1
|
Chua KO, Liew YJM, See-Too WS, Tan JY, Yong HS, Yin WF, Chan KG. Formicincola oecophyllae gen. nov. sp. nov., a novel member of the family Acetobacteraceae isolated from the weaver ant Oecophylla smaragdina. Antonie van Leeuwenhoek 2022; 115:995-1007. [DOI: 10.1007/s10482-022-01750-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 05/12/2022] [Indexed: 11/28/2022]
|
2
|
Chua KO, Fatima I, Lau YY, Hong KW, Yin WF, Mardaryev A, Chan KG, Chang CY. Bacterial microbiome of faecal samples of naked mole-rat collected from the toilet chamber. BMC Res Notes 2022; 15:107. [PMID: 35303951 PMCID: PMC8932300 DOI: 10.1186/s13104-022-06000-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/09/2022] [Indexed: 01/04/2023] Open
Abstract
Objective The naked mole rats (NMRs, Heterocephalus glaber) are subterranean rodents that belong to the family Bathyergidae. They gained the attention of the scientific community for their exceptionally long lifespan of up to 30 years and have become an animal model of biomedical research on neurodegenerative diseases, aging and cancer. NMRs dig and survive in a maze of underground tunnels and chambers and demarcate toilet chambers for defecation and urination. Due to their coprophagic behaviours, we believed that the toilet chamber might play a role in maintaining optimal health of the NMRs. A 16S rRNA gene amplicon sequencing was performed to characterize the bacterial microbiome of faecal samples collected from the toilet chamber of a laboratory NMR colony. Results Four faecal samples were collected at different time points from the same toilet chamber of a laboratory NMR colony for analysis. The 16S rRNA gene amplicon sequencing revealed that bacterial phyla Firmicutes and Bacteroidetes were the dominant taxa in the bacterial microbiome of NMRs. The relative abundance of the bacterial taxa shifted substantially between time points, indicating a dynamic microbiome in the toilet chamber. The data provided an insight to the faecal microbiome of NMRs in the toilet chamber. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-022-06000-8.
Collapse
Affiliation(s)
- Kah-Ooi Chua
- Centre for Research in Biotechnology for Agriculture, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Iqra Fatima
- Centre for Skin Sciences, School of Chemistry and Biosciences, University of Bradford, Bradford, BD7 1DP, UK
| | - Yin Yin Lau
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University Kuala Lumpur, 56000, Kuala Lumpur, Malaysia
| | - Kar Wai Hong
- International Genome Centre, Jiangsu University, Zhenjiang, China.,Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Institute of Marine Sciences, Shantou University, Shantou, 515063, China
| | - Andrei Mardaryev
- Centre for Skin Sciences, School of Chemistry and Biosciences, University of Bradford, Bradford, BD7 1DP, UK
| | - Kok-Gan Chan
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University Kuala Lumpur, 56000, Kuala Lumpur, Malaysia. .,International Genome Centre, Jiangsu University, Zhenjiang, China. .,Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Chien-Yi Chang
- School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4BW, UK.
| |
Collapse
|
3
|
Chua KO, See-Too WS, Yong HS, Song SL, Yin WF, Chan KG. Plasmid localization of sole rrn operon in genomes of Oecophyllibacter saccharovorans (Acetobacteraceae). Plasmid 2021; 114:102559. [PMID: 33476637 DOI: 10.1016/j.plasmid.2021.102559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/26/2020] [Accepted: 12/01/2020] [Indexed: 11/15/2022]
Abstract
The bacterium Oecophyllibacter saccharovorans of family Acetobacteraceae is a symbiont of weaver ant Oecophylla smaragdina. In our previous study, we published the finding of novel O. saccharovorans strains Ha5T, Ta1 and Jb2 (Chua et al. 2020) but their plasmid sequences have not been reported before. Here, we demonstrate for the first time that the sole rrn operon of their genomes was detected on a 6.6 kb circular replicon. This replicon occurred in high copy number, much smaller size and lower G + C content than the main chromosome. Based on these features, the 6.6 kb circular replicon was regarded as rrn operon-containing plasmid. Further restriction analysis on the plasmids confirmed their circular conformation. A Southern hybridization analysis also corroborated the presence of 16S rRNA gene and thus the rrn operon on a single locus in the genome of the O. saccharovorans strains. However, similar genome architecture was not observed in other closely related bacterial strains. Additional survey also detected no plasmid-borne rrn operon in available genomes of validly described taxa of family Acetobacteraceae. To date, plasmid localization of rrn operon is rarely documented. This study reports the occurrence of rrn operon on the smallest bacterial plasmid in three O. saccharovorans strains and discusses its possible importance in enhancing their competitive fitness as bacterial symbiont of O. smaragdina.
Collapse
Affiliation(s)
- Kah-Ooi Chua
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Wah-Seng See-Too
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Hoi-Sen Yong
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Sze-Looi Song
- Institute of Ocean and Earth Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia; China-ASEAN College of Marine Sciences, Xiamen University Malaysia, 43900 Sepang, Selangor, Malaysia
| | - Wai-Fong Yin
- Guangdong Provincial Key Laboratory of Marine Biology, & Institute of Marine Sciences, Shantou University, Shantou 515063, China
| | - Kok-Gan Chan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia; International Genome Centre, Jiangsu University, Zhenjiang, China.
| |
Collapse
|
4
|
Lau YY, How KY, Yin WF, Chan KG. Functional characterization of quorum sensing LuxR-type transcriptional regulator, EasR in Enterobacter asburiae strain L1. PeerJ 2020; 8:e10068. [PMID: 33150063 PMCID: PMC7585371 DOI: 10.7717/peerj.10068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 09/08/2020] [Indexed: 01/17/2023] Open
Abstract
Over the past decades, Enterobacter spp. have been identified as challenging and important pathogens. The emergence of multidrug-resistant Enterobacteria especially those that produce Klebsiella pneumoniae carbapenemase has been a very worrying health crisis. Although efforts have been made to unravel the complex mechanisms that contribute to the pathogenicity of different Enterobacter spp., there is very little information associated with AHL-type QS mechanism in Enterobacter spp. Signaling via N-acyl homoserine lactone (AHL) is the most common quorum sensing (QS) mechanism utilized by Proteobacteria. A typical AHL-based QS system involves two key players: a luxI gene homolog to synthesize AHLs and a luxR gene homolog, an AHL-dependent transcriptional regulator. These signaling molecules enable inter-species and intra-species interaction in response to external stimuli according to population density. In our recent study, we reported the genome of AHL-producing bacterium, Enterobacter asburiae strain L1. Whole genome sequencing and in silico analysis revealed the presence of a pair of luxI/R genes responsible for AHL-type QS, designated as easI/R, in strain L1. In a QS system, a LuxR transcriptional protein detects and responds to the concentration of a specific AHL controlling gene expression. In E. asburiae strain L1, EasR protein binds to its cognate AHLs, N-butanoyl homoserine lactone (C4-HSL) and N–hexanoyl homoserine lactone (C6-HSL), modulating the expression of targeted genes. In this current work, we have cloned the 693 bp luxR homolog of strain L1 for further characterization. The functionality and specificity of EasR protein in response to different AHL signaling molecules to activate gene transcription were tested and validated with β-galactosidase assays. Higher β-galactosidase activities were detected for cells harboring EasR, indicating EasR is a functional transcriptional regulator. This is the first report documenting the cloning and characterization of transcriptional regulator, luxR homolog of E. asburiae.
Collapse
Affiliation(s)
- Yin Yin Lau
- International Genome Centre, Jiangsu University, Zhenjiang, China.,Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Malaysia
| | - Kah Yan How
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Malaysia
| | - Kok-Gan Chan
- International Genome Centre, Jiangsu University, Zhenjiang, China.,Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Malaysia
| |
Collapse
|
5
|
Chua KO, See-Too WS, Ee R, Lim YL, Yin WF, Chan KG. In silico Analysis Reveals Distribution of Quorum Sensing Genes and Consistent Presence of LuxR Solos in the Pandoraea Species. Front Microbiol 2019; 10:1758. [PMID: 31447806 PMCID: PMC6691176 DOI: 10.3389/fmicb.2019.01758] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 07/16/2019] [Indexed: 01/11/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- Kah-Ooi Chua
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Wah-Seng See-Too
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Robson Ee
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Yan-Lue Lim
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.,International Genome Centre, Jiangsu University, Zhenjiang, China
| |
Collapse
|
6
|
Tan LTH, Chan KG, Pusparajah P, Yin WF, Khan TM, Lee LH, Goh BH. Mangrove derived Streptomyces sp. MUM265 as a potential source of antioxidant and anticolon-cancer agents. BMC Microbiol 2019; 19:38. [PMID: 30760201 PMCID: PMC6375222 DOI: 10.1186/s12866-019-1409-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 01/31/2019] [Indexed: 01/11/2023] Open
Abstract
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. Electronic supplementary material The online version of this article (10.1186/s12866-019-1409-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Loh Teng-Hern Tan
- Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, People's Republic of China.,Biofunctional Molecule Exploratory (BMEX) Research Group, School of Pharmacy, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.,Novel Bacteria and Drug Discovery (NBDD) Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Kok-Gan Chan
- International Genome Centre, Jiangsu University, Zhenjiang, China. .,Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia.
| | - Priyia Pusparajah
- Medical Health and Translational Research Group, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Tahir Mehmood Khan
- Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, People's Republic of China.,Biofunctional Molecule Exploratory (BMEX) Research Group, School of Pharmacy, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.,Medical Health and Translational Research Group, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Learn-Han Lee
- Novel Bacteria and Drug Discovery (NBDD) Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia. .,Institute of Pharmaceutical Science, University of Veterinary and Animal Science, Lahore, Pakistan. .,Center of Health Outcomes Research and Therapeutic Safety (Cohorts), School of Pharmaceutical Sciences, University of Phayao, Phayao, Thailand.
