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Gosset-Erard C, Han G, Kyrko D, Hueber A, Nay B, Eparvier V, Touboul D. Structural characterization of N-acyl-homoserine lactones from bacterial quorum sensing using LC-MS/MS analyses after Paternò-Büchi derivatization in solution. Anal Bioanal Chem 2024; 416:5431-5443. [PMID: 38842688 DOI: 10.1007/s00216-024-05355-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/05/2024] [Accepted: 05/07/2024] [Indexed: 06/07/2024]
Abstract
Bacterial quorum sensing is a chemical language allowing bacteria to interact through the excretion of molecules called autoinducers, like N-acyl-homoserine lactones (AHLs) produced by Gram-negative Burkholderia and Paraburkholderia bacteria known as opportunistic pathogens. The AHLs differ in their acyl-chain length and may be modified by a 3-oxo or 3-hydroxy substituent, or C = C double bonds at different positions. As the bacterial signal specificity depends on all of these chemical features, their structural characterization is essential to have a better understanding of the population regulation and virulence phenomenon. This study aimed at enabling the localization of the C = C double bond on such specialized metabolites while using significantly lower amounts of biological material. The approach is based on LC-MS/MS analyses of bacterial extracts after in-solution derivatization by a photochemical Paternò-Büchi reaction, leading to the formation of an oxetane ring and subsequently to specific fragmentations when performing MS/MS experiments. The in-solution derivatization of AHLs was optimized on several standards, and then the matrix effect of bacterial extracts on the derivatization was assessed. As a proof of concept, the optimized conditions were applied to a bacterial extract enabling the localization of C = C bonds on unsaturated AHLs.
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Affiliation(s)
- Clarisse Gosset-Erard
- Université Paris-Saclay, CNRS, Institut de Chimie Des Substances Naturelles, UPR 2301, 91198, Gif-Sur-Yvette, France
| | - Guanghui Han
- Laboratoire de Synthèse Organique (LSO), CNRS UMR 7652, Ecole Polytechnique, ENSTA, Institut Polytechnique de Paris, 91128, Palaiseau, France
| | - Dimitra Kyrko
- Université Paris-Saclay, CNRS, Institut de Chimie Des Substances Naturelles, UPR 2301, 91198, Gif-Sur-Yvette, France
| | - Amandine Hueber
- Université Paris-Saclay, CNRS, Institut de Chimie Des Substances Naturelles, UPR 2301, 91198, Gif-Sur-Yvette, France
| | - Bastien Nay
- Laboratoire de Synthèse Organique (LSO), CNRS UMR 7652, Ecole Polytechnique, ENSTA, Institut Polytechnique de Paris, 91128, Palaiseau, France
| | - Véronique Eparvier
- Université Paris-Saclay, CNRS, Institut de Chimie Des Substances Naturelles, UPR 2301, 91198, Gif-Sur-Yvette, France
| | - David Touboul
- Université Paris-Saclay, CNRS, Institut de Chimie Des Substances Naturelles, UPR 2301, 91198, Gif-Sur-Yvette, France.
- Laboratoire de Chimie Moléculaire (LCM), CNRS UMR 9168, Ecole Polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, France.
