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Lee SQE, Ma GL, Candra H, Khandelwal S, Pang LM, Low ZJ, Cheang QW, Liang ZX. Streptomyces sungeiensis SD3 as a Microbial Chassis for the Heterologous Production of Secondary Metabolites. ACS Synth Biol 2024; 13:1259-1272. [PMID: 38513222 DOI: 10.1021/acssynbio.3c00750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
We present the newly isolated Streptomyces sungeiensis SD3 strain as a promising microbial chassis for heterologous production of secondary metabolites. S. sungeiensis SD3 exhibits several advantageous traits as a microbial chassis, including genetic tractability, rapid growth, susceptibility to antibiotics, and metabolic capability supporting secondary metabolism. Genomic and transcriptomic sequencing unveiled the primary metabolic capabilities and secondary biosynthetic pathways of S. sungeiensis SD3, including a previously unknown pathway responsible for the biosynthesis of streptazone B1. The unique placement of S. sungeiensis SD3 in the phylogenetic tree designates it as a type strain, setting it apart from other frequently employed Streptomyces chassis. This distinction makes it the preferred chassis for expressing biosynthetic gene clusters (BGCs) derived from strains within the same phylogenetic or neighboring phylogenetic clade. The successful expression of secondary biosynthetic pathways from a closely related yet slow-growing strain underscores the utility of S. sungeiensis SD3 as a heterologous expression chassis. Validation of CRISPR/Cas9-assisted genetic tools for chromosomal deletion and insertion paved the way for further strain improvement and BGC refactoring through rational genome editing. The addition of S. sungeiensis SD3 to the heterologous chassis toolkit will facilitate the discovery and production of secondary metabolites.
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Affiliation(s)
- Sean Qiu En Lee
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Guang-Lei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hartono Candra
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Srashti Khandelwal
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Li Mei Pang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Zhen Jie Low
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Qing Wei Cheang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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2
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Cheng T, Cheang QW, Xu L, Sheng S, Li Z, Shi Y, Zhang H, Pang LM, Liu DX, Yang L, Liang ZX, Wang J. A PilZ domain protein interacts with the transcriptional regulator HinK to regulate type VI secretion system in Pseudomonas aeruginosa. J Biol Chem 2024; 300:105741. [PMID: 38340793 PMCID: PMC10912698 DOI: 10.1016/j.jbc.2024.105741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/29/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024] Open
Abstract
Type VI secretion systems (T6SS) are bacterial macromolecular complexes that secrete effectors into target cells or the extracellular environment, leading to the demise of adjacent cells and providing a survival advantage. Although studies have shown that the T6SS in Pseudomonas aeruginosa is regulated by the Quorum Sensing system and second messenger c-di-GMP, the underlying molecular mechanism remains largely unknown. In this study, we discovered that the c-di-GMP-binding adaptor protein PA0012 has a repressive effect on the expression of the T6SS HSI-I genes in P. aeruginosa PAO1. To probe the mechanism by which PA0012 (renamed TssZ, Type Six Secretion System -associated PilZ protein) regulates the expression of HSI-I genes, we conducted yeast two-hybrid screening and identified HinK, a LasR-type transcriptional regulator, as the binding partner of TssZ. The protein-protein interaction between HinK and TssZ was confirmed through co-immunoprecipitation assays. Further analysis suggested that the HinK-TssZ interaction was weakened at high c-di-GMP concentrations, contrary to the current paradigm wherein c-di-GMP enhances the interaction between PilZ proteins and their partners. Electrophoretic mobility shift assays revealed that the non-c-di-GMP-binding mutant TssZR5A/R9A interacts directly with HinK and prevents it from binding to the promoter of the quorum-sensing regulator pqsR. The functional connection between TssZ and HinK is further supported by observations that TssZ and HinK impact the swarming motility, pyocyanin production, and T6SS-mediated bacterial killing activity of P. aeruginosa in a PqsR-dependent manner. Together, these results unveil a novel regulatory mechanism wherein TssZ functions as an inhibitor that interacts with HinK to control gene expression.
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Affiliation(s)
- Tianfang Cheng
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Qing Wei Cheang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Linghui Xu
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Shuo Sheng
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China; Key Laboratory of Basic Pharmacology of the Ministry of Education, Joint International Research Laboratory of Ethnomedicine of the Ministry of Education and Key Laboratory of Basic Pharmacology of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou, China
| | - Zhaoting Li
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Yu Shi
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Huiyan Zhang
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Li Mei Pang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Ding Xiang Liu
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Liang Yang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Junxia Wang
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China.
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Yang Y, Guo S, Hong CJ, Liang ZX, Ho CL. Initial cyclic-di-GMP upregulation triggers sporadic cellular expansion leading to improved cellular survival. Biotechnol J 2024; 19:e2300542. [PMID: 38403404 DOI: 10.1002/biot.202300542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/29/2023] [Accepted: 01/18/2024] [Indexed: 02/27/2024]
Abstract
Bacterial second messenger c-di-GMP upregulation is associated with the transition from planktonic to sessile microbial lifestyle, inhibiting cellular motility, and virulence. However, in-depth elucidation of the cellular processes resulting from c-di-GMP upregulation has not been fully explored. Here, we report the role of upregulated cellular c-di-GMP in promoting planktonic cell growth of Escherichia coli K12 and Pseudomonas aeruginosa PAO1. We found a rapid expansion of cellular growth during initial cellular c-di-GMP upregulation, resulting in a larger planktonic bacterial population. The initial increase in c-di-GMP levels promotes bacterial swarming motility during the growth phase, which is subsequently inhibited by the continuous increase of c-di-GMP, and ultimately facilitates the formation of biofilms. We demonstrated that c-di-GMP upregulation triggers key bacterial genes linked to bacterial growth, swarming motility, and biofilm formation. These genes are mainly controlled by the master regulatory genes csgD and csrA. This study provides us a glimpse of the bacterial behavior of evading potential threats through adapting lifestyle changes via c-di-GMP regulation.
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Affiliation(s)
- Yongshuai Yang
- Department of Biomedical Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Siyu Guo
- Department of Biomedical Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Can-Jian Hong
- Department of Biomedical Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Zhao-Xun Liang
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chun Loong Ho
- Department of Biomedical Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology (SIAT), Chinese Academy of Sciences, Shenzhen, China
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Liao Y, Wang XJ, Ma GL, Candra H, Qiu En SL, Khandelwal S, Liang ZX. Biosynthesis of Octacosamicin A: Uncommon Starter/extender Units and Product Releasing via Intermolecular Amidation. Chembiochem 2024; 25:e202300590. [PMID: 37908177 DOI: 10.1002/cbic.202300590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/02/2023]
Abstract
Octacosamicin A is an antifungal metabolite featuring a linear polyene-polyol chain flanked by N-hydroxyguanidine and glycine moieties. We report here that sub-inhibitory concentrations of streptomycin elicited the production of octacosamicin A in Amycolatopsis azurea DSM 43854T . We identified the biosynthetic gene cluster (oca BGC) that encodes a modular polyketide synthase (PKS) system for assembling the polyene-polyol chain of octacosamicin A. Our analysis suggested that the N-hydroxyguanidine unit originates from a 4-guanidinobutyryl-CoA starter unit, while the PKS incorporates an α-hydroxyketone moiety using a (2R)-hydroxymalonyl-CoA extender unit. The modular PKS system contains a non-canonical terminal module that lacks thioesterase (TE) and acyl carrier protein (ACP) domains, indicating the biosynthesis is likely to employ an unconventional and cryptic off-loading mechanism that attaches glycine to the polyene-polyol chain via an intermolecular amidation reaction.
