined a Malaysian Y-shaped Sungai Klah hot spring located within a wooded area. The fallen foliage that formed a thick layer of biomass bed under the heated water of the Y-shaped Sungai Klah hot spring was an ideal environment for the discovery and analysis of microbial biomass decay communities. We sequenced the hypervariable regions of bacterial and archaeal 16S rRNA genes using total community DNA extracted from the hot spring. Data suggested that 25 phyla, 58 classes, 110 orders, 171 families, and 328 genera inhabited this hot spring. Among the detected genera, members of Acidimicrobium, Aeropyrum, Caldilinea, Caldisphaera, Chloracidobacterium, Chloroflexus, Desulfurobacterium, Fervidobacterium, Geobacillus, Meiothermus, Melioribacter, Methanothermococcus, Methanotorris, Roseiflexus, Thermoanaerobacter, Thermoanaerobacterium, Thermoanaerobaculum, and Thermosipho were the main thermophiles containing various GHs that play an important role in cellulose and hemicellulose breakdown. Collectively, the results suggest that the microbial community in this hot spring represents a good source for isolating efficient biomass degrading thermophiles and thermozymes.

Fulltext In silico Analysis Reveals Distribution of Quorum Sensing Genes and Consistent Presence of LuxR Solos in the Pandoraea Species

Chua KO, See-Too WS, Ee R, Lim YL, Yin WF, Chan KG

Front Microbiol, 2019;10:1758.

PMID: 31447806 DOI: 10.3389/fmicb.2019.01758

The most common quorum sensing (QS) system in Gram-negative bacteria consists of signaling molecules called N-acyl-homoserine lactones (AHLs), which are synthesized by an enzyme AHL synthase (LuxI) and detected by a transcriptional regulator (LuxR) that are usually located in close proximity. However, many recent studies have also evidenced the presence of LuxR solos that are LuxR-related proteins in Proteobacteria that are devoid of a cognate LuxI AHL synthase. Pandoraea species are opportunistic pathogens frequently isolated from sputum specimens of cystic fibrosis (CF) patients. We have previously shown that P. pnomenusa strains possess QS activity. In this study, we examined the presence of QS activity in all type strains of Pandoraea species and acquired their complete genome sequences for holistic bioinformatics analyses of QS-related genes. Only four out of nine type strains (P. pnomenusa, P. sputorum, P. oxalativorans, and P. vervacti) showed QS activity, and C8-HSL was the only AHL detected. A total of 10 canonical luxIs with adjacent luxRs were predicted by bioinformatics from the complete genomes of aforementioned species and publicly available Pandoraea genomes. No orphan luxI was identified in any of the genomes. However, genes for two LuxR solos (LuxR2 and LuxR3 solos) were identified in all Pandoraea genomes (except two draft genomes with one LuxR solo gene), and P. thiooxydans was the only species that harbored no QS-related activity and genes. Except the canonical LuxR genes, LuxIs and LuxR solos of Pandoraea species were distantly related to the other well-characterized QS genes based on phylogenetic clustering. LuxR2 and LuxR3 solos might represent two novel evolutionary branches of LuxR system as they were found exclusively only in the genus. As a few luxR solos were located in close proximity with prophage sequence regions in the genomes, we thus postulated that these luxR solos could be transmitted into genus Pandoraea by transduction process mediated by bacteriophage. The bioinformatics approach developed in this study forms the basis for further characterization of closely related species. Overall, our findings improve the current understanding of QS in Pandoraea species, which is a potential pharmacological target in battling Pandoraea infections in CF patients.

Comprehensive genomic and phenotypic metal resistance profile of Pseudomonas putida strain S13.1.2 isolated from a vineyard soil

Chong TM, Yin WF, Chen JW, Mondy S, Grandclément C, Faure D, et al.

AMB Express, 2016 Dec;6(1):95.

PMID: 27730570

Trace metals are required in many cellular processes in bacteria but also induce toxic effects to cells when present in excess. As such, various forms of adaptive responses towards extracellular trace metal ions are essential for the survival and fitness of bacteria in their environment. A soil Pseudomonas putida, strain S13.1.2 has been isolated from French vineyard soil samples, and shown to confer resistance to copper ions. Further investigation revealed a high capacity to tolerate elevated concentrations of various heavy metals including nickel, cobalt, cadmium, zinc and arsenic. The complete genome analysis was conducted using single-molecule real-time (SMRT) sequencing and the genome consisted in a single chromosome at the size of 6.6 Mb. Presence of operons and gene clusters such as cop, cus, czc, nik, and asc systems were detected and accounted for the observed resistance phenotypes. The unique features in terms of specificity and arrangements of some genetic determinants were also highlighted in the study. Our findings has provided insights into the adaptation of this strain to accumulation and persistence of copper and other heavy metals in vineyard soil environment.

Fulltext Insights of biosurfactant producing Serratia marcescens strain W2.3 isolated from diseased tilapia fish: a draft genome analysis

Chan XY, Chang CY, Hong KW, Tee KK, Yin WF, Chan KG

Gut Pathog, 2013;5(1):29.