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Li J, Xiong M, Fu XH, Fan Y, Dong C, Sun X, Zheng F, Wang SW, Liu L, Xu M, Wang C, Ping J, Che S, Wang Q, Yang K, Zuo Y, Lu X, Zheng Z, Lan T, Wang S, Ma S, Sun S, Zhang B, Chen CS, Cheng KY, Ye J, Qu J, Xue Y, Yang YG, Zhang F, Zhang W, Liu GH. Determining a multimodal aging clock in a cohort of Chinese women. MED 2023; 4:825-848.e13. [PMID: 37516104 DOI: 10.1016/j.medj.2023.06.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/25/2023] [Accepted: 06/30/2023] [Indexed: 07/31/2023]
Abstract
BACKGROUND Translating aging rejuvenation strategies into clinical practice has the potential to address the unmet needs of the global aging population. However, to successfully do so requires precise quantification of aging and its reversal in a way that encompasses the complexity and variation of aging. METHODS Here, in a cohort of 113 healthy women, tiled in age from young to old, we identified a repertoire of known and previously unknown markers associated with age based on multimodal measurements, including transcripts, proteins, metabolites, microbes, and clinical laboratory values, based on which an integrative aging clock and a suite of customized aging clocks were developed. FINDINGS A unified analysis of aging-associated traits defined four aging modalities with distinct biological functions (chronic inflammation, lipid metabolism, hormone regulation, and tissue fitness), and depicted waves of changes in distinct biological pathways peak around the third and fifth decades of life. We also demonstrated that the developed aging clocks could measure biological age and assess partial aging deceleration by hormone replacement therapy, a prevalent treatment designed to correct hormonal imbalances. CONCLUSIONS We established aging metrics that capture systemic physiological dysregulation, a valuable framework for monitoring the aging process and informing clinical development of aging rejuvenation strategies. FUNDING This work was supported by the National Natural Science Foundation of China (32121001), the National Key Research and Development Program of China (2022YFA1103700 and 2020YFA0804000), the National Natural Science Foundation of China (81502304), and the Quzhou Technology Projects (2022K46).
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Affiliation(s)
- Jiaming Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Muzhao Xiong
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xiang-Hong Fu
- Center for Reproductive Medicine, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, China; Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, China
| | - Yanling Fan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Chen Dong
- State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, Beijing 100876, China
| | - Xiaoyan Sun
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Zheng
- Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, China
| | - Si-Wei Wang
- Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, China
| | - Lixiao Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ming Xu
- State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, Beijing 100876, China
| | - Cui Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jiale Ping
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Shanshan Che
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Qiaoran Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Kuan Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yuesheng Zuo
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyong Lu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zikai Zheng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Tian Lan
- Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, China
| | - Si Wang
- Aging Biomarker Consortium, Beijing 100101, China; Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Shuai Ma
- Aging Biomarker Consortium, Beijing 100101, China; State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Shuhui Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Bin Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Chen-Shui Chen
- Department of Respiratory and Critical Care Medicine, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, China; Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, China
| | - Ke-Yun Cheng
- Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, China
| | - Jinlin Ye
- Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, China
| | - Jing Qu
- Aging Biomarker Consortium, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Yongbiao Xue
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yun-Gui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
| | - Feng Zhang
- Center for Reproductive Medicine, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, China; The Joint Innovation Center for Engineering in Medicine, Quzhou People's Hospital, Quzhou 324000, China; Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, China.
| | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Aging Biomarker Consortium, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China.
| | - Guang-Hui Liu
- Aging Biomarker Consortium, Beijing 100101, China; State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
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Tan KY, Deng S, Tan TK, Hari R, Sitam FT, Othman RY, Wong KT, Mohidin TBM, Choo SW. Genome sequence analysis of Malayan pangolin ( Manis javanica) forensic samples reveals the presence of Paraburkholderia fungorum sequences. PeerJ 2023; 11:e16002. [PMID: 37810781 PMCID: PMC10559893 DOI: 10.7717/peerj.16002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 08/09/2023] [Indexed: 10/10/2023] Open
Abstract
Background The Malayan pangolin (Manis javanica) is a placental mammal and is listed as Critically Endangered on the IUCN Red List of Threatened Species. Most previous attempts to breed pangolins in captivity have met with little success because of dietary issues, infections, and other complications, although a previous study reported breeding pangolins in captivity to the third generation. In our previous pangolin genome sequencing data analysis, we obtained a considerable amount of bacterial DNA from a pregnant female Malayan pangolin (named "UM3"), which was likely infected by Paraburkholderia fungorum-an agent of biodegradation and bioremediation in agriculture. Methodology Here, we further confirmed and characterized this bacterial species using PCR, histological staining, whole-genome sequencing, and bioinformatics approaches. PCR assays with in-house designed primer sets and 16S universal primers showed clear positive bands in the cerebrum, cerebellum, lung, and blood of UM3 suggesting that UM3 might have developed septicaemia. Histological staining showed the presence of Gram-negative rod-shaped bacteria in the pangolin brain and lungs, indicating the colonization of the bacteria in these two organs. In addition, PCR screening of UM3's fetal tissues revealed the presence of P. fungorum in the gastrocnemius muscle, but not in other tissues that we examined. We also sequenced and reconstructed the genome of pangolin P. fungorum, which has a genome size of 7.7 Mbps. Conclusion Our study is the first to present detailed evidence of the presence of P. fungorum in a pangolin and her fetus (although preliminary results were presented in our previous article). Here, we raise the concern that P. fungorum may potentially infect humans, especially YOPI (young, old, pregnant, and immunocompromised) people. Therefore, caution should be exercised when using this bacterial species as biodegradation or bioremediation agents in agriculture.