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Affiliation(s)
- Yanghui Liao
- School of Biological Sciences, Nanyang Technological University, Singapore, 67551, Singapore
| | - Xue-Jiao Wang
- School of Biological Sciences, Nanyang Technological University, Singapore, 67551, Singapore
| | - Guang-Lei Ma
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314102, China
| | - Hartono Candra
- School of Biological Sciences, Nanyang Technological University, Singapore, 67551, Singapore
| | - Sean Lee Qiu En
- School of Biological Sciences, Nanyang Technological University, Singapore, 67551, Singapore
| | - Srashti Khandelwal
- School of Biological Sciences, Nanyang Technological University, Singapore, 67551, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore, 67551, Singapore
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Wang LS, Tang YB, Liang ZX. [Research progress on the preventive and therapeutic effects of exercise on gestational diabetes mellitus]. Zhonghua Yu Fang Yi Xue Za Zhi 2023; 57:1808-1812. [PMID: 38008570 DOI: 10.3760/cma.j.cn112150-20230119-00047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/28/2023]
Abstract
Gestational diabetes mellitus (GDM) is one of the most common complications of pregnancy, which poses a serious health risk to mothers and infants. In recent years, many studies have revealed the important role of exercise in preventing GDM, regulating blood glucose and ameliorating insulin resistance, as well as its potential value as an emerging therapeutic approach in improving maternal and infant outcomes and long-term health. This review discusses the latest research progress on the effect of exercise on the prevention and treatment of GDM, aims to deepen the knowledge of exercise therapy for GDM and provides guidance and assistance for the clinical treatment of GDM.
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Affiliation(s)
- L S Wang
- Department of Obstetric, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Y B Tang
- Department of Obstetric, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Z X Liang
- Department of Obstetric, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
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Turner MS, Xiang Y, Liang ZX, Marcellin E, Pham HT. Cyclic-di-AMP signalling in lactic acid bacteria. FEMS Microbiol Rev 2023:7177525. [PMID: 37222477 DOI: 10.1093/femsre/fuad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
Cyclic-di-AMP is a nucleotide second messenger present in Gram-positive bacteria and some Gram-negative bacteria and Archaea. The intracellular concentration of cyclic-di-AMP is adjusted in response to environmental and cellular cues, primarily through the activities of synthesis and degradation enzymes. It performs its role by binding to protein and riboswitch receptors, many of which contribute to osmoregulation. Imbalances in cyclic-di-AMP can lead to pleiotropic phenotypes, affecting aspects such as growth, biofilm formation, virulence and resistance to osmotic, acid and antibiotic stressors. This review focuses on cyclic-di-AMP signalling in lactic acid bacteria (LAB) incorporating recent experimental discoveries and presenting an analysis of signalling components from a variety of LAB including those found in food, and commensal, probiotic and pathogenic species. All LAB possess enzymes for the synthesis and degradation of cyclic-di-AMP, but they are highly variable with regards to the receptors they possess. Studies in Lactococcus and Streptococcus have revealed a conserved function for c-di-AMP in inhibiting the transport of potassium and glycine betaine, either through direct binding to transporters or to a transcriptional regulator. Structural analysis of several cyclic-di-AMP receptors from LAB has also provided insights into how this nucleotide exerts its influence.
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Affiliation(s)
- Mark S Turner
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Yuwei Xiang
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
| | - Huong Thi Pham
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia
- The University of Danang, University of Science and Technology, Da Nang, Vietnam
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7
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Zhu SQ, Tang YB, Liang ZX. [New research advances in the prospective cohort study of gestational diabetes mellitus]. Zhonghua Yu Fang Yi Xue Za Zhi 2023; 57:771-777. [PMID: 37165826 DOI: 10.3760/cma.j.cn112150-20220530-00546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Gestational diabetes mellitus (GDM) is associated with an increased risk of suffering diverse adverse pregnancy outcomes, threating maternal and child health seriously, with an increasing incidence rate year by year. However, the exact cause of GDM is still unknown. Prospective cohort studies obtain data through follow-up, which is helpful to clarify the causal relationship, so as to draw more accurate and reliable conclusions. In recent years, numerous prospective cohort studies on the GDM have emerged. This article elaborates along the occurrence and development process of GDM, in order to provide useful reference for the establishment of relevant high-quality prospective cohort studies in China.
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Affiliation(s)
- S Q Zhu
- Obstetrical Department, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China
| | - Y B Tang
- Obstetrical Department, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China
| | - Z X Liang
- Obstetrical Department, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China
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8
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Ye LY, Zhu SQ, Liang ZX. [Research progress on the relationship between persistent organic pollutants and gestational diabetes]. Zhonghua Yu Fang Yi Xue Za Zhi 2023; 57:166-171. [PMID: 36797572 DOI: 10.3760/cma.j.cn112150-20220417-00376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Gestational diabetes mellitus(GDM)is one of the common complications during pregnancy. It is associated with many adverse pregnancy outcomes, threatening maternal and child health seriously. The exact pathogenesis of GDM remains unclear. Long term exposure to persistent organic pollutants (POPs) is considered to be one of the risk factors for GDM. More and more studies are concerned about the relationship between them. Based on the literature published at home and abroad, this article summarizes the correlation and possibly related mechanism of POPs and GDM, and explores the correlation between pops and GDM, so as to provide a new idea for the prevention of gestational diabetes.
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Affiliation(s)
- L Y Ye
- Department of Obstetrics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China Department of Obstetrics,Taizhou Hospital, Zhejiang University, Taizhou 317000, China
| | - S Q Zhu
- Department of Obstetrics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China
| | - Z X Liang
- Department of Obstetrics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China
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Candra H, Ma GL, En SLQ, Liang ZX. Enaminone Formation Drives the Coupling of Biosynthetic Pathways to Generate Cyclic Lipopeptides. Chembiochem 2022; 23:e202200457. [PMID: 36161451 DOI: 10.1002/cbic.202200457] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 08/08/2022] [Revised: 09/17/2022] [Indexed: 02/03/2023]
Abstract
A family of novel cyclic lipopeptides named tasikamides A-H (Tsk A-H) were discovered recently in Streptomyces tasikensis P46. Aside from the unique cyclic pentapeptide scaffold shared by the tasikamides, Tsk A-C contain a hydrazone bridge that connects the cyclic pentapeptide to the lipophilic alkyl 5-hydroxylanthranilate (AHA) moiety. Here we report the production of tasikamides I-K (Tsk I-K) by a mutant strain of S. tasikensis P46 that overexpresses two pathway-specific transcription regulators. Unlike Tsk A-C, Tsk I-K feature a rare enaminone-bridge that links the cyclic peptide scaffold to the AHA moiety. Our experimental data suggest that Tsk I-K are generated by the coupling of two biosynthetic pathways via a nonenzymatic condensation reaction between an arylamine and a β-keto aldehyde-containing precursor. The results underscore the nucleophilic and electrophilic reactivity of the β-keto aldehyde moiety and its ability to promote fragment coupling reactions in live microbial cells.