| | - Bey-Hing Goh
- Biofunctional Molecule Exploratory (BMEX) Research Group, School of Pharmacy, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia. .,Institute of Pharmaceutical Science, University of Veterinary and Animal Science, Lahore, Pakistan. .,Center of Health Outcomes Research and Therapeutic Safety (Cohorts), School of Pharmaceutical Sciences, University of Phayao, Phayao, Thailand.
| |
Collapse
|
7
|
Kher HL, Krishnan T, Letchumanan V, Hong KW, How KY, Lee LH, Tee KK, Yin WF, Chan KG. Characterization of quorum sensing genes and N-acyl homoserine lactones in Citrobacter amalonaticus strain YG6. Gene 2018; 684:58-69. [PMID: 30321658 DOI: 10.1016/j.gene.2018.10.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 07/27/2018] [Accepted: 10/11/2018] [Indexed: 11/26/2022]
Abstract
In the phylum of Proteobacteria, quorum sensing (QS) system is widely driven by synthesis and response of N-acyl homoserine lactone (AHL) signalling molecules. AHL is synthesized by LuxI homologue and sensed by LuxR homologue. Once the AHL concentration achieves a threshold level, it triggers the regulation of target genes. In this study, QS activity of Citrobacter amalonaticus strain YG6 which was isolated from clams was investigated. In order to characterise luxI/R homologues, the genome of C. amalonaticus strain YG6 (4.95 Mbp in size) was sequenced using Illumina MiSeq sequencer. Through in silico analysis, a pair of canonical luxI/R homologues and an orphan luxR homologue were identified and designated as camI, camR, and camR2, respectively. A putative lux box was identified at the upstream of camI. The camI gene was cloned and overexpressed in E. coli BL21 (DE3)pLysS. High-resolution triple quadrupole liquid chromatography mass spectrometry (LC-MS/MS) analysis verified that the CamI is a functional AHL synthase which produced multiple AHL species, namely N‑butyryl‑l‑homoserine lactone (C4-HSL), N‑hexanoyl‑l‑homoserine lactone (C6-HSL), N‑octanoyl‑l‑homoserine lactone (C8-HSL), N‑tetradecanoyl‑l‑homoserine lactone (C14-HSL) and N‑hexadecanoyl‑l‑homoserine lactone (C16-HSL) in C. amalonaticus strain YG6 and camI gene in recombinant E. coli BL21(DE3)pLysS. To our best knowledge, this is the first functional study report of camI as well as the first report describing the production of C14-HSL by C. amalonaticus.
Collapse
Affiliation(s)
- Heng-Leong Kher
- Institute of Graduate Studies, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Thiba Krishnan
- Division of Genetics and Molecular Biology, Institute of Biological Science, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Vengadesh Letchumanan
- Division of Genetics and Molecular Biology, Institute of Biological Science, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia; Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia
| | - Kar-Wai Hong
- Division of Genetics and Molecular Biology, Institute of Biological Science, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Kah-Yan How
- Division of Genetics and Molecular Biology, Institute of Biological Science, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Learn-Han Lee
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia.
| | - Kok-Keng Tee
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia.
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Science, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Science, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia; International Genome Centre, Jiangsu University, Zhenjiang, China.
| |
Collapse
|
8
|
Phan MD, Nhu NTK, Achard MES, Forde BM, Hong KW, Chong TM, Yin WF, Chan KG, West NP, Walker MJ, Paterson DL, Beatson SA, Schembri MA. Modifications in the pmrB gene are the primary mechanism for the development of chromosomally encoded resistance to polymyxins in uropathogenic Escherichia coli. J Antimicrob Chemother 2018; 72:2729-2736. [PMID: 29091192 DOI: 10.1093/jac/dkx204] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/26/2017] [Indexed: 01/08/2023] Open
Abstract
Objectives Polymyxins remain one of the last-resort drugs to treat infections caused by MDR Gram-negative pathogens. Here, we determined the mechanisms by which chromosomally encoded resistance to colistin and polymyxin B can arise in the MDR uropathogenic Escherichia coli ST131 reference strain EC958. Methods Two complementary approaches, saturated transposon mutagenesis and spontaneous mutation induction with high concentrations of colistin and polymyxin B, were employed to select for mutations associated with resistance to polymyxins. Mutants were identified using transposon-directed insertion-site sequencing or Illumina WGS. A resistance phenotype was confirmed by MIC and further investigated using RT-PCR. Competitive growth assays were used to measure fitness cost. Results A transposon insertion at nucleotide 41 of the pmrB gene (EC958pmrB41-Tn5) enhanced its transcript level, resulting in a 64- and 32-fold increased MIC of colistin and polymyxin B, respectively. Three spontaneous mutations, also located within the pmrB gene, conferred resistance to both colistin and polymyxin B with a corresponding increase in transcription of the pmrCAB genes. All three mutations incurred a fitness cost in the absence of colistin and polymyxin B. Conclusions This study identified the pmrB gene as the main chromosomal target for induction of colistin and polymyxin B resistance in E. coli.
Collapse
Affiliation(s)
- Minh-Duy Phan
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Nguyen Thi Khanh Nhu
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Maud E S Achard
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Brian M Forde
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Queensland, Australia
| | - Kar Wai Hong
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala, Lumpur, Malaysia
| | - Teik Min Chong
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala, Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala, Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala, Lumpur, Malaysia
| | - Nicholas P West
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Mark J Walker
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - David L Paterson
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.,The University of Queensland Centre for Clinical Research, The University of Queensland, Brisbane, Queensland, Australia
| | - Scott A Beatson
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Queensland, Australia
| | - Mark A Schembri
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| |
Collapse
|
9
|
Priya K, Sulaiman J, How KY, Yin WF, Chan KG. Production of N-acyl homoserine lactones by Chromobacterium haemolyticum KM2 isolated from the river water in Malaysia. Arch Microbiol 2018; 200:1135-1142. [PMID: 29796703 DOI: 10.1007/s00203-018-1526-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 03/16/2018] [Accepted: 05/14/2018] [Indexed: 10/16/2022]
Abstract
Quorum sensing (QS) is a term used to describe cell-to-cell communication that enables bacteria to orchestrate group behaviours according to density of bacterial cells. In Gram-negative bacteria, this signalling system is widely known to regulate a variety of different phenotypes such as antibiotic production and biofilm formation. In this study, we report the production of N-acyl homoserine lactones produced by Chromobacterium haemolyticum strain KM2, a bacterium isolated from a river water of a reserved tropical national park. Preliminary screening of QS activity using biosensor reporter assays indicated that C. haemolyticum strain KM2 produces both short- and long-chain AHLs. Analysis with high-resolution liquid chromatography-mass spectrometry (LC-MS/MS) analysis revealed the production of three AHLs by strain KM2: N-octanoyl-L-homoserine lactone (C8-HSL), N-dodecanoyl-L-homoserine lactone (C12-HSL), and N-3-oxo-dodecanoyl-L-homoserine lactone (OC12-HSL). This bacterial isolate also exhibited strong β-haemolytic activity. To the best of our knowledge, this is the first documentation of QS activity and multiple AHLs production by C. haemolyticum strain KM2.
Collapse
Affiliation(s)
- Kumutha Priya
- International Genome Centre, Jiangsu University, Zhenjiang, China.,Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | - Joanita Sulaiman
- Institute for Public Health, National Institutes of Health Malaysia, Jalan Bangsar, 50590, Kuala Lumpur, Malaysia
| | - Kah Yan How
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | - Wai-Fong Yin
- International Genome Centre, Jiangsu University, Zhenjiang, China.,Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | - Kok-Gan Chan
- International Genome Centre, Jiangsu University, Zhenjiang, China. .,Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia.
| |
Collapse
|
10
|
Lee LS, Goh KM, Chan CS, Annie Tan GY, Yin WF, Chong CS, Chan KG. Microbial diversity of thermophiles with biomass deconstruction potential in a foliage-rich hot spring. Microbiologyopen 2018; 7:e00615. [PMID: 29602271 PMCID: PMC6291792 DOI: 10.1002/mbo3.615] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 01/29/2018] [Accepted: 02/12/2018] [Indexed: 11/12/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Li Sin Lee
- ISB (Genetics), Faculty of Science, University of Malaysia, Kuala Lumpur, Malaysia
| | - Kian Mau Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Chia Sing Chan
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Geok Yuan Annie Tan
- ISB (Genetics), Faculty of Science, University of Malaysia, Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- ISB (Genetics), Faculty of Science, University of Malaysia, Kuala Lumpur, Malaysia
| | - Chun Shiong Chong
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Kok-Gan Chan
- ISB (Genetics), Faculty of Science, University of Malaysia, Kuala Lumpur, Malaysia.,Jiangsu University, Zhenjiang, China
| |
Collapse
|
11
|
Ser HL, Tan WS, Mutalib NSA, Yin WF, Chan KG, Goh BH, Lee LH. Genome sequence of Streptomyces gilvigriseus MUSC 26 T isolated from mangrove forest. Braz J Microbiol 2018; 49:207-209. [PMID: 29428207 PMCID: PMC5913758 DOI: 10.1016/j.bjm.2017.04.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/22/2017] [Accepted: 04/03/2017] [Indexed: 11/07/2022] Open
Abstract
Streptomycetes remain as one of the important sources for bioactive products. Isolated from the mangrove forest, Streptomyces gilvigriseus MUSC 26T was previously characterised as a novel streptomycete. The high quality draft genome of MUSC 26T contained 5,213,277 bp with G + C content of 73.0%. Through genome mining, several gene clusters associated with secondary metabolites production were revealed in the genome of MUSC 26T. These findings call for further investigations into the potential exploitation of the strain for production of pharmaceutically important compounds.