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Affiliation(s)
- Ka Yun Tan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Siwei Deng
- College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang, China
| | - Tze King Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ranjeev Hari
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Frankie Thomas Sitam
- National Wildlife Forensic Laboratory, Department of Wildlife and National Parks (PERHILITAN), Kuala Lumpur, Malaysia
| | - Rofina Yasmin Othman
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Kum Thong Wong
- Department of Pathology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Siew Woh Choo
- College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou, Zhejiang, China
- Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang, China
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5
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Keaney D, Lucey B, Quinn N, Finn K. The Effects of Freeze-Thaw and UVC Radiation on Microbial Survivability in a Selected Mars-like Environment. Microorganisms 2022; 10:microorganisms10030576. [PMID: 35336151 PMCID: PMC8956125 DOI: 10.3390/microorganisms10030576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/23/2022] [Accepted: 03/04/2022] [Indexed: 02/06/2023] Open
Abstract
The purpose of this study was to determine survivability of Escherichia coli, Deinococcus radiodurans and Paraburkholderia fungorum under Mars-simulated conditions for freeze-thawing (−80 °C to +30 °C) and UV exposure alone and in combination. E. coli ATCC 25922, D. radiodurans and P. fungorum remained viable following 20 successive freeze-thaw cycles, exhibiting viabilities of 2.3%, 96% and 72.6%, respectively. E. coli ATCC 9079 was non-recoverable by cycle 9. When exposed to UV irradiation, cells withstood doses of 870 J/m2 (E. coli ATCC 25922), 200 J/m2 (E. coli ATCC 9079), 50,760 J/m2 (D. radiodurans) and 44,415 J/m2 (P. fungorum). Data suggests P. fungorum is highly UV-resistant. Combined freeze-thawing with UV irradiation showed freezing increased UV resistance in E. coli ATCC 25922, E. coli DSM 9079 and D. radiodurans by 6-fold, 30-fold and 1.2-fold, respectively. Conversely, freezing caused P. fungorum to exhibit a 1.75-fold increase in UV susceptibility. Strain-dependent experimentation demonstrated that freezing increases UV resistance and prolongs survival. These findings suggest that exposure to short wavelength UV rays (254 nm) and temperature cycles resembling the daily fluctuating conditions on Mars do not significantly affect survival of D. radiodurans, P. fungorum and E. coli ATCC 25922 following 20 days of exposure.
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Affiliation(s)
- Daniel Keaney
- Department of Biological Sciences, Munster Technological University, Bishopstown, T12 P928 Cork, Ireland; (D.K.); (B.L.)
| | - Brigid Lucey
- Department of Biological Sciences, Munster Technological University, Bishopstown, T12 P928 Cork, Ireland; (D.K.); (B.L.)
| | - Noreen Quinn
- Department of Mathematics, Munster Technological University, Bishopstown, T12 P928 Cork, Ireland;
| | - Karen Finn
- Department of Analytical, Biopharmaceutical and Medical Sciences, Galway-Mayo Institute of Technology, Old Dublin Road, H91 T8NW Galway, Ireland
- Correspondence:
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TIONG V, LOONG SK, MOHAMAD WALI HA, TAN KK, JEE PF, LIM FS, KHOO JJ, WONG PF, CHANG LY, ABUBAKAR S. Isolation of Streptococcus cuniculi from corneal lesion in laboratory-raised mice. J Vet Med Sci 2021; 83:280-284. [PMID: 33441499 PMCID: PMC7972885 DOI: 10.1292/jvms.20-0070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 09/14/2020] [Indexed: 11/22/2022] Open
Abstract
Corneal lesions appearing as white mass beneath intact epithelium, with ocular discharge in one mouse, was observed in a batch of laboratory-raised BALB/c mice (n=9 of 56). The affected mice remained active, well-groomed and had normal appetite. Isolates recovered from swab cultures of the external and internal contents of the eye had partial 16S rRNA gene sequence of 99.1% similarity to Streptococcus cuniculi. No previous report of S. cuniculi infection in laboratory rodents has been presented. The isolate was susceptible to all antibiotics tested. We suggest S. cuniculi is an opportunistic bacteria in laboratory mice but are uncertain of its source. Our findings revealed that S. cuniculi is able to colonize laboratory mice and should be considered when mice present with eye lesion or ocular discharge.