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Affiliation(s)
- Hartono Candra
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Guang-Lei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Sean Lee Qiu En
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
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Gakuubi MM, Ching KC, Munusamy M, Wibowo M, Lim CT, Ma GL, Liang ZX, Kanagasundaram Y, Ng SB. CRISPR/Cas9 RNP-assisted validation of palmarumycin biosynthetic gene cluster in Lophiotrema sp. F6932. Front Microbiol 2022; 13:1012115. [PMID: 36246293 PMCID: PMC9556985 DOI: 10.3389/fmicb.2022.1012115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 08/05/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Lophiotrema is a genus of ascomycetous fungi within the family Lophiotremataceae. Members of this genus have been isolated as endophytes from a wide range of host plants and also from plant debris within terrestrial and marine habitats, where they are thought to function as saprobes. Lophiotrema sp. F6932 was isolated from white mangrove (Avicennia officinalis) in Pulau Ubin Island, Singapore. Crude extracts from the fungus exhibited strong antibacterial activity, and bioassay-guided isolation and structure elucidation of bioactive constituents led to the isolation of palmarumycin C8 and a new analog palmarumycin CP30. Whole-genome sequencing analysis resulted in the identification of a putative type 1 iterative PKS (iPKS) predicated to be involved in the biosynthesis of palmarumycins. To verify the involvement of palmarumycin (PAL) gene cluster in the biosynthesis of these compounds, we employed ribonucleoprotein (RNP)-mediated CRISPR-Cas9 to induce targeted deletion of the ketosynthase (KS) domain in PAL. Double-strand breaks (DSBs) upstream and downstream of the KS domain was followed by homology-directed repair (HDR) with a hygromycin resistance cassette flanked by a 50 bp of homology on both sides of the DSBs. The resultant deletion mutants displayed completely different phenotypes compared to the wild-type strain, as they had different colony morphology and were no longer able to produce palmarumycins or melanin. This study, therefore, confirms the involvement of PAL in the biosynthesis of palmarumycins, and paves the way for implementing a similar approach in the characterization of other gene clusters of interest in this largely understudied fungal strain.
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Affiliation(s)
- Martin Muthee Gakuubi
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kuan Chieh Ching
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Madhaiyan Munusamy
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Mario Wibowo
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chun Teck Lim
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Guang-Lei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yoganathan Kanagasundaram
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- *Correspondence: Siew Bee Ng,
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Gakuubi MM, Ching KC, Munusamy M, Wibowo M, Liang ZX, Kanagasundaram Y, Ng SB. Enhancing the Discovery of Bioactive Secondary Metabolites From Fungal Endophytes Using Chemical Elicitation and Variation of Fermentation Media. Front Microbiol 2022; 13:898976. [PMID: 35733953 PMCID: PMC9207341 DOI: 10.3389/fmicb.2022.898976] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/05/2022] [Indexed: 11/26/2022] Open
Abstract
Endophytic microorganisms are an important source of bioactive secondary metabolites. In this study, fungal endophytes obtained from A*STAR’s Natural Product Library (NPL) and previously isolated from different habitats of Singapore were investigated for their diversity, antimicrobial, and cytotoxic activities. A total of 222 fungal strains were identified on the basis of sequence analysis of ITS region of the rDNA gene. The identified fungal strains belong to 59 genera distributed in 20 orders. Majority of the identified strains (99%; 219 strains) belong to the phylum Ascomycota, while two strains belonged to the phylum Basidiomycota, and only one strain was from Mucoromycota phylum. The most dominant genus was Colletotrichum accounting for 27% of all the identified strains. Chemical elicitation using 5-azacytidine and suberoylanilide hydroxamic acid (SAHA) and variation of fermentation media resulted in the discovery of more bioactive strains. Bioassay-guided isolation and structure elucidation of active constituents from three prioritized fungal strains: Lophiotrema sp. F6932, Muyocopron laterale F5912, and Colletotrichum tropicicola F10154, led to the isolation of a known compound; palmarumycin C8 and five novel compounds; palmarumycin CP30, muyocopronol A-C and tropicicolide. Tropicicolide displayed the strongest antifungal activity against Aspergillus fumigatus with an IC50 value of 1.8 μg/ml but with a weaker activity against the Candida albicans presenting an IC50 of 7.1 μg/ml. Palmarumycin C8 revealed the best antiproliferative activity with IC50 values of 1.1 and 2.1 μg/ml against MIA PaCa-2 and PANC-1 cells, respectively.
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Affiliation(s)
- Martin Muthee Gakuubi
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kuan Chieh Ching
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Madhaiyan Munusamy
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Mario Wibowo
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yoganathan Kanagasundaram
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- *Correspondence: Siew Bee Ng,
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Ma GL, Candra H, Pang LM, Xiong J, Ding Y, Tran HT, Low ZJ, Ye H, Liu M, Zheng J, Fang M, Cao B, Liang ZX. Biosynthesis of Tasikamides via Pathway Coupling and Diazonium-Mediated Hydrazone Formation. J Am Chem Soc 2022; 144:1622-1633. [DOI: 10.1021/jacs.1c10369] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Guang-Lei Ma
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Hartono Candra
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Li Mei Pang
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Juan Xiong
- School of Pharmacy, Fudan University, Shanghai 201203, P. R. China
| | - Yichen Ding
- Temasek Life Sciences Laboratory Limited, Research Link, National University of Singapore, 117604 Singapore
| | - Hoa Thi Tran
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Zhen Jie Low
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Hong Ye
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Min Liu
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798 Singapore
| | - Jie Zheng
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798 Singapore
| | - Mingliang Fang
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798 Singapore
| | - Bin Cao
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798 Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551 Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
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13
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Gakuubi MM, Munusamy M, Liang ZX, Ng SB. Fungal Endophytes: A Promising Frontier for Discovery of Novel Bioactive Compounds. J Fungi (Basel) 2021; 7:786. [PMID: 34682208 PMCID: PMC8538612 DOI: 10.3390/jof7100786] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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: 09/01/2021] [Revised: 09/10/2021] [Accepted: 09/16/2021] [Indexed: 12/13/2022] Open
Abstract
For years, fungi have served as repositories of bioactive secondary metabolites that form the backbone of many existing drugs. With the global rise in infections associated with antimicrobial resistance, in addition to the growing burden of non-communicable disease, such as cancer, diabetes and cardiovascular ailments, the demand for new drugs that can provide an improved therapeutic outcome has become the utmost priority. The exploration of microbes from understudied and specialized niches is one of the promising ways of discovering promising lead molecules for drug discovery. In recent years, a special class of plant-associated fungi, namely, fungal endophytes, have emerged as an important source of bioactive compounds with unique chemistry and interesting biological activities. The present review focuses on endophytic fungi and their classification, rationale for selection and prioritization of host plants for fungal isolation and examples of strategies that have been adopted to induce the activation of cryptic biosynthetic gene clusters to enhance the biosynthetic potential of fungal endophytes.