Collapse
Affiliation(s)
- Hooi-Leng Ser
- Monash University Malaysia, School of Pharmacy, Novel Bacteria and Drug Discovery Research Group (NBDD), Selangor Darul Ehsan, Malaysia; Monash University Malaysia, Jeffrey Cheah School of Medicine and Health Sciences, Biomedical Research Laboratory, Selangor Darul Ehsan, Malaysia; Monash University Malaysia, School of Pharmacy, Biofunctional Molecule Exploratory Research Group (BMEX), Bandar Sunway, Malaysia
| | - Wen-Si Tan
- University of Malaya, Faculty of Science, Institute of Biological Sciences, Division of Genetics and Molecular Biology, Malaysia
| | - Nurul-Syakima Ab Mutalib
- Universiti Kebangsaan Malaysia, UKM Medical Centre, UKM Medical Molecular Biology Institute (UMBI), Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- University of Malaya, Faculty of Science, Institute of Biological Sciences, Division of Genetics and Molecular Biology, Malaysia
| | - Kok-Gan Chan
- University of Malaya, Faculty of Science, Institute of Biological Sciences, Division of Genetics and Molecular Biology, Malaysia; Vice Chancellor Office, Jiangsu University, Zhenjiang 212013, PR China
| | - Bey-Hing Goh
- Monash University Malaysia, School of Pharmacy, Novel Bacteria and Drug Discovery Research Group (NBDD), Selangor Darul Ehsan, Malaysia; Monash University Malaysia, School of Pharmacy, Biofunctional Molecule Exploratory Research Group (BMEX), Bandar Sunway, Malaysia; University of Phayao, School of Pharmaceutical Sciences, Center of Health Outcomes Research and Therapeutic Safety (Cohorts), Phayao, Thailand; Monash University Malaysia, Global Asia in the 21st Century (GA21) Platform, Health and Well-being Cluster, Implementation and Clinical Outcomes (PICO), Asian Centre for Evidence Synthesis in Population, Bandar Sunway, Malaysia
| | - Learn-Han Lee
- Monash University Malaysia, School of Pharmacy, Novel Bacteria and Drug Discovery Research Group (NBDD), Selangor Darul Ehsan, Malaysia; Monash University Malaysia, Jeffrey Cheah School of Medicine and Health Sciences, Biomedical Research Laboratory, Selangor Darul Ehsan, Malaysia; Monash University Malaysia, School of Pharmacy, Biofunctional Molecule Exploratory Research Group (BMEX), Bandar Sunway, Malaysia; University of Phayao, School of Pharmaceutical Sciences, Center of Health Outcomes Research and Therapeutic Safety (Cohorts), Phayao, Thailand; Monash University Malaysia, Global Asia in the 21st Century (GA21) Platform, Health and Well-being Cluster, Implementation and Clinical Outcomes (PICO), Asian Centre for Evidence Synthesis in Population, Bandar Sunway, Malaysia.
| |
Collapse
|
12
|
Yu CY, Ang GY, Chong TM, Chin PS, Ngeow YF, Yin WF, Chan KG. Complete genome sequencing revealed novel genetic contexts of the mcr-1 gene in Escherichia coli strains. J Antimicrob Chemother 2018; 72:1253-1255. [PMID: 28031273 DOI: 10.1093/jac/dkw541] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Choo Yee Yu
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia.,Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, Selangor, Malaysia
| | - Geik Yong Ang
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia.,Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, Selangor, Malaysia
| | - Teik-Min Chong
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Pui San Chin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Yun Fong Ngeow
- Department of Pre-clinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Selangor, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| |
Collapse
|
13
|
Chong TM, Chen JW, See-Too WS, Yu CY, Ang GY, Lim YL, Yin WF, Grandclément C, Faure D, Dessaux Y, Chan KG. Phenotypic and genomic survey on organic acid utilization profile of Pseudomonas mendocina strain S5.2, a vineyard soil isolate. AMB Express 2017; 7:138. [PMID: 28655216 PMCID: PMC5484659 DOI: 10.1186/s13568-017-0437-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/19/2017] [Indexed: 12/30/2022] Open
Abstract
Root exudates are chemical compounds that are released from living plant roots and provide significant energy, carbon, nitrogen and phosphorus sources for microbes inhabiting the rhizosphere. The exudates shape the microflora associated with the plant, as well as influences the plant health and productivity. Therefore, a better understanding of the trophic link that is established between the plant and the associated bacteria is necessary. In this study, a comprehensive survey on the utilization of grapevine and rootstock related organic acids were conducted on a vineyard soil isolate which is Pseudomonas mendocina strain S5.2. Phenotype microarray analysis has demonstrated that this strain can utilize several organic acids including lactic acid, succinic acid, malic acid, citric acid and fumaric acid as sole growth substrates. Complete genome analysis using single molecule real-time technology revealed that the genome consists of a 5,120,146 bp circular chromosome and a 252,328 bp megaplasmid. A series of genetic determinants associated with the carbon utilization signature of the strain were subsequently identified in the chromosome. Of note, the coexistence of genes encoding several iron-sulfur cluster independent isoenzymes in the genome indicated the importance of these enzymes in the events of iron deficiency. Synteny and comparative analysis have also unraveled the unique features of D-lactate dehydrogenase of strain S5.2 in the study. Collective information of this work has provided insights on the metabolic role of this strain in vineyard soil rhizosphere.
Collapse
Affiliation(s)
- Teik Min Chong
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Jian-Woon Chen
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- UM Omics Centre, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Wah-Seng See-Too
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Choo-Yee Yu
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, 40450 Shah Alam, Selangor Malaysia
| | - Geik-Yong Ang
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, 40450 Shah Alam, Selangor Malaysia
| | - Yan Lue Lim
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Catherine Grandclément
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-Sur-Yvette, France
| | - Denis Faure
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-Sur-Yvette, France
| | - Yves Dessaux
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-Sur-Yvette, France
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- UM Omics Centre, University of Malaya, 50603 Kuala Lumpur, Malaysia
| |
Collapse
|
14
|
Hong KW, Asmah Hani A, Nurul Aina Murni C, Pusparani R, Chong CK, Verasahib K, Yusoff WNW, Noordin NM, Tee KK, Yin WF, Yu CY, Ang GY, Chan KG. Comparative genomic and phylogenetic analysis of a toxigenic clinical isolate of Corynebacterium diphtheriae strain B-D-16-78 from Malaysia. Infection, Genetics and Evolution 2017; 54:263-270. [DOI: 10.1016/j.meegid.2017.07.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 06/11/2017] [Accepted: 07/11/2017] [Indexed: 11/24/2022]
|
15
|
See-Too WS, Ee R, Lim YL, Convey P, Pearce DA, Mohidin TBM, Yin WF, Chan KG. Complete genome of Arthrobacter alpinus strain R3.8, bioremediation potential unraveled with genomic analysis. Stand Genomic Sci 2017; 12:52. [PMID: 28904741 PMCID: PMC5586057 DOI: 10.1186/s40793-017-0264-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 08/23/2017] [Indexed: 11/10/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Wah-Seng See-Too
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.,National Antarctic Research Centre (NARC), Institute of Postgraduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Robson Ee
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Yan-Lue Lim
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Peter Convey
- National Antarctic Research Centre (NARC), Institute of Postgraduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia.,British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge, CB3 OET UK
| | - David A Pearce
- National Antarctic Research Centre (NARC), Institute of Postgraduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia.,British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge, CB3 OET UK.,Faculty of Health and Life Sciences, University of Northumbria, Newcastle Upon Tyne, NE1 8ST UK
| | - Taznim Begam Mohd Mohidin
- Division of Microbiology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.,UM Omics Centre, University of Malaya, Kuala Lumpur, Malaysia.,Vice Chancellor Office, Jiangsu University, Zhenjiang, 212013 People's Republic of China
| |
Collapse
|
16
|
Ser HL, Tan WS, Ab Mutalib NS, Yin WF, Chan KG, Goh BH, Lee LH. Genome sequence of Streptomyces mangrovisoli MUSC 149 T isolated from intertidal sediments. Braz J Microbiol 2017; 49:13-15. [PMID: 28927873 PMCID: PMC5790589 DOI: 10.1016/j.bjm.2017.01.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 01/31/2017] [Indexed: 11/16/2022] Open
Abstract
As the largest genus in Actinobacteria family, Streptomyces species have the ability to synthesize numerous compounds of diverse structures with bioactivities. Streptomyces mangrovisoli MUSC 149T was previously isolated as a novel streptomycete from mangrove forest in east coast of Peninsular Malaysia. The high quality draft genome of MUSC 149T comprises 9,165,825bp with G+C content of 72.5%. Through bioinformatics analysis, 21 gene clusters identified in the genome were associated with the production of bioactive secondary metabolites. The presence of these biosynthetic gene clusters in MUSC 149T suggests the potential exploitation of the strain for production of medically important compounds.