PMID: 24148830 DOI: 10.1186/1757-4749-5-29

Serratia marcescens is an opportunistic bacterial pathogen with broad range of host ranging from vertebrates, invertebrates and plants. S. marcescens strain W2.3 was isolated from a diseased tilapia fish and it was suspected to be the causal agent for the fish disease as virulence genes were found within its genome. In this study, for the first time, the genome sequences of S. marcescens strain W2.3 were sequenced using the Illumina MiSeq platform.

Fulltext Methylome Characterization of Burkholderia pseudomallei Strain 982 at Single-Base Resolution

Hong KW, Tee KK, Yin WF, Roberts RJ, Chan KG

Microbiol Resour Announc, 2019 Oct 24;8(43).

PMID: 31649075 DOI: 10.1128/MRA.00898-19

Burkholderia pseudomallei is the etiological agent of melioidosis, which has been studied by transcriptome and secretome analyses. However, little is known about the methylome of this pathogen. Here, we present the complete genome and methylome of melioidosis-causing B. pseudomallei strain 982.

Complete genome sequence of oxalate-degrading bacterium Pandoraea vervacti DSM 23571(T)

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.

Complete genome of Pseudomonas sp. strain L10.10, a psychrotolerant biofertilizer that could promote plant growth

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.

Complete genome of Planococcus rifietoensis M8(T), a halotolerant and potentially plant growth promoting bacterium

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.

Complete genome of Pandoraea pnomenusa RB-38, an oxalotrophic bacterium isolated from municipal solid waste landfill site

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.

Complete genome sequence of Serratia fonticola DSM 4576 T, a potential plant growth promoting bacterium

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.

Complete genome sequence of Serratia multitudinisentens RB-25(T), a novel chitinolytic bacterium

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.

Fulltext Mangrove derived Streptomyces sp. MUM265 as a potential source of antioxidant and anticolon-cancer agents

Tan LT, Chan KG, Pusparajah P, Yin WF, Khan TM, Lee LH, et al.

BMC Microbiol, 2019 02 13;19(1):38.

PMID: 30760201 DOI: 10.1186/s12866-019-1409-7

BACKGROUND: Colon cancer is the third most commonly diagnosed cancer worldwide, with a commensurately high mortality rate. The search for novel antioxidants and specific anticancer agents which may inhibit, delay or reverse the development of colon cancer is thus an area of great interest; Streptomyces bacteria have been demonstrated to be a source of such agents.

RESULTS: The extract from Streptomyces sp. MUM265- a strain which was isolated and identified from Kuala Selangor mangrove forest, Selangor, Malaysia- was analyzed and found to exhibit antioxidant properties as demonstrated via metal-chelating ability as well as superoxide anion, DPPH and ABTS radical scavenging activities. This study also showed that MUM265 extract demonstrated cytotoxicity against colon cancer cells as evidenced by the reduced cell viability of Caco-2 cell line. Treatment with MUM265 extract induced depolarization of mitochondrial membrane potential and accumulation of subG1 cells in cell cycle analysis, suggesting that MUM265 exerted apoptosis-inducing effects on Caco-2 cells.

CONCLUSION: These findings indicate that mangrove derived Streptomyces sp. MUM265 represents a valuable bioresource of bioactive compounds for the future development of chemopreventive agents, with particular promise suggested for treatment of colon cancer.

Emergence of mcr-1-mediated colistin resistance in Escherichia coli in Malaysia

Yu CY, Ang GY, Chin PS, Ngeow YF, Yin WF, Chan KG

Int J Antimicrob Agents, 2016 Jun;47(6):504-5.

PMID: 27208898 DOI: 10.1016/j.ijantimicag.2016.04.004

Emergence of ST119 Acinetobacter pittii co-harbouring NDM-1 and OXA-58 in Malaysia

Ang GY, Yu CY, Cheong YM, Yin WF, Chan KG

Int J Antimicrob Agents, 2016 Feb;47(2):168-9.

PMID: 26742728 DOI: 10.1016/j.ijantimicag.2015.11.008

Fulltext Heavy-metal resistance of a France vineyard soil bacterium, Pseudomonas mendocina strain S5.2, revealed by whole-genome sequencing

Chong TM, Yin WF, Mondy S, Grandclément C, Dessaux Y, Chan KG

J Bacteriol, 2012 Nov;194(22):6366.

PMID: 23105092 DOI: 10.1128/JB.01702-12

Here we present the draft genome of Pseudomonas mendocina strain S5.2, possessing tolerance to a high concentration of copper. In addition to being copper resistant, the genome of P. mendocina strain S5.2 contains a number of heavy-metal-resistant genes known to confer resistance to multiple heavy-metal ions.

Fulltext Draft genome sequence of an Aeromonas sp. strain 159 clinical isolate that shows quorum-sensing activity

Chan XY, Chua KH, Puthucheary SD, Yin WF, Chan KG

J Bacteriol, 2012 Nov;194(22):6350.

PMID: 23105081 DOI: 10.1128/JB.01642-12

Aeromonas is a pathogenic organism that is often found to infect humans. Here we report the draft genome of a clinical isolate in Malaysia, Aeromonas sp. strain 159, which shows N-acylhomoserine lactone production. In the draft genome of strain 159, luxI and luxR homologue genes were found to be located at contig 47, and these genes are believed to be important for the quorum-sensing system present in this pathogen.

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