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Affiliation(s)
- Martin Muthee Gakuubi
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore; (M.M.G.); (M.M.)
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore;
| | - Madhaiyan Munusamy
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore; (M.M.G.); (M.M.)
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore;
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore; (M.M.G.); (M.M.)
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14
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Ma GL, Tran HT, Low ZJ, Candra H, Pang LM, Cheang QW, Fang M, Liang ZX. Pathway Retrofitting Yields Insights into the Biosynthesis of Anthraquinone-Fused Enediynes. J Am Chem Soc 2021; 143:11500-11509. [PMID: 34293863 DOI: 10.1021/jacs.1c03911] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Anthraquinone-fused enediynes (AQEs) are renowned for their distinctive molecular architecture, reactive enediyne warhead, and potent anticancer activity. Although the first members of AQEs, i.e., dynemicins, were discovered three decades ago, how their nitrogen-containing carbon skeleton is synthesized by microbial producers remains largely a mystery. In this study, we showed that the recently discovered sungeidine pathway is a "degenerative" AQE pathway that contains upstream enzymes for AQE biosynthesis. Retrofitting the sungeidine pathway with genes from the dynemicin pathway not only restored the biosynthesis of the AQE skeleton but also produced a series of novel compounds likely as the cycloaromatized derivatives of chemically unstable biosynthetic intermediates. The results suggest a cascade of highly surprising biosynthetic steps leading to the formation of the anthraquinone moiety, the hallmark C8-C9 linkage via alkyl-aryl cross-coupling, and the characteristic epoxide functionality. The findings provide unprecedented insights into the biosynthesis of AQEs and pave the way for examining these intriguing biosynthetic enzymes.
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Affiliation(s)
- Guang-Lei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Hoa Thi Tran
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Zhen Jie Low
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Hartono Candra
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Li Mei Pang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Qing Wei Cheang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Mingliang Fang
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
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15
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Xu Y, Wu T, Wang P, Liang ZX, Shi SS, Xu SF, Liu XJ, Tian Q. Perfluorocarbon Protects against Lipopolysaccharide-Induced Apoptosis of Endothelial Cells in Pulmonary Microvessels. Bull Exp Biol Med 2021; 170:410-414. [PMID: 33725245 DOI: 10.1007/s10517-021-05077-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 05/30/2020] [Indexed: 10/21/2022]
Abstract
This study was aimed to explore the effect and mechanisms of action of perfluorocarbon on LPS-induced apoptosis of pulmonary microvascular endothelial cells (PMVEC) isolated from Sprague-Dawley rats. Apoptosis rates were assessed by flow cytometry. Ultrastructural characteristics of PMVEC were evaluated by transmission electron microscopy. The protein expression of cleaved caspase-3 was measured using Western blotting. LPS significantly increased the level of apoptosis, induced the appearance of ultrastructural changes typical of apoptosis, up-regulated the expression of active caspase-3 protein. These effects of LPS were attenuated by co-administration of perfluorocarbon. These results suggest that perfluorocarbon can attenuate LPS-induced apoptosis of PMVEC by inhibiting TLR-4 signaling and caspase-3 activation.
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Affiliation(s)
- Y Xu
- Department of Respiratory Diseases, the First Medical Center, Chinese PLA General Hospital, Beijing, P.R. China
| | - T Wu
- Department of Respiratory Diseases, the First Hospital of Qinhuangdao, Qinhuangdao, P.R. China
| | - P Wang
- Department of Respiratory Diseases, the First Medical Center, Chinese PLA General Hospital, Beijing, P.R. China
| | - Z X Liang
- Department of Respiratory Diseases, the First Medical Center, Chinese PLA General Hospital, Beijing, P.R. China
| | - S S Shi
- Department of Respiratory Diseases, the First Hospital of Qinhuangdao, Qinhuangdao, P.R. China
| | - S F Xu
- Department of Respiratory Diseases, the First Hospital of Qinhuangdao, Qinhuangdao, P.R. China.
| | - X J Liu
- Department of Respiratory Diseases, the First Hospital of Qinhuangdao, Qinhuangdao, P.R. China
| | - Q Tian
- Department of Respiratory Diseases, the First Hospital of Qinhuangdao, Qinhuangdao, P.R. China
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16
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Chen LA, She DY, Liang ZX, Liang LL, Chen RC, Ye F, Li YP, Zhou Y, Chen XH, Fang SF, Lai GX, Hu Q, Xie BS, Yao XJ, Shi Y, Su X, He LX, Zhou JY, Zhong SC, Zhang QL, Xiong SD, Qu JM, Tong ZH, Jiang SJ, Liu J, Xu F, He B, Li ER, Yuan YD, Zhang XY, Sun TY, Liu YN. [A prospective multi-center clinical investigation of HIV-negative pulmonary cryptococcosis in China]. Zhonghua Jie He He Hu Xi Za Zhi 2021; 44:14-27. [PMID: 33412620 DOI: 10.3760/cma.j.cn112147-20200122-00034] [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] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the current status of the diagnosis and treatment of pulmonary cryptococcosis in respiratory medicine and improve the understanding of the clinical characteristics of HIV-negative pulmonary cryptococcosis in China. Methods: A prospective multi-center open cohort study was designed to screen for pulmonary cryptococcosis in the general wards and intensive care units of the Department of Respiratory Diseases in 22 hospitals. The HIV-negative patients with positive cryptococcal etiological diagnosis based on smear culture, antigen detection and histopathology were enrolled in the study. The clinical data of enrolled patients were collected and analyzed. Results: A total of 457 cases of pulmonary cryptococcosis were enrolled, among which 3.28% (15/457) were disseminated infections. The case fatality rate was 0.88% (4/457). The majority of the cases were diagnosed by histopathological examinations (74.40%, 340/457) and cryptococcus antigen detection (37.64%, 172/457). Patients with pulmonary cryptococcosis accounted for 2.04‰ (457/223 748) of the total hospitalized patients in the Department of Respiratory Diseases during the same period, and the ratio was the highest in south and east China. Meanwhile, 70.24% (321/457) of the patients had no underlying diseases, while 87.75% (401/457) were found to have immunocompetent status. Cough and expectoration were the most common clinical symptoms in patients with pulmonary cryptococcosis. However, 25.16% (115/457) of the patients had no clinical symptom or physical signs. In terms of imaging features on pulmonary CT, multiple pulmonary lesions were more common than isolated lesions, and there were more subpleural lesions than perihilar or medial lesions. Morphologically, most of the lesions were middle-sized nodules (1-5 cm) or small-sized nodules (3 mm to 1 cm). The sensitivity of serum cryptococcus antigen test was 71.99% (203/282). Moreover, antigen-positive patients differed from antigen-negative patients in terms of basic immune status, clinical symptoms, imaging features and infection types. Meanwhile, immunocompromised patients differed from immunocompetent patients in terms of clinical symptoms, physical signs, infection-related inflammation indicator levels, imaging features, serum cryptococcus antigen positive rate and prognosis. Conclusions: The majority of cases of HIV-negative pulmonary cryptococcosis in China had no underlying disease or immunocompromised status, and the overrall prognosis was favorable. However, early diagnosis of HIV-negative pulmonary cryptococcosis remains challenging due to the complicated manifestations of the disease.