Collapse
Affiliation(s)
- Hooi-Leng Ser
- Monash University Malaysia, School of Pharmacy, Novel Bacteria and Drug Discovery (NBDD) Research Group, Selangor Darul Ehsan, Malaysia; Monash University Malaysia, Jeffrey Cheah School of Medicine and Health Sciences, Biomedical Research Laboratory, Selangor Darul Ehsan, Malaysia
| | - Wen-Si Tan
- University of Malaya, Institute of Biological Sciences, Division of Genetics and Molecular Biology, Kuala Lumpur, Malaysia
| | - Nurul-Syakima Ab Mutalib
- University Kebangsaan Malaysia, UKM Medical Centre, UKM Medical Molecular Biology Institute (UMBI), Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- University of Malaya, Institute of Biological Sciences, Division of Genetics and Molecular Biology, Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- University of Malaya, Institute of Biological Sciences, Division of Genetics and Molecular Biology, Kuala Lumpur, Malaysia
| | - Bey-Hing Goh
- Monash University Malaysia, School of Pharmacy, Novel Bacteria and Drug Discovery (NBDD) Research Group, Selangor Darul Ehsan, Malaysia; University Kebangsaan Malaysia, UKM Medical Centre, UKM Medical Molecular Biology Institute (UMBI), Kuala Lumpur, Malaysia; University of Phayao, School of Pharmaceutical Sciences, Center of Health Outcomes Research and Therapeutic Safety (Cohorts), Phayao, Thailand
| | - Learn-Han Lee
- Monash University Malaysia, School of Pharmacy, Novel Bacteria and Drug Discovery (NBDD) Research Group, Selangor Darul Ehsan, Malaysia; University Kebangsaan Malaysia, UKM Medical Centre, UKM Medical Molecular Biology Institute (UMBI), Kuala Lumpur, Malaysia; University of Phayao, School of Pharmaceutical Sciences, Center of Health Outcomes Research and Therapeutic Safety (Cohorts), Phayao, Thailand.
| |
Collapse
|
17
|
See-Too WS, Chua KO, Lim YL, Chen JW, Convey P, Mohd Mohidin TB, Yin WF, Chan KG. Complete genome sequence of Planococcus donghaensis JH1 T, a pectin-degrading bacterium. J Biotechnol 2017; 252:11-14. [PMID: 28483443 DOI: 10.1016/j.jbiotec.2017.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 05/04/2017] [Accepted: 05/05/2017] [Indexed: 11/29/2022]
Abstract
The type strain Planococcus donghaensis JH1T is a psychrotolerant and halotolerant bacterium with starch-degrading ability. Here, we determine the carbon utilization profile of P. donghaensis JH1T and 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.
Collapse
Affiliation(s)
- Wah-Seng See-Too
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia; National Antarctic Research Centre (NARC), Institute of Postgraduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kah-Ooi Chua
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Yan-Lue Lim
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Jian-Woon Chen
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia; UM Omics Centre, University of Malaya, Kuala Lumpur, Malaysia
| | - Peter Convey
- National Antarctic Research Centre (NARC), Institute of Postgraduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia; British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge CB3 OET, UK
| | - Taznim Begam Mohd Mohidin
- Division of Microbiology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia; UM Omics Centre, University of Malaya, Kuala Lumpur, Malaysia.
| |
Collapse
|
18
|
|
19
|
Abstract
A large number of Vibrio sp. thrive in the marine environment and they are notable to cause food borne infection associated with undercooked seafood. In this study, we report the whole genome sequence of Vibrio sinaloensis T47 which was isolated from coastal marine water in Morib Beach, Hulu Selangor. The genome is made up of approximately 4.59 Mbp with 80 contigs and 46% G+C content. From the annotated genome, genes associated with quorum sensing (QS) were identified. This research provides a genetic basis for better understanding of QS pathway which contributes to the physiological traits of strain T47 to thrive in the marine environment.
Collapse
Affiliation(s)
- Nur Izzati Mohamad
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603 Malaysia
| | - Kah Yan How
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603 Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603 Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603 Malaysia
| |
Collapse
|
20
|
See-Too WS, Ee R, Lim YL, Convey P, Pearce DA, Yin WF, Chan KG. AidP, a novel N-Acyl homoserine lactonase gene from Antarctic Planococcus sp. Sci Rep 2017; 7:42968. [PMID: 28225085 PMCID: PMC5320481 DOI: 10.1038/srep42968] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/17/2017] [Indexed: 11/29/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Wah Seng See-Too
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science University of Malaya, 50603 Kuala Lumpur, Malaysia.,National Antarctic Research Centre (NARC), Institute of Postgraduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Robson Ee
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Yan-Lue Lim
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Peter Convey
- National Antarctic Research Centre (NARC), Institute of Postgraduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia.,British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge CB3 OET, UK
| | - David A Pearce
- National Antarctic Research Centre (NARC), Institute of Postgraduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia.,British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge CB3 OET, UK.,Faculty of Health and Life Sciences, University of Northumbria, Newcastle Upon Tyne NE1 8ST, UK
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science University of Malaya, 50603 Kuala Lumpur, Malaysia.,UM Omics Centre, University of Malaya, Kuala Lumpur, Malaysia
| |
Collapse
|
21
|
Tan KH, How KY, Tan JY, Yin WF, Chan KG. Cloning and Characterization of the Autoinducer Synthase Gene from Lipid-Degrading Bacterium Cedecea neteri. Front Microbiol 2017; 8:72. [PMID: 28197135 PMCID: PMC5281573 DOI: 10.3389/fmicb.2017.00072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 01/11/2017] [Indexed: 11/13/2022] Open
Abstract
The process of intercellular communication among bacteria, termed quorum sensing (QS), is mediated by small diffusible molecules known as the autoinducers. QS allows the population to react to the change of cell density in unison, in processes such as biofilm formation, plasmid conjugation, virulence, motility and root nodulation. In Gram-negative proteobacteria, N-acyl homoserine lactone (AHL) is the common "language" to coordinate gene expression. This signaling molecule is usually synthesized by LuxI-type proteins. We have previously discovered that a rare bacterium, Cedecea neteri, exhibits AHL-type QS activity. With information generated from genome sequencing, we have identified the luxIR gene pair responsible for AHL-type QS and named it cneIR. In this study, we have cloned and expressed the 636 bp luxI homolog in an Escherichia coli host for further characterization. Our findings show that E. coli harboring cneI produced the same AHL profile as the wild type C. neteri, with the synthesis of AHL known as N-butyryl-homoserine lactone. This 25 kDa LuxI homolog shares high similarity with other AHL synthases from closely related species. This work is the first documentation of molecular cloning and characterization of luxI homolog from C. neteri.
Collapse
Affiliation(s)
- Kian-Hin Tan
- Division of Genetic and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| | - Kah-Yan How
- Division of Genetic and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| | - Jia-Yi Tan
- Division of Genetic and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetic and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetic and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| |
Collapse
|
22
|
Chong TM, Yin WF, Chen JW, Mondy S, Grandclément C, Faure D, Dessaux Y, Chan KG. Comprehensive genomic and phenotypic metal resistance profile of Pseudomonas putida strain S13.1.2 isolated from a vineyard soil. AMB Express 2016; 6:95. [PMID: 27730570 PMCID: PMC5059233 DOI: 10.1186/s13568-016-0269-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 10/04/2016] [Indexed: 11/17/2022] Open
Abstract
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.
Collapse
|
23
|
Yong D, Tee KK, Yin WF, Chan KG. Characterization and Comparative Overview of Complete Sequences of the First Plasmids of Pandoraea across Clinical and Non-clinical Strains. Front Microbiol 2016; 7:1606. [PMID: 27790203 PMCID: PMC5064223 DOI: 10.3389/fmicb.2016.01606] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/26/2016] [Indexed: 11/25/2022] Open
Abstract
To date, information on plasmid analysis in Pandoraea spp. is scarce. To address the gap of knowledge on this, the complete sequences of eight plasmids from Pandoraea spp. namely Pandoraea faecigallinarum DSM 23572T (pPF72-1, pPF72-2), Pandoraea oxalativorans DSM 23570T (pPO70-1, pPO70-2, pPO70-3, pPO70-4), Pandoraea vervacti NS15 (pPV15) and Pandoraea apista DSM 16535T (pPA35) were studied for the first time in this study. The information on plasmid sequences in Pandoraea spp. is useful as the sequences did not match any known plasmid sequence deposited in public databases. Replication genes were not identified in some plasmids, a situation that has led to the possibility of host interaction involvement. Some plasmids were also void of par genes and intriguingly, repA gene was also not discovered in these plasmids. This further leads to the hypothesis of host-plasmid interaction. Plasmid stabilization/stability protein-encoding genes were observed in some plasmids but were not established for participating in plasmid segregation. Toxin-antitoxin systems MazEF, VapBC, RelBE, YgiT-MqsR, HigBA, and ParDE were identified across the plasmids and their presence would improve plasmid maintenance. Conjugation genes were identified portraying the conjugation ability amongst Pandoraea plasmids. Additionally, we found a shared region amongst some of the plasmids that consists of conjugation genes. The identification of genes involved in replication, segregation, toxin-antitoxin systems and conjugation, would aid the design of drugs to prevent the survival or transmission of plasmids carrying pathogenic properties. Additionally, genes conferring virulence and antibiotic resistance were identified amongst the plasmids. The observed features in the plasmids shed light on the Pandoraea spp. as opportunistic pathogens.