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Affiliation(s)
- Vunjia TIONG
- Tropical Infectious Diseases Research & Education
Centre, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Shih-Keng LOONG
- Tropical Infectious Diseases Research & Education
Centre, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | | | - Kim-Kee TAN
- Tropical Infectious Diseases Research & Education
Centre, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Pui-Fong JEE
- Department of Medical Microbiology, Faculty of Medicine,
University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Fang-Shiang LIM
- Tropical Infectious Diseases Research & Education
Centre, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Jing-Jing KHOO
- Tropical Infectious Diseases Research & Education
Centre, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Pooi-Fong WONG
- Animal Experimental Unit, Faculty of Medicine, University of
Malaya, 50603 Kuala Lumpur, Malaysia
- Department of Pharmacology, Faculty of Medicine, University
of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Li-Yen CHANG
- Department of Medical Microbiology, Faculty of Medicine,
University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Sazaly ABUBAKAR
- Tropical Infectious Diseases Research & Education
Centre, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Department of Medical Microbiology, Faculty of Medicine,
University of Malaya, 50603 Kuala Lumpur, Malaysia
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7
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Tan KY, Dutta A, Tan TK, Hari R, Othman RY, Choo SW. Comprehensive genome analysis of a pangolin-associated Paraburkholderia fungorum provides new insights into its secretion systems and virulence. PeerJ 2020; 8:e9733. [PMID: 32953261 PMCID: PMC7474880 DOI: 10.7717/peerj.9733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/25/2020] [Indexed: 12/26/2022] Open
Abstract
Background Paraburkholderia fungorum (P. fungorum) is a Gram-negative environmental species that has been commonly used as a beneficial microorganism in agriculture as an agent for biocontrol and bioremediation. Its use in agriculture is controversial as many people believe that it could harm human health; however, there is no clear evidence to support. Methodology The pangolin P. fungorum (pangolin Pf) genome has a genomic size of approximately 7.7 Mbps with N50 of 69,666 bps. Our study showed that pangolin Pf is a Paraburkholderia fungorum supported by evidence from the core genome SNP-based phylogenetic analysis and the ANI analysis. Functional analysis has shown that the presence of a considerably large number of genes related to stress response, virulence, disease, and defence. Interestingly, we identified different types of secretion systems in the genome of pangolin Pf, which are highly specialized and responsible for a bacterium’s response to its environment and in physiological processes such as survival, adhesion, and adaptation. The pangolin Pf also shared some common virulence genes with the known pathogenic member of the Burkholderiales. These genes play important roles in adhesion, motility, and invasion. Conclusion This study may provide better insights into the functions, secretion systems and virulence of this pangolin-associated bacterial strain. The addition of this genome sequence is also important for future comparative analysis and functional work of P. fungorum.
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Affiliation(s)
- Ka Yun Tan
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia.,Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), High Impact Research Building, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Avirup Dutta
- Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), High Impact Research Building, Universiti Malaya, Kuala Lumpur, Malaysia.,Current affiliation: The Novo Nordisk Foundation Center for Basic Metabolic Research, Human Genomics and Metagenomics in Metabolism, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tze King Tan
- Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), High Impact Research Building, Universiti Malaya, Kuala Lumpur, Malaysia.,Current affiliation: Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ranjeev Hari
- Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), High Impact Research Building, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Rofina Y Othman
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia.,Centre for Research in Biotechnology for Agriculture (CEBAR), Level 3, Research Management & Innovation Complex, Universiti Malaya, Copenhagen, Kuala Lumpur, Malaysia
| | - Siew Woh Choo
- College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
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