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Affiliation(s)
- L A Chen
- Department of Pulmonary and Critical Care Medicine, the First Medical Center of General Hospital of Chinese People's Liberation Army, Beijing 100853, China
| | - D Y She
- Department of Pulmonary and Critical Care Medicine, the First Medical Center of General Hospital of Chinese People's Liberation Army, Beijing 100853, China
| | - Z X Liang
- Department of Pulmonary and Critical Care Medicine, the First Medical Center of General Hospital of Chinese People's Liberation Army, Beijing 100853, China
| | - L L Liang
- Department of Pulmonary and Critical Care Medicine, the First Medical Center of General Hospital of Chinese People's Liberation Army, Beijing 100853, China
| | - R C Chen
- Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - F Ye
- Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Y P Li
- Department of Pulmonary and Critical Care Medicine, the First Affiliated Hospital of Wenzhou Medical University,Wenzhou 325000, China
| | - Y Zhou
- Department of Pulmonary and Critical Care Medicine, the First Affiliated Hospital of Wenzhou Medical University,Wenzhou 325000, China
| | - X H Chen
- Department of Pulmonary and Critical Care Medicine, Fuzhou Pulmonary Hospital of Fujian, Fuzhou 350008, China
| | - S F Fang
- Department of Pulmonary and Critical Care Medicine, Fuzhou Pulmonary Hospital of Fujian, Fuzhou 350008, China
| | - G X Lai
- Department of Pulmonary and Critical Care Medicine, 900 Hospital of the Joint Logistics Team Support Force,Fuzhou 350025, China
| | - Q Hu
- Department of Pulmonary and Critical Care Medicine, 900 Hospital of the Joint Logistics Team Support Force,Fuzhou 350025, China
| | - B S Xie
- Department of Pulmonary and Critical Care Medicine, Fujian Provincial Hospital,Fuzhou 350001, China
| | - X J Yao
- Department of Pulmonary and Critical Care Medicine, Fujian Provincial Hospital,Fuzhou 350001, China
| | - Y Shi
- Department of Pulmonary and Critical Care Medicine, the General Hospital of Eastern Theater Command;,Nanjing 210002, China
| | - X Su
- Department of Pulmonary and Critical Care Medicine, the General Hospital of Eastern Theater Command;,Nanjing 210002, China
| | - L X He
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University,Shanghai 200032, China
| | - J Y Zhou
- Department of Pulmonary and Critical Care Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - S C Zhong
- Department of Pulmonary and Critical Care Medicine, Longyan First Hospital,Longyan 364000, China
| | - Q L Zhang
- Department of Neurology Medicine, Jiangxi Chest Hospital,Nanchang 330006, China
| | - S D Xiong
- Department of Pulmonary and Critical Care Medicine, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - J M Qu
- Department of Pulmonary and Critical Care Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai 200040, China
| | - Z H Tong
- Department of Pulmonary and Critical Care Medicine, Beijing Chao-Yang Hospital, Capital Medical University,Beijing 100020, China
| | - S J Jiang
- Department of Pulmonary and Critical Care Medicine, Shandong Provincial Hospital,Jinan 250021, China
| | - J Liu
- Department of Pulmonary and Critical Care Medicine, the Second Hospital of Jilin University, Changchun 130041, China
| | - F Xu
- Department of Pulmonary and Critical Care Medicine, the First Affiliated Hospital of Nanchang University,Nanchang 330006, China
| | - B He
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital,Beijing 100191, China
| | - E R Li
- Department of Pulmonary and Critical Care Medicine, the First Hospital of China Medical University,Shenyang 110001, China
| | - Y D Yuan
- Department of Pulmonary and Critical Care Medicine, the Second Hospital of Hebei Medical University, Shijiazhuang 050000, China
| | - X Y Zhang
- Department of Pulmonary and Critical Care Medicine, Guzhou Provincial People's Hospital,Guiyang 550002, China
| | - T Y Sun
- Department of Pulmonary and Critical Care Medicine, Beijing Hospital,Beijing 100730, China
| | - Y N Liu
- Department of Pulmonary and Critical Care Medicine, the First Medical Center of General Hospital of Chinese People's Liberation Army, Beijing 100853, China
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17
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Ma GL, Chandra H, Liang ZX. Taming the flagellar motor of pseudomonads with a nucleotide messenger. Environ Microbiol 2020; 22:2496-2513. [PMID: 32329141 DOI: 10.1111/1462-2920.15036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 01/11/2023]
Abstract
Pseudomonads rely on the flagellar motor to rotate a polar flagellum for swimming and swarming, and to sense surfaces for initiating the motile-to-sessile transition to adopt a surface-dwelling lifestyle. Deciphering the function and regulation of the flagellar motor is of paramount importance for understanding the behaviours of environmental and pathogenic pseudomonads. Recent studies disclosed the preeminent role played by the messenger c-di-GMP in controlling the real-time performance of the flagellar motor in pseudomonads. The studies revealed that c-di-GMP controls the dynamic exchange of flagellar stator units to regulate motor torque/speed and modulates the frequency of flagellar motor switching via the chemosensory signalling pathways. Apart from being a rotary motor, the flagellar motor is emerging as a mechanosensor that transduces surface-induced mechanical signals into an increase of cellular c-di-GMP concentration to initiate the cellular programs required for long-term colonization. Collectively, the studies generate long-awaited mechanistic insights into how c-di-GMP regulates bacterial motility and the motile-to-sessile transition. The new findings also raise the fundamental questions of how cellular c-di-GMP concentrations are dynamically coupled to flagellar output and the proton-motive force, and how c-di-GMP signalling is coordinated spatiotemporally to fine-tune flagellar response and the behaviour of pseudomonads in solutions and on surfaces.
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Affiliation(s)
- Guang-Lei Ma
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, S637551, Singapore
| | - Hartono Chandra
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, S637551, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, S637551, Singapore.,Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, S637551, Singapore
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18
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Mayandi V, Wen Choong AC, Dhand C, Lim FP, Aung TT, Sriram H, Dwivedi N, Periayah MH, Sridhar S, Fazil MHUT, Goh ETL, Orive G, W Beuerman R, Barkham TMS, Loh XJ, Liang ZX, Barathi VA, Ramakrishna S, Chong SJ, Verma NK, Lakshminarayanan R. Multifunctional Antimicrobial Nanofiber Dressings Containing ε-Polylysine for the Eradication of Bacterial Bioburden and Promotion of Wound Healing in Critically Colonized Wounds. ACS Appl Mater Interfaces 2020; 12:15989-16005. [PMID: 32172559 DOI: 10.1021/acsami.9b21683] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bacterial colonization of acute and chronic wounds is often associated with delayed wound healing and prolonged hospitalization. The rise of multi-drug resistant bacteria and the poor biocompatibility of topical antimicrobials warrant safe and effective antimicrobials. Antimicrobial agents that target microbial membranes without interfering with the mammalian cell proliferation and migration hold great promise in the treatment of traumatic wounds. This article reports the utility of superhydrophilic electrospun gelatin nanofiber dressings (NFDs) containing a broad-spectrum antimicrobial polymer, ε-polylysine (εPL), crosslinked by polydopamine (pDA) for treating second-degree burns. In a porcine model of partial thickness burns, NFDs promoted wound closure and reduced hypertrophic scarring compared to untreated burns. Analysis of NFDs in contact with the burns indicated that the dressings trap early colonizers and elicit bactericidal activity, thus creating a sterile wound bed for fibroblasts migration and re-epithelialization. In support of these observations, in porcine models of Pseudomonas aeruginosa and Staphylococcus aureus colonized partial thickness burns, NFDs decreased bacterial bioburden and promoted wound closure and re-epithelialization. NFDs displayed superior clinical outcome than standard-of-care silver dressings. The excellent biocompatibility and antimicrobial efficacy of the newly developed dressings in pre-clinical models demonstrate its potential for clinical use to manage infected wounds without compromising tissue regeneration.