Collapse
Affiliation(s)
- Delicia Yong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya Kuala Lumpur, Malaysia
| | - Kok Keng Tee
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| |
Collapse
|
24
|
Ser HL, Tan WS, Ab Mutalib NS, Yin WF, Chan KG, Goh BH, Lee LH. Draft Genome Sequence of Mangrove-Derived Streptomyces sp. MUSC 125 with Antioxidant Potential. Front Microbiol 2016; 7:1470. [PMID: 27695452 PMCID: PMC5023686 DOI: 10.3389/fmicb.2016.01470] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/02/2016] [Indexed: 12/03/2022] Open
Affiliation(s)
- Hooi-Leng Ser
- Novel Bacteria and Drug Discovery Research Group, School of Pharmacy, Monash University Malaysia Bandar Sunway, Malaysia
| | - Wen-Si Tan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute, UKM Medical Centre, Universiti Kebangsaan Malaysia Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Bey-Hing Goh
- Novel Bacteria and Drug Discovery Research Group, School of Pharmacy, Monash University MalaysiaBandar Sunway, Malaysia; Center of Health Outcomes Research and Therapeutic Safety (Cohorts), School of Pharmaceutical Sciences, University of PhayaoPhayao, Thailand
| | - Learn-Han Lee
- Novel Bacteria and Drug Discovery Research Group, School of Pharmacy, Monash University MalaysiaBandar Sunway, Malaysia; Center of Health Outcomes Research and Therapeutic Safety (Cohorts), School of Pharmaceutical Sciences, University of PhayaoPhayao, Thailand
| |
Collapse
|
25
|
Ee R, Lim YL, Yin WF, See-Too WS, Roberts RJ, Chan KG. Novel Methyltransferase Recognition Motif Identified in Chania multitudinisentens RB-25(T) gen. nov., sp. nov. Front Microbiol 2016; 7:1362. [PMID: 27630623 PMCID: PMC5005818 DOI: 10.3389/fmicb.2016.01362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 08/17/2016] [Indexed: 11/13/2022] Open
Affiliation(s)
- Robson Ee
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Yan-Lue Lim
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Wah-Seng See-Too
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | | | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| |
Collapse
|
26
|
Chan KG, Chong TM, Adrian TGS, Kher HL, Grandclément C, Faure D, Yin WF, Dessaux Y, Hong KW. Pseudomonas lini Strain ZBG1 Revealed Carboxylic Acid Utilization and Copper Resistance Features Required for Adaptation to Vineyard Soil Environment: A Draft Genome Analysis. J Genomics 2016; 4:26-8. [PMID: 27512520 PMCID: PMC4978946 DOI: 10.7150/jgen.16146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Pseudomonas lini strain ZBG1 was isolated from the soil of vineyard in Zellenberg, France and the draft genome was reported in this study. Bioinformatics analyses of the genome revealed presence of genes encoding tartaric and malic acid utilization as well as copper resistance that correspond to the adaptation this strain in vineyard soil environment.
Collapse
Affiliation(s)
- Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Teik-Min Chong
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Tan-Guan-Sheng Adrian
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Heng Leong Kher
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Catherine Grandclément
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Denis Faure
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Yves Dessaux
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Kar-Wai Hong
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| |
Collapse
|
27
|
Chan KG, Priya K, Chang CY, Abdul Rahman AY, Tee KK, Yin WF. Transcriptome analysis of Pseudomonas aeruginosa PAO1 grown at both body and elevated temperatures. PeerJ 2016; 4:e2223. [PMID: 27547539 PMCID: PMC4957987 DOI: 10.7717/peerj.2223] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 06/15/2016] [Indexed: 01/15/2023] Open
Abstract
Functional genomics research can give us valuable insights into bacterial gene function. RNA Sequencing (RNA-seq) can generate information on transcript abundance in bacteria following abiotic stress treatments. In this study, we used the RNA-seq technique to study the transcriptomes of the opportunistic nosocomial pathogen Pseudomonas aeruginosa PAO1 following heat shock. Samples were grown at both the human body temperature (37 °C) and an arbitrarily-selected temperature of 46 °C. In this work using RNA-seq, we identified 133 genes that are differentially expressed at 46 °C compared to the human body temperature. Our work identifies some key P. aeruginosa PAO1 genes whose products have importance in both environmental adaptation as well as in vivo infection in febrile hosts. More importantly, our transcriptomic results show that many genes are only expressed when subjected to heat shock. Because the RNA-seq can generate high throughput gene expression profiles, our work reveals many unanticipated genes with further work to be done exploring such genes products.
Collapse
Affiliation(s)
- Kok-Gan Chan
- ISB (Genetics & Molecular Biology), Faculty of Science, University of Malaya , Kuala Lumpur , Malaysia
| | - Kumutha Priya
- ISB (Genetics & Molecular Biology), Faculty of Science, University of Malaya , Kuala Lumpur , Malaysia
| | - Chien-Yi Chang
- School of Life Sciences, Heriot-Watt University , Edinburgh , United Kingdom
| | | | - Kok Keng Tee
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya , Kuala Lumpur , Malaysia
| | - Wai-Fong Yin
- ISB (Genetics & Molecular Biology), Faculty of Science, University of Malaya , Kuala Lumpur , Malaysia
| |
Collapse
|
28
|
Ser HL, Tan LTH, Palanisamy UD, Abd Malek SN, Yin WF, Chan KG, Goh BH, Lee LH. Streptomyces antioxidans sp. nov., a Novel Mangrove Soil Actinobacterium with Antioxidative and Neuroprotective Potentials. Front Microbiol 2016; 7:899. [PMID: 27379040 PMCID: PMC4909769 DOI: 10.3389/fmicb.2016.00899] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/26/2016] [Indexed: 11/16/2022] Open
Abstract
A novel strain, Streptomyces antioxidans MUSC 164T was recovered from mangrove forest soil located at Tanjung Lumpur, Malaysia. The Gram-positive bacterium forms yellowish-white aerial and brilliant greenish yellow substrate mycelium on ISP 2 agar. A polyphasic approach was used to determine the taxonomy status of strain MUSC 164T. The strain showed a spectrum 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(H6) and MK-9(H8), while the identified polar lipids consisted of aminolipid, diphosphatidylglycerol, glycolipid, hydroxyphosphatidylethanolamine, phospholipid, phosphatidylinositol, phosphatidylethanolamine, phosphatidylglycerol and lipid. The cell wall sugars consist of galactose, glucose and ribose. The predominant cellular fatty acids (>10.0%) were identified as iso-C15:0 (34.8%) and anteiso-C15:0(14.0%). Phylogenetic analysis identified that closely related strains for MUSC 164T as Streptomyces javensis NBRC 100777T (99.6% sequence similarity), Streptomyces yogyakartensis NBRC 100779T (99.6%) and Streptomyces violaceusniger NBRC 13459T (99.6%). The DNA–DNA relatedness values between MUSC 164T and closely related type strains ranged from 23.8 ± 0.3% to 53.1 ± 4.3%. BOX-PCR fingerprints comparison showed that MUSC 164T exhibits a unique DNA profile, with DNA G + C content determined to be 71.6 mol%. Based on the polyphasic study of MUSC 164T, it is concluded that this strain represents a novel species, for which the name Streptomyces antioxidans sp. nov. is proposed. The type strain is MUSC 164T (=DSM 101523T = MCCC 1K01590T). The extract of MUSC 164T showed potent antioxidative and neuroprotective activities against hydrogen peroxide. The chemical analysis of the extract revealed that the strain produces pyrazines and phenolic-related compounds that could explain for the observed bioactivities.
Collapse
Affiliation(s)
- Hooi-Leng Ser
- Novel Bacteria and Drug Discovery Research Group, School of Pharmacy, Monash University MalaysiaBandar Sunway, Malaysia; Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University MalaysiaBandar Sunway, Malaysia
| | - Loh Teng-Hern Tan
- Novel Bacteria and Drug Discovery Research Group, School of Pharmacy, Monash University MalaysiaBandar Sunway, Malaysia; Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University MalaysiaBandar Sunway, Malaysia
| | - Uma D Palanisamy
- Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia Bandar Sunway, Malaysia
| | - Sri N Abd Malek
- Biochemistry Program, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Bey-Hing Goh
- Novel Bacteria and Drug Discovery Research Group, School of Pharmacy, Monash University MalaysiaBandar Sunway, Malaysia; Center of Health Outcomes Research and Therapeutic Safety (Cohorts), School of Pharmaceutical Sciences, University of PhayaoPhayao, Thailand
| | - Learn-Han Lee
- Novel Bacteria and Drug Discovery Research Group, School of Pharmacy, Monash University MalaysiaBandar Sunway, Malaysia; Center of Health Outcomes Research and Therapeutic Safety (Cohorts), School of Pharmaceutical Sciences, University of PhayaoPhayao, Thailand
| |
Collapse
|
29
|
Abstract
Kocuria rhizophila is a ubiquitous bacterium which is well known for its industrial value. Here, we present the draft genome of Kocuria rhizophila strain TPW45 which was isolated from Sungai Gabai, Selangor, Malaysia. The assembled genome comprised of 46 contigs and the estimated genome size is 2.7 Mb. Based on the RAST annotation, a gene cluster responsible for aromatic compound degradation was identified in this strain.
Collapse
Affiliation(s)
- Tan-Guan-Sheng Adrian
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Pui-Wan Tan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Jian-Woon Chen
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| |
Collapse
|
30
|
See-Too WS, Tan JY, Ee R, Lim YL, Convey P, Pearce DA, Yin WF, Chan KG. De novo assembly of complete genome sequence of Planococcus kocurii ATCC 43650(T), a potential plant growth promoting bacterium. Mar Genomics 2016; 28:33-35. [PMID: 27117861 DOI: 10.1016/j.margen.2016.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 04/17/2016] [Accepted: 04/17/2016] [Indexed: 10/21/2022]
Abstract
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.