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Affiliation(s)
- Venkatesh Mayandi
- Anti-Infectives Research Group, Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower, 169856 Singapore
- School of Biological Sciences, Nanyang Technological University Singapore, 60 Nanyang Drive, 637551 Singapore
| | - Alvin Chua Wen Choong
- Department of Plastic Reconstructive & Aesthetic Surgery, Singapore General Hospital, 20 College Road, 169856 Singapore
- Skin Bank Unit, Singapore General Hospital, 169608 Singapore
| | - Chetna Dhand
- Anti-Infectives Research Group, Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower, 169856 Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Graduate Medical School, 169857 Singapore
| | - Fui Ping Lim
- Alice Lee Centre for Nursing Studies, National University of Singapore, 117597 Singapore
| | - Thet Tun Aung
- Anti-Infectives Research Group, Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower, 169856 Singapore
- Department of Microbiology and Immunology, National University of Singapore, 119077 Singapore
| | - Harini Sriram
- Anti-Infectives Research Group, Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower, 169856 Singapore
| | - Neeraj Dwivedi
- Department of Electrical and Computer Engineering, National University of Singapore, 117583 Singapore
| | - Mercy Halleluyah Periayah
- Anti-Infectives Research Group, Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower, 169856 Singapore
| | - Sreepathy Sridhar
- Anti-Infectives Research Group, Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower, 169856 Singapore
| | - Mobashar Hussain Urf Turabe Fazil
- Lee Kong Chian School of Medicine, Clinical Sciences Building, Nanyang Technological University Singapore, 11 Mandalay Road, 308232 Singapore
| | - Eunice Tze Leng Goh
- Anti-Infectives Research Group, Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower, 169856 Singapore
| | - Gorka Orive
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country UPV/EHU, Paseo de la Universidad 7, Vitoria-Gasteiz 01006, Spain
- Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Vitoria-Gasteiz 01006, Spain
- University Institute for Regenerative Medicine and Oral Implantology - UIRMI (UPV/EHU-Fundación Eduardo Anitua), Vitoria 01006, Spain
| | - Roger W Beuerman
- Anti-Infectives Research Group, Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower, 169856 Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Graduate Medical School, 169857 Singapore
| | | | - Xian Jun Loh
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 138634 Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University Singapore, 60 Nanyang Drive, 637551 Singapore
| | - Veluchamy Amutha Barathi
- Anti-Infectives Research Group, Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower, 169856 Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Graduate Medical School, 169857 Singapore
| | - Seeram Ramakrishna
- Center for Nanofibers & Nanotechnology, National University of Singapore, 119077 Singapore
| | - Si Jack Chong
- Department of Plastic Reconstructive & Aesthetic Surgery, Singapore General Hospital, 20 College Road, 169856 Singapore
- Skin Bank Unit, Singapore General Hospital, 169608 Singapore
| | - Navin Kumar Verma
- Anti-Infectives Research Group, Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower, 169856 Singapore
- Lee Kong Chian School of Medicine, Clinical Sciences Building, Nanyang Technological University Singapore, 11 Mandalay Road, 308232 Singapore
- Skin Research Institute of Singapore, Clinical Sciences Building, 11 Mandalay Road, 308232 Singapore
| | - Rajamani Lakshminarayanan
- Anti-Infectives Research Group, Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower, 169856 Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Graduate Medical School, 169857 Singapore
- Department of Pharmacy, National University of Singapore, 18 Science Drive, 117543 Singapore
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19
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Low ZJ, Ma GL, Tran HT, Zou Y, Xiong J, Pang L, Nuryyeva S, Ye H, Hu JF, Houk KN, Liang ZX. Sungeidines from a Non-canonical Enediyne Biosynthetic Pathway. J Am Chem Soc 2020; 142:1673-1679. [PMID: 31922407 DOI: 10.1021/jacs.9b10086] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the genome-guided discovery of sungeidines, a class of microbial secondary metabolites with unique structural features. Despite evolutionary relationships with dynemicin-type enediynes, the sungeidines are produced by a biosynthetic gene cluster (BGC) that exhibits distinct differences from known enediyne BGCs. Our studies suggest that the sungeidines are assembled from two octaketide chains that are processed differently than those of the dynemicin-type enediynes. The biosynthesis also involves a unique activating sulfotransferase that promotes a dehydration reaction. The loss of genes, including a putative epoxidase gene, is likely to be the main cause of the divergence of the sungeidine pathway from other canonical enediyne pathways. The findings disclose the surprising evolvability of enediyne pathways and set the stage for characterizing the intriguing enzymatic steps in sungeidine biosynthesis.
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Affiliation(s)
- Zhen Jie Low
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore
| | - Guang-Lei Ma
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore
| | - Hoa Thi Tran
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore
| | - Yike Zou
- Department of Chemistry & Biochemistry , University of California , Los Angeles , California 90095 , United States
| | - Juan Xiong
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore.,School of Pharmacy , Fudan University , Shanghai 200433 , China
| | - Limei Pang
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore
| | - Selbi Nuryyeva
- Department of Chemistry & Biochemistry , University of California , Los Angeles , California 90095 , United States
| | - Hong Ye
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore
| | - Jin-Feng Hu
- School of Pharmacy , Fudan University , Shanghai 200433 , China
| | - K N Houk
- Department of Chemistry & Biochemistry , University of California , Los Angeles , California 90095 , United States
| | - Zhao-Xun Liang
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore
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20
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Low ZJ, Xiong J, Xie Y, Ma GL, Saw H, Thi Tran H, Wong SL, Pang LM, Fong J, Lu P, Hu JF, Yang L, Miao Y, Liang ZX. Correction: Discovery, biosynthesis and antifungal mechanism of the polyene-polyol meijiemycin. Chem Commun (Camb) 2020; 56:826. [PMID: 31897459 DOI: 10.1039/c9cc90554e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Correction for 'Discovery, biosynthesis and antifungal mechanism of the polyene-polyol meijiemycin' by Zhen Jie Low et al., Chem. Commun., 2020, DOI: .
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Affiliation(s)
- Zhen Jie Low
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Juan Xiong
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore. and School of Pharmacy, Fudan University, Shanghai, China
| | - Ying Xie
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Guang-Lei Ma
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Howard Saw
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Hoa Thi Tran
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Soo Lin Wong
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Li Mei Pang
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - July Fong
- The Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 637551, Singapore
| | - Peng Lu
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Jin-Feng Hu
- School of Pharmacy, Fudan University, Shanghai, China
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore. and The Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 637551, Singapore
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21
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Low ZJ, Xiong J, Xie Y, Ma GL, Saw H, Thi Tran H, Wong SL, Pang LM, Fong J, Lu P, Hu JF, Yang L, Miao Y, Liang ZX. Discovery, biosynthesis and antifungal mechanism of the polyene-polyol meijiemycin. Chem Commun (Camb) 2019; 56:822-825. [PMID: 31848534 DOI: 10.1039/c9cc08908j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Produced by a newly isolated Streptomycetes strain, meijiemycin is a gigantic linear polyene-polyol that exhibits structural features not seen in other members of the polyene-polyol family. We propose a biosynthetic mechanism and demonstrate that meijiemycin inhibits hyphal growth by inducing the aggregation of ergosterol and restructuring of the fungal plasma membrane.
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Affiliation(s)
- Zhen Jie Low
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Juan Xiong
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore. and School of Pharmacy, Fudan University, Shanghai, China
| | - Ying Xie
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Guang-Lei Ma
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Howard Saw
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Hoa Thi Tran
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Soo Lin Wong
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Li Mei Pang
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - July Fong
- The Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 637551, Singapore
| | - Peng Lu
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Jin-Feng Hu
- School of Pharmacy, Fudan University, Shanghai, China
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore. and The Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 637551, Singapore
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22
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Xin L, Zeng Y, Sheng S, Chea RA, Liu Q, Li HY, Yang L, Xu L, Chiam KH, Liang ZX. Regulation of flagellar motor switching by c-di-GMP phosphodiesterases in Pseudomonas aeruginosa. J Biol Chem 2019; 294:13789-13799. [PMID: 31350333 DOI: 10.1074/jbc.ra119.009009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/23/2019] [Indexed: 12/12/2022] Open
Abstract
The second messenger cyclic diguanylate (c-di-GMP) plays a prominent role in regulating flagellum-dependent motility in the single-flagellated pathogenic bacterium Pseudomonas aeruginosa The c-di-GMP-mediated signaling pathways and mechanisms that control flagellar output remain to be fully unveiled. Studying surface-tethered and free-swimming P. aeruginosa PAO1 cells, we found that the overexpression of an exogenous diguanylate cyclase (DGC) raises the global cellular c-di-GMP concentration and thereby inhibits flagellar motor switching and decreases motor speed, reducing swimming speed and reversal frequency, respectively. We noted that the inhibiting effect of c-di-GMP on flagellar motor switching, but not motor speed, is exerted through the c-di-GMP-binding adaptor protein MapZ and associated chemotactic pathways. Among the 22 putative c-di-GMP phosphodiesterases, we found that three of them (DipA, NbdA, and RbdA) can significantly inhibit flagellar motor switching and swimming directional reversal in a MapZ-dependent manner. These results disclose a network of c-di-GMP-signaling proteins that regulate chemotactic responses and flagellar motor switching in P. aeruginosa and establish MapZ as a key signaling hub that integrates inputs from different c-di-GMP-signaling pathways to control flagellar output and bacterial motility. We rationalized these experimental findings by invoking a model that postulates the regulation of flagellar motor switching by subcellular c-di-GMP pools.
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Affiliation(s)
- Lingyi Xin
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Yukai Zeng
- Bioinformatics Institute (A*STAR), S138671, Singapore
| | - Shuo Sheng
- Guangdong Innovative and Entrepreneurial Research Team of Sociomicrobiology Basic Science and Frontier Technology, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Rachel Andrea Chea
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Qiong Liu
- Guangdong Innovative and Entrepreneurial Research Team of Sociomicrobiology Basic Science and Frontier Technology, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Hoi Yeung Li
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Liang Yang
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.,Interdisciplinary Graduate School, Nanyang Technological University, S637551, Singapore.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Linghui Xu
- Guangdong Innovative and Entrepreneurial Research Team of Sociomicrobiology Basic Science and Frontier Technology, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China.,Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, South China Agricultural University, Guangzhou 510642, China
| | | | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore .,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
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23
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Sheng S, Xin L, Yam JKH, Salido MM, Khong NZJ, Liu Q, Chea RA, Li HY, Yang L, Liang ZX, Xu L. The MapZ-Mediated Methylation of Chemoreceptors Contributes to Pathogenicity of Pseudomonas aeruginosa. Front Microbiol 2019; 10:67. [PMID: 30804897 PMCID: PMC6370697 DOI: 10.3389/fmicb.2019.00067] [Citation(s) in RCA: 7] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/15/2019] [Indexed: 12/22/2022] Open
Abstract
The pathogenic bacterium Pseudomonas aeruginosa is notorious for causing acute and chronic infections in humans. The ability to infect host by P. aeruginosa is dependent on a complex cellular signaling network, which includes a large number of chemosensory signaling pathways that rely on the methyl-accepting chemotaxis proteins (MCPs). We previously found that the second messenger c-di-GMP-binding adaptor MapZ modulates the methylation of an amino acid-detecting MCP by directly interacting with a chemotaxis methyltransferase CheR1. The current study further expands our understanding of the role of MapZ in regulating chemosensory pathways by demonstrating that MapZ suppresses the methylation of multiple MCPs in P. aeruginosa PAO1. The MCPs under the control of MapZ include five MCPs (Aer, CtpH, CptM, PctA, and PctB) for detecting oxygen/energy, inorganic phosphate, malate and amino acids, and three MCPs (PA1251, PA1608, and PA2867) for detecting unknown chemoattractant or chemorepellent. Chemotaxis assays showed that overexpression of MapZ hampered the taxis of P. aeruginosa toward chemoattractants and scratch-wounded human cells. Mouse infection experiments demonstrated that a dysfunction in MapZ regulation had a profound negative impact on the dissemination of P. aeruginosa and resulted in attenuated bacterial virulence. Together, the results imply that by controlling the methylation of various MCPs via the adaptor protein MapZ, c-di-GMP exerts a profound influence on chemotactic responses and bacterial pathogenesis.