Collapse
Affiliation(s)
- Wah-Seng See-Too
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia; National Antarctic Research Centre (NARC), Institute of Postgraduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Jia Yi Tan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Robson Ee
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Yan-Lue Lim
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Peter Convey
- National Antarctic Research Centre (NARC), Institute of Postgraduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia; British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge CB3 OET, UK
| | - David A Pearce
- National Antarctic Research Centre (NARC), Institute of Postgraduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia; British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge CB3 OET, UK; Faculty of Health and Life Sciences, University of Northumbria, Newcastle Upon Tyne NE1 8ST, UK
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia; UM Omics Centre, University of Malaya, Kuala Lumpur, Malaysia.
| |
Collapse
|
31
|
Yu CY, Ang GY, Chin PS, Ngeow YF, Yin WF, Chan KG. Emergence of mcr-1-mediated colistin resistance in Escherichia coli in Malaysia. Int J Antimicrob Agents 2016; 47:504-5. [PMID: 27208898 DOI: 10.1016/j.ijantimicag.2016.04.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 04/14/2016] [Accepted: 04/16/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Choo Yee Yu
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia; Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, Puncak Alam, Malaysia.
| | - Geik Yong Ang
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia; Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, Puncak Alam, Malaysia
| | - Pui San Chin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Yun Fong Ngeow
- Department of Pre-clinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Kampar, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia.
| |
Collapse
|
32
|
Ser HL, Palanisamy UD, Yin WF, Chan KG, Goh BH, Lee LH. Streptomyces malaysiense sp. nov.: A novel Malaysian mangrove soil actinobacterium with antioxidative activity and cytotoxic potential against human cancer cell lines. Sci Rep 2016; 6:24247. [PMID: 27072394 PMCID: PMC4829849 DOI: 10.1038/srep24247] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 03/23/2016] [Indexed: 12/31/2022] Open
Abstract
Actinobacteria from the unique intertidal ecosystem of the mangroves are known to produce novel, bioactive secondary metabolites. A novel strain known as MUSC 136T (=DSM 100712T = MCCC 1K01246T) which was isolated from Malaysian mangrove forest soil has proven to be no exception. Assessed by a polyphasic approach, its taxonomy showed a range of phylogenetic and chemotaxonomic properties consistent with the genus of Streptomyces. Phylogenetically, highest similarity was to Streptomyces misionensis NBRC 13063T (99.6%) along with two other strains (>98.9% sequence similarities). The DNA–DNA relatedness between MUSC 136T and these type strains ranged from 22.7 ± 0.5% to 46.5 ± 0.2%. Overall, polyphasic approach studies indicated this strain represents a novel species, for which the name Streptomyces malaysiense sp. nov. is proposed. The potential bioactivities of this strain were explored by means of antioxidant and cytotoxic assays. Intriguingly, MUSC 136T exhibited strong antioxidative activities as evaluated by a panel of antioxidant assays. It was also found to possess high cytotoxic effect against HCT-116 cells, which probably mediated through altering p53 protein and intracellular glutathione levels. Chemical analysis of the extract using GC-MS further affirms that the strain produces chemopreventive related metabolites.
Collapse
Affiliation(s)
- Hooi-Leng Ser
- School of Pharmacy, Monash University Malaysia, 47500 Bandar Sunway, Malaysia.,Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Uma Devi Palanisamy
- Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Bey-Hing Goh
- School of Pharmacy, Monash University Malaysia, 47500 Bandar Sunway, Malaysia.,Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia.,Center of Health Outcomes Research and Therapeutic Safety (Cohorts), School of Pharmaceutical Sciences, University of Phayao, Phayao, Thailand
| | - Learn-Han Lee
- School of Pharmacy, Monash University Malaysia, 47500 Bandar Sunway, Malaysia.,Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia.,Center of Health Outcomes Research and Therapeutic Safety (Cohorts), School of Pharmaceutical Sciences, University of Phayao, Phayao, Thailand
| |
Collapse
|
33
|
Yu CY, Ang GY, Cheng HJ, Cheong YM, Yin WF, Chan KG. Draft genome sequence of a multidrug-resistant Chryseobacterium indologenes isolate from Malaysia. Genom Data 2016; 7:185-6. [PMID: 26981402 PMCID: PMC4778611 DOI: 10.1016/j.gdata.2015.12.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 12/29/2015] [Indexed: 11/16/2022]
Abstract
Chryseobacterium indologenes is an emerging pathogen which poses a threat in clinical healthcare setting due to its multidrug-resistant phenotype and its common association with nosocomial infections. Here, we report the draft genome of a multidrug-resistant C. indologenes CI_885 isolated in 2014 from Malaysia. The 908,704-kb genome harbors a repertoire of putative antibiotic resistance determinants which may elucidate the molecular basis and underlying mechanisms of its resistant to various classes of antibiotics. The genome sequence has been deposited in DDBJ/EMBL/GenBank under the accession number LJOD00000000.
Collapse
Affiliation(s)
- Choo Yee Yu
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Geik Yong Ang
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Huey Jia Cheng
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Yuet Meng Cheong
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, s46150 Bandar Sunway, Selangor, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| |
Collapse
|
34
|
Ee R, Madhaiyan M, Ji L, Lim YL, Nor NM, Tee KK, Chen JW, Yin WF. Chania multitudinisentens gen. nov., sp. nov., an N-acyl-homoserine-lactone-producing bacterium in the family Enterobacteriaceae isolated from landfill site soil. Int J Syst Evol Microbiol 2016; 66:2297-2304. [PMID: 26978486 DOI: 10.1099/ijsem.0.001025] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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).
Collapse
Affiliation(s)
- Robson Ee
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Munusamy Madhaiyan
- Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Lianghui Ji
- Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Yan-Lue Lim
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Nuruddin Muhammad Nor
- Department of Microbiology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Kok-Keng Tee
- Centre of Excellence for Research in AIDS (CERiA), Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Jian-Woon Chen
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| |
Collapse
|
35
|
Chan KG, Yin WF, Chan XY. Whole genome analysis of Klebsiella pneumoniae T2-1-1 from human oral cavity. Genomics Data 2016; 7:105-6. [PMID: 26981378 PMCID: PMC4778642 DOI: 10.1016/j.gdata.2015.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 12/15/2015] [Indexed: 11/27/2022]
|
36
|
Lim YL, Ee R, Yong D, Yu CY, Ang GY, Tee KK, Yin WF, Chan KG. Complete Genome Sequence Analysis of Pandoraea pnomenusa Type Strain DSM 16536(T) Isolated from a Cystic Fibrosis Patient. Front Microbiol 2016; 7:109. [PMID: 26903988 PMCID: PMC4744841 DOI: 10.3389/fmicb.2016.00109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 01/21/2016] [Indexed: 01/07/2023] Open
Affiliation(s)
- Yan-Lue Lim
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Robson Ee
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Delicia Yong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya Kuala Lumpur, Malaysia
| | - Choo-Yee Yu
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Geik-Yong Ang
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Kok-Keng Tee
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| |
Collapse
|
37
|
Chan XY, How KY, Yin WF, Chan KG. N-Acyl Homoserine Lactone-Mediated Quorum Sensing in Aeromonas veronii biovar sobria Strain 159: Identification of LuxRI Homologs. Front Cell Infect Microbiol 2016; 6:7. [PMID: 26909339 PMCID: PMC4754395 DOI: 10.3389/fcimb.2016.00007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 01/14/2016] [Indexed: 11/13/2022] Open
Affiliation(s)
- Xin-Yue Chan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Kah-Yan How
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| |
Collapse
|
38
|
Chan KG, Yong D, Ee R, Lim YL, Yu CY, Tee KK, Yin WF, Ang GY. Complete genome sequence of Pandoraea oxalativorans DSM 23570(T), an oxalate metabolizing soil bacterium. J Biotechnol 2016; 219:124-5. [PMID: 26742625 DOI: 10.1016/j.jbiotec.2015.12.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 12/23/2015] [Indexed: 11/24/2022]
Abstract
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.
Collapse
Affiliation(s)
- Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.
| | - Delicia Yong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Robson Ee
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Yan-Lue Lim
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Choo-Yee Yu
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok-Keng Tee
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Geik-Yong Ang
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| |
Collapse
|
39
|
Zainal N, Ser HL, Yin WF, Tee KK, Lee LH, Chan KG. Streptomyces humi sp. nov., an actinobacterium isolated from soil of a mangrove forest. Antonie Van Leeuwenhoek 2016; 109:467-74. [PMID: 26786500 DOI: 10.1007/s10482-016-0653-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 01/13/2016] [Indexed: 11/30/2022]
Abstract
A novel Streptomyces strain, MUSC 119(T), was isolated from a soil collected from a mangrove forest. Cells of MUSC 119(T) stained Gram-positive and formed light brownish grey aerial mycelium and grayish yellowish brown substrate mycelium on ISP 2 medium. A polyphasic approach was used to determine the taxonomic status of strain MUSC 119(T), which shows a range of phylogenetic and chemotaxonomic properties consistent with those of the genus Streptomyces. The cell wall peptidoglycan consisted of LL-diaminopimelic acid. The predominant menaquinones were identified as MK-9(H8), MK-9(H6) and MK-9(H4). The polar lipid profile consisted of phosphatidylinositol, phosphatidylethanolamine, glycolipids, diphosphatidylglycerol and four phospholipids. The predominant cellular fatty acids were anteiso-C15:0, iso-C16:0, and anteiso-C17:0. The cell wall sugars were glucose, mannose, ribose and rhamnose. The phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain MUSC119(T) to be closely related to Streptomyces rhizophilus JR-41(T) (99.0 % sequence similarity), S. panaciradicis 1MR-8(T) (98.9 %), S. gramineus JR-43(T) (98.8 %) and S. graminisoli JR-19(T) (98.7 %). These results suggest that MUSC 119(T) should be placed within the genus Streptomyces. DNA-DNA relatedness values between MUSC 119(T) to closely related strains ranged from 14.5 ± 1.3 to 27.5 ± 0.7 %. The G+C content was determined to be 72.6 mol %. The polyphasic study of MUSC 119(T) showed that this strain represents a novel species, for which the name Streptomyces humi sp. nov. is proposed. The type strain of S. humi is MUSC 119(T) (=DSM 42174(T) = MCCC 1K00505(T)).
Collapse
Affiliation(s)
- Nurullhudda Zainal
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 46150, Bandar Sunway, Selangor Darul Ehsan, Malaysia.,Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Hooi-Leng Ser
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 46150, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Kok-Keng Tee
- Department of Medicine, Faculty of Medicine, Centre of Excellent for Research in AIDS (CERiA), University of Malaya, Kuala Lumpur, Malaysia
| | - Learn-Han Lee
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 46150, Bandar Sunway, Selangor Darul Ehsan, Malaysia.
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| |
Collapse
|
40
|
Ser HL, Ab Mutalib NS, Yin WF, Chan KG, Goh BH, Lee LH. Evaluation of Antioxidative and Cytotoxic Activities of Streptomyces pluripotens MUSC 137 Isolated from Mangrove Soil in Malaysia. Front Microbiol 2015; 6:1398. [PMID: 26733951 PMCID: PMC4679926 DOI: 10.3389/fmicb.2015.01398] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 11/24/2015] [Indexed: 12/30/2022] Open
Abstract
Streptomyces pluripotens MUSC 137 was isolated from mangrove soil obtained from Tanjung Lumpur, Pahang, Malaysia. We investigated the phylogenetic, genomic, biochemical, and phenotypic characteristics of this strain. Uniquely adapted microorganisms from mangrove habitats have previously yielded compounds of biopharmaceutical interest. In order to examine the bioactivities possessed by the strain, fermentation extract was prepared through solvent extraction method prior to bioactivities screenings. Antioxidant activity was examined via DPPH assay while the cytotoxic effect was assessed by means of examining the activity of the extract against selected human cancer cell lines, namely colon cancer cells (HCT-116, Caco-2, SW480, and HT-29), breast cancer cell (MCF-7), lung cancer cell (A549), prostate cancer cell (DU145), and cervical cancer cell (Ca Ski). The results revealed MUSC 137 possesses significant antioxidant activity and demonstrates cytotoxic effect against several cancer cell lines tested. The results indicated MCF-7 cells were most susceptible to the extract with the lowest IC50 (61.33 ± 17.10 μg/mL), followed by HCT-116 and A549. Additionally, selective index (SI) showed that MUSC 137 extract was less toxic against normal cell lines when compared to MCF-7 and HCT-116 cells. The extract was further subjected to chemical analysis using GC–MS and revealed the presence of deferoxamine and pyrrolizidines related compounds which may account for the antioxidant and cytotoxic properties observed.
Collapse
Affiliation(s)
- Hooi-Leng Ser
- Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia Bandar Sunway, Malaysia
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute-UKM Medical Centre, Universiti Kebangsaan Malaysia Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| | - Bey-Hing Goh
- Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia Bandar Sunway, Malaysia
| | - Learn-Han Lee
- Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia Bandar Sunway, Malaysia
| |
Collapse
|
41
|
Letchumanan V, Pusparajah P, Tan LTH, Yin WF, Lee LH, Chan KG. Occurrence and Antibiotic Resistance of Vibrio parahaemolyticus from Shellfish in Selangor, Malaysia. Front Microbiol 2015; 6:1417. [PMID: 26697003 PMCID: PMC4678184 DOI: 10.3389/fmicb.2015.01417] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/27/2015] [Indexed: 01/19/2023] Open
Abstract
High consumer demand for shellfish has led to the need for large-scale, reliable shellfish supply through aquaculture or shellfish farming. However, bacterial infections which can spread rapidly among shellfish poses a major threat to this industry. Shellfish farmers therefore often resort to extensive use of antibiotics, both prophylactically and therapeutically, in order to protect their stocks. The extensive use of antibiotics in aquaculture has been postulated to represent a major contributing factor in the rising incidence of antimicrobial resistant pathogenic bacteria in shellfish. This study aimed to investigate the incidence of pathogenic Vibrio parahaemolyticus and determine the antibiotic resistance profile as well as to perform plasmid curing in order to determine the antibiotic resistance mediation. Based on colony morphology, all 450 samples tested were positive for Vibrio sp; however, tox-R assay showed that only 44.4% (200/450) of these were V. parahaemolyticus. Out of these 200 samples, 6.5% (13/200) were trh-positive while none were tdh-positive. Antibiotic resistance was determined for all V. parahaemolyticus identified against 14 commonly used antibiotics and the multiple antibiotic resistance index (MAR) was calculated. The isolates demonstrated high resistance to several antibiotics tested- including second and third-line antibiotics- with 88% resistant to ampicillin, 81% to amikacin,70.5% to kanamycin, 73% to cefotaxime, and 51.5% to ceftazidime. The MAR index ranged from 0.00 to 0.79 with the majority of samples having an index of 0.36 (resistant to five antibiotics). Among the 13 trh-positive strains, almost 70% (9/13) demonstrated resistance to 4 or more antibiotics. Plasmid profiling for all V. parahaemolyticus isolates revealed that 86.5% (173/200) contained plasmids - ranging from 1 to 7 plasmids with DNA band sizes ranging from 1.2 kb to greater than 10 kb. 6/13 of the pathogenic V. pathogenic strains contained plasmid. After plasmid curing, the plasmid containing pathogenic strains isolated in our study have chromosomally mediated ampicillin resistance while the remaining resistance phenotypes are plasmid mediated. Overall, our results indicate that while the incidence of pathogenic V. parahaemolyticus in shellfish in Selangor still appears to be at relatively reassuring levels, antibiotic resistance is a real concern and warrants ongoing surveillance.
Collapse
Affiliation(s)
- Vengadesh Letchumanan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia ; Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia Bandar Sunway, Malaysia
| | - Priyia Pusparajah
- Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia Bandar Sunway, Malaysia
| | - Loh Teng-Hern Tan
- Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia Bandar Sunway, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| | - Learn-Han Lee
- Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia Bandar Sunway, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| |
Collapse
|
42
|
Ang GY, Yu CY, Cheong YM, Yin WF, Chan KG. Emergence of ST119 Acinetobacter pittii co-harbouring NDM-1 and OXA-58 in Malaysia. Int J Antimicrob Agents 2015; 47:168-9. [PMID: 26742728 DOI: 10.1016/j.ijantimicag.2015.11.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 11/16/2022]
Affiliation(s)
- Geik Yong Ang
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia.
| | - Choo Yee Yu
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Yuet Meng Cheong
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University, Bandar Sunway, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia.
| |
Collapse
|
43
|
Tan LTH, Ser HL, Yin WF, Chan KG, Lee LH, Goh BH. Investigation of Antioxidative and Anticancer Potentials of Streptomyces sp. MUM256 Isolated from Malaysia Mangrove Soil. Front Microbiol 2015; 6:1316. [PMID: 26635777 PMCID: PMC4659911 DOI: 10.3389/fmicb.2015.01316] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/09/2015] [Indexed: 12/24/2022] Open
Abstract
A Streptomyces strain, MUM256 was isolated from Tanjung Lumpur mangrove soil in Malaysia. Characterization of the strain showed that it has properties consistent with those of the members of the genus Streptomyces. In order to explore the potential bioactivities, extract of the fermented broth culture of MUM256 was prepared with organic solvent extraction method. DPPH and SOD activity were utilized to examine the antioxidant capacity and the results have revealed the potency of MUM256 in superoxide anion scavenging activity in dose-dependent manner. The cytotoxicity of MUM256 extract was determined using cell viability assay against 8 different panels of human cancer cell lines. Among all the tested cancer cells, HCT116 was the most sensitive toward the extract treatment. At the highest concentration of tested extract, the result showed 2.3-, 2.0-, and 1.8-folds higher inhibitory effect against HCT116, HT29, and Caco-2 respectively when compared to normal cell line. This result has demonstrated that MUM256 extract was selectively cytotoxic toward colon cancer cell lines. In order to determine the constituents responsible for its bioactivities, the extract was then subjected to chemical analysis using GC-MS. The analysis resulted in the identification of chemical constituents including phenolic and pyrrolopyrazine compounds which may responsible for antioxidant and anticancer activities observed. Based on the findings of this study, the presence of bioactive constituents in MUM256 extract could be a potential source for the development of antioxidative and chemopreventive agents.
Collapse
Affiliation(s)
- Loh Teng-Hern Tan
- Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia Bandar Sunway, Malaysia
| | - Hooi-Leng Ser
- Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia Bandar Sunway, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| | - Learn-Han Lee
- Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia Bandar Sunway, Malaysia
| | - Bey-Hing Goh
- Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia Bandar Sunway, Malaysia
| |
Collapse
|
44
|
Ahmad N, Chong TM, Hashim R, Shukor S, Yin WF, Chan KG. Draft Genome of Multidrug-Resistant Klebsiella pneumoniae 223/14 Carrying KPC-6, Isolated from a General Hospital in Malaysia. J Genomics 2015; 3:97-8. [PMID: 26816553 PMCID: PMC4716803 DOI: 10.7150/jgen.13910] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We performed whole genome sequencing on a clinical multidrug-resistant Klebsiella pneumoniae strain 223/14. Investigation into its draft genome revealed the presence of KPC-6 variant, suggesting carbapenemase is present in this isolate. We found a plasmid-borne KPC gene (882 bp) inserted between two transposase genes in the genome of K. pneumoniae 223/14.
Collapse
Affiliation(s)
- Norazah Ahmad
- 1. Bacteriology Unit, Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| | - Teik Min Chong
- 2. Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Rohaidah Hashim
- 1. Bacteriology Unit, Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| | - Surianti Shukor
- 1. Bacteriology Unit, Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- 2. Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Kok-Gan Chan
- 2. Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| |
Collapse
|
45
|
Azman AS, Zainal N, Mutalib NSA, Yin WF, Chan KG, Lee LH. Monashia flava gen. nov., sp. nov., an actinobacterium of the family Intrasporangiaceae. Int J Syst Evol Microbiol 2015; 66:554-561. [PMID: 26556816 DOI: 10.1099/ijsem.0.000753] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinobacterial strain, MUSC 78T, was isolated from a mangrove soil collected from Peninsular Malaysia. The taxonomic status of this strain was determined using a polyphasic approach. Comparative 16S rRNA gene sequence analysis revealed that strain MUSC 78T represented a novel lineage within the class Actinobacteria. Strain MUSC 78T formed a distinct clade in the family Intrasporangiaceae and was related most closely to members of the genera Terrabacter (98.3-96.8 % 16S rRNA gene sequence similarity), Intrasporangium (98.2-96.8 %), Humibacillus (97.2 %), Janibacter (97.0-95.3 %), Terracoccus (96.8 %), Kribbia (96.6 %), Phycicoccus (96.2-94.7 %), Knoellia (96.1-94.8 %), Tetrasphaera (96.0-94.9 %) and Lapillicoccus (95.9 %). Cells were irregular rod-shaped or cocci and stained Gram-positive. The cell-wall peptidoglycan type was A3γ, with ll-diaminopimelic acid as the diagnostic diamino acid. The main cell-wall sugar was mannose and lower amounts of galactose and rhamnose were present. The predominant menaquinone was MK-8(H4). The polar lipid profile consisted of phosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine, diphosphatidylglycerol and phosphoglycolipid. The predominant fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0. The DNA G+C content was 73.1 mol%. Based on this polyphasic study, MUSC 78T exhibited phylogenetic and phenotypic differences from members of the genera of the family Intrasporangiaceae, and therefore a novel species of a new genus, Monashia flava gen. nov., sp. nov., is proposed. The type strain of Monashia flava is MUSC 78T ( = DSM 29621T = MCCC 1K00454T = NBRC 110749T).
Collapse
Affiliation(s)
- Adzzie-Shazleen Azman
- Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences,Monash University Malaysia, 46150 Bandar Sunway, Selangor Darul Ehsan,Malaysia
| | - Nurullhudda Zainal
- Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences,Monash University Malaysia, 46150 Bandar Sunway, Selangor Darul Ehsan,Malaysia.,Division of Genetics and Molecular Biology,Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur,Malaysia
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI),UKM Medical Centre, Bandar Tun Razak, 56000 Cheras, Kuala Lumpur,Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology,Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur,Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology,Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur,Malaysia
| | - Learn-Han Lee
- Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences,Monash University Malaysia, 46150 Bandar Sunway, Selangor Darul Ehsan,Malaysia
| |
Collapse
|
46
|
Zowawi HM, Forde BM, Alfaresi M, Alzarouni A, Farahat Y, Chong TM, Yin WF, Chan KG, Li J, Schembri MA, Beatson SA, Paterson DL. Stepwise evolution of pandrug-resistance in Klebsiella pneumoniae. Sci Rep 2015; 5:15082. [PMID: 26478520 PMCID: PMC4609946 DOI: 10.1038/srep15082] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 09/01/2015] [Indexed: 01/21/2023] Open
Abstract
Carbapenem resistant Enterobacteriaceae (CRE) pose an urgent risk to global human health. CRE that are non-susceptible to all commercially available antibiotics threaten to return us to the pre-antibiotic era. Using Single Molecule Real Time (SMRT) sequencing we determined the complete genome of a pandrug-resistant Klebsiella pneumoniae isolate, representing the first complete genome sequence of CRE resistant to all commercially available antibiotics. The precise location of acquired antibiotic resistance elements, including mobile elements carrying genes for the OXA-181 carbapenemase, were defined. Intriguingly, we identified three chromosomal copies of an ISEcp1-bla(OXA-181) mobile element, one of which has disrupted the mgrB regulatory gene, accounting for resistance to colistin. Our findings provide the first description of pandrug-resistant CRE at the genomic level, and reveal the critical role of mobile resistance elements in accelerating the emergence of resistance to other last resort antibiotics.
Collapse
Affiliation(s)
- Hosam M Zowawi
- The University of Queensland, Centre for Clinical Research (UQCCR), Herston QLD 4029, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia.,College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,World Health Organization Collaborating Centre for Infection Prevention and Control, and the Gulf Cooperation Council Center for Infection Control, Riyadh, Saudi Arabia
| | - Brian M Forde
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Mubarak Alfaresi
- Pathology and Laboratory Medicine Department at Sheikh Khalifa General Hospital, Umm Al Quwain, United Arab Emirates
| | - Abdulqadir Alzarouni
- Urology Department, Sheikh Khalifa General Hospital, Umm Al Quwain, United Arab Emirates
| | - Yasser Farahat
- Urology Department, Sheikh Khalifa General Hospital, Umm Al Quwain, United Arab Emirates
| | - Teik-Min Chong
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Jian Li
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Mark A Schembri
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Scott A Beatson
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - David L Paterson
- The University of Queensland, Centre for Clinical Research (UQCCR), Herston QLD 4029, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia
| |
Collapse
|
47
|
Ser HL, Tan WS, Ab Mutalib NS, Cheng HJ, Yin WF, Chan KG, Lee LH. Genome sequence of Streptomyces pluripotens MUSC 135(T) exhibiting antibacterial and antioxidant activity. Mar Genomics 2015; 24 Pt 3:281-3. [PMID: 26452302 DOI: 10.1016/j.margen.2015.09.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/01/2015] [Accepted: 09/30/2015] [Indexed: 10/22/2022]
Abstract
Isolated from intertidal soil, Streptomyces pluripotens MUSC 135(T) produces a broad-spectrum bacteriocin against the pathogens methicillin-resistant Staphylococcus aureus (MRSA) ATCC BAA-44(T), Salmonella typhi ATCC 19430(T) and Aeromonas hydrophila ATCC 7966(T). Along with antibacterial activity, fermentation studies on strain MUSC 135(T) revealed production of antioxidant(s). The high quality draft genome of MUSC 135(T) comprises 7,480,269 bp with G+C content of 70.00%. Through bioinformatics analysis, 72 gene clusters identified in the genome were associated with the production of secondary metabolites, which may shed light on the identity of these bioactive compounds.
Collapse
Affiliation(s)
- Hooi-Leng Ser
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 46150 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Wen-Si Tan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), UKM Medical Centre, Bandar Tun Razak, 56000 Cheras, Kuala Lumpur, Malaysia
| | - Huey-Jia Cheng
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Learn-Han Lee
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 46150 Bandar Sunway, Selangor Darul Ehsan, Malaysia.
| |
Collapse
|
48
|
Lim YL, Ee R, Yong D, Tee KK, Yin WF, Chan KG. Complete genome of Pandoraea pnomenusa RB-38, an oxalotrophic bacterium isolated from municipal solid waste landfill site. J Biotechnol 2015; 214:83-4. [PMID: 26393955 DOI: 10.1016/j.jbiotec.2015.09.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 09/16/2015] [Indexed: 10/23/2022]
Abstract
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.
Collapse
Affiliation(s)
- Yan-Lue Lim
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Robson Ee
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Delicia Yong
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kok-Keng Tee
- Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| |
Collapse
|
49
|
Tan KH, Tan JY, Yin WF, Chan KG. Genome analysis of quorum sensing Cedecea neteri SSMD04 leads to identification of its novel signaling synthase (cneI), cognate receptor (cneR) and an orphan receptor. PeerJ 2015; 3:e1216. [PMID: 26355540 PMCID: PMC4562240 DOI: 10.7717/peerj.1216] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 08/05/2015] [Indexed: 11/20/2022] Open
Abstract
Cedecea neteri is a very rare human pathogen. We have isolated a strain of C. neteri SSMD04 from pickled mackerel sashimi identified using molecular and phenotypics approaches. Using the biosensor Chromobacterium violaceum CV026, we have demonstrated the presence of short chain N-acyl-homoserine lactone (AHL) type quorum sensing (QS) activity in C. neteri SSMD04. Triple quadrupole LC/MS analysis revealed that C. neteri SSMD04 produced short chain N-butyryl-homoserine lactone (C4-HSL). With the available genome information of C. neteri SSMD04, we went on to analyse and identified a pair of luxI/R homologues in this genome that share the highest similarity with croI/R homologues from Citrobacter rodentium. The AHL synthase, which we named cneI(636 bp), was found in the genome sequences of C. neteri SSMD04. At a distance of 8bp from cneI is a sequence encoding a hypothetical protein, potentially the cognate receptor, a luxR homologue which we named it as cneR. Analysis of this protein amino acid sequence reveals two signature domains, the autoinducer-binding domain and the C-terminal effector which is typical characteristic of luxR. In addition, we found that this genome harboured an orphan luxR that is most closely related to easR in Enterobacter asburiae. To our knowledge, this is the first report on the AHL production activity in C. neteri, and the discovery of its luxI/R homologues, the orphan receptor and its whole genome sequence.
Collapse
Affiliation(s)
- Kian-Hin Tan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya , Kuala Lumpur , Malaysia
| | - Jia-Yi Tan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya , Kuala Lumpur , Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya , Kuala Lumpur , Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya , Kuala Lumpur , Malaysia
| |
Collapse
|
50
|
Lim YL, Ee R, How KY, Lee SK, Yong D, Tee KK, Yin WF, Chan KG. Complete genome sequencing of Pandoraea pnomenusa RB38 and Molecular Characterization of Its N-acyl homoserine lactone synthase gene ppnI. PeerJ 2015; 3:e1225. [PMID: 26336650 PMCID: PMC4556143 DOI: 10.7717/peerj.1225] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 08/11/2015] [Indexed: 01/05/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- Yan-Lue Lim
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya , Kuala Lumpur , Malaysia
| | - Robson Ee
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya , Kuala Lumpur , Malaysia
| | - Kah-Yan How
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya , Kuala Lumpur , Malaysia
| | - Siew-Kim Lee
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya , Kuala Lumpur , Malaysia
| | - Delicia Yong
- Department of Medicine, Faculty of Medicine, University of Malaya , Kuala Lumpur , Malaysia
| | - Kok Keng Tee
- Department of Medicine, Faculty of Medicine, University of Malaya , Kuala Lumpur , Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya , Kuala Lumpur , Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya , Kuala Lumpur , Malaysia
| |
Collapse
|