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Affiliation(s)
- Shuo Sheng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.,Guangdong Innovative and Entrepreneurial Research Team of Sociomicrobiology, South China Agricultural University, Guangzhou, China
| | - Lingyi Xin
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Joey Kuok Hoong Yam
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,Interdisciplinary Graduate School, Nanyang Technological University, Singapore, Singapore
| | - May Margarette Salido
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,Interdisciplinary Graduate School, Nanyang Technological University, Singapore, Singapore
| | - Nicole Zi Jia Khong
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Qiong Liu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.,Guangdong Innovative and Entrepreneurial Research Team of Sociomicrobiology, South China Agricultural University, Guangzhou, China
| | - Rachel Andrea Chea
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Hoi Yeung Li
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Liang Yang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,Interdisciplinary Graduate School, Nanyang Technological University, Singapore, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Linghui Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.,Guangdong Innovative and Entrepreneurial Research Team of Sociomicrobiology, South China Agricultural University, Guangzhou, China
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24
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Ding CYG, Pang LM, Liang ZX, Goh KKK, Glukhov E, Gerwick WH, Tan LT. MS/MS-Based Molecular Networking Approach for the Detection of Aplysiatoxin-Related Compounds in Environmental Marine Cyanobacteria. Mar Drugs 2018; 16:md16120505. [PMID: 30551660 PMCID: PMC6315786 DOI: 10.3390/md16120505] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/05/2018] [Accepted: 12/10/2018] [Indexed: 12/20/2022] Open
Abstract
Certain strains of cyanobacteria produce a wide array of cyanotoxins, such as microcystins, lyngbyatoxins and aplysiatoxins, that are associated with public health issues. In this pilot study, an approach combining LC-MS/MS and molecular networking was employed as a rapid analytical method to detect aplysiatoxins present in four environmental marine cyanobacterial samples collected from intertidal areas in Singapore. Based on 16S-ITS rRNA gene sequences, these filamentous cyanobacterial samples collected from Pulau Hantu were determined as Trichodesmium erythraeum, Oscillatoria sp. PAB-2 and Okeania sp. PNG05-4. Organic extracts were prepared and analyzed on LC-HRMS/MS and Global Natural Product Social Molecular Networking (GNPS) for the presence of aplysiatoxin-related molecules. From the molecular networking, six known compounds, debromoaplysiatoxin (1), anhydrodebromoaplysiatoxin (2), 3-methoxydebromoaplysiatoxin (3), aplysiatoxin (4), oscillatoxin A (5) and 31-noroscillatoxin B (6), as well as potential new analogues, were detected in these samples. In addition, differences and similarities in molecular networking clusters related to the aplysiatoxin molecular family were observed in extracts of Trichodesmium erythraeum collected from two different locations and from different cyanobacterial species found at Pulau Hantu, respectively.
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Affiliation(s)
- Chi Ying Gary Ding
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore 637616, Singapore.
| | - Li Mei Pang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
| | - Kau Kiat Kelvin Goh
- Singapore Phenome Centre, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, (K.K.K.G.).
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093, USA.
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093, USA.
| | - Lik Tong Tan
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore 637616, Singapore.
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25
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Pham HT, Nhiep NTH, Vu TNM, Huynh TN, Zhu Y, Huynh ALD, Chakrabortti A, Marcellin E, Lo R, Howard CB, Bansal N, Woodward JJ, Liang ZX, Turner MS. Enhanced uptake of potassium or glycine betaine or export of cyclic-di-AMP restores osmoresistance in a high cyclic-di-AMP Lactococcus lactis mutant. PLoS Genet 2018; 14:e1007574. [PMID: 30074984 PMCID: PMC6108528 DOI: 10.1371/journal.pgen.1007574] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 08/24/2018] [Accepted: 07/20/2018] [Indexed: 11/22/2022] Open
Abstract
The broadly conserved bacterial signalling molecule cyclic-di-adenosine monophosphate (c-di-AMP) controls osmoresistance via its regulation of potassium (K+) and compatible solute uptake. High levels of c-di-AMP resulting from inactivation of c-di-AMP phosphodiesterase activity leads to poor growth of bacteria under high osmotic conditions. To better understand how bacteria can adjust in response to excessive c-di-AMP levels and to identify signals that feed into the c-di-AMP network, we characterised genes identified in a screen for osmoresistant suppressor mutants of the high c-di-AMP Lactococcus ΔgdpP strain. Mutations were identified which increased the uptake of osmoprotectants, including gain-of-function mutations in a Kup family K+ importer (KupB) and inactivation of the glycine betaine transporter transcriptional repressor BusR. The KupB mutations increased the intracellular K+ level while BusR inactivation increased the glycine betaine level. In addition, BusR was found to directly bind c-di-AMP and repress expression of the glycine betaine transporter in response to elevated c-di-AMP. Interestingly, overactive KupB activity or loss of BusR triggered c-di-AMP accumulation, suggesting turgor pressure changes act as a signal for this second messenger. In another group of suppressors, overexpression of an operon encoding an EmrB family multidrug resistance protein allowed cells to lower their intracellular level of c-di-AMP through active export. Lastly evidence is provided that c-di-AMP levels in several bacteria are rapidly responsive to environmental osmolarity changes. Taken together, this work provides evidence for a model in which high c-di-AMP containing cells are dehydrated due to lower K+ and compatible solute levels and that this osmoregulation system is able to sense and respond to cellular water stress.
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Affiliation(s)
- Huong Thi Pham
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia
- The University of Danang, University of Science and Technology, Da Nang, Vietnam
| | - Nguyen Thi Hanh Nhiep
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Thu Ngoc Minh Vu
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - TuAnh Ngoc Huynh
- Department of Microbiology, University of Washington, Seattle, WA, United States of America
| | - Yan Zhu
- Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Anh Le Diep Huynh
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia
| | | | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
| | - Raquel Lo
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Christopher B. Howard
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
| | - Nidhi Bansal
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Joshua J. Woodward
- Department of Microbiology, University of Washington, Seattle, WA, United States of America
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Mark S. Turner
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
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26
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Chin KH, Liang JM, Yang JG, Shih MS, Tu ZL, Wang YC, Sun XH, Hu NJ, Liang ZX, Dow JM, Ryan RP, Chou SH. Correction to "Structural Insights into the Distinct Binding Mode of Cyclic Di-AMP with SaCpaA_RCK". Biochemistry 2018; 57:4236. [PMID: 29984582 DOI: 10.1021/acs.biochem.8b00686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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Abstract
C-di-GMP has emerged as a prevalent bacterial messenger that controls a multitude of bacterial behaviors. Having access to milligram or gram quantities of c-di-GMP is essential for the biochemical and structural characterization of enzymes and effectors involved in c-di-GMP signaling. Although c-di-GMP can be synthesized using chemical methods, diguanylate cyclases (DGC)-based enzymatic synthesis is the most efficient method of preparing c-di-GMP today. Many DGCs are not suitable for c-di-GMP production because of poor protein stability and the presence of a c-di-GMP-binding inhibitory site (I-site) in most DGCs. We have identified and engineered a thermophilic DGC for efficient production of c-di-GMP for characterizing c-di-GMP signaling proteins and riboswitches. Importantly, residue replacement in the inhibitory I-site of the thermophilic DGC drastically relieved product inhibition to enable the production of hundreds of milligrams of c-di-GMP using 5-10 mg of this robust biocatalyst.
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Affiliation(s)
- Prabhadevi Venkataramani
- Division of Chemical Biology and Biotechnology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Zhao-Xun Liang
- Division of Chemical Biology and Biotechnology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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28
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Yan XF, Xin L, Yen JT, Zeng Y, Jin S, Cheang QW, Fong RACY, Chiam KH, Liang ZX, Gao YG. Structural analyses unravel the molecular mechanism of cyclic di-GMP regulation of bacterial chemotaxis via a PilZ adaptor protein. J Biol Chem 2017; 293:100-111. [PMID: 29146598 DOI: 10.1074/jbc.m117.815704] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/10/2017] [Indexed: 01/09/2023] Open
Abstract
The bacterial second messenger cyclic di-GMP (c-di-GMP) has emerged as a prominent mediator of bacterial physiology, motility, and pathogenicity. c-di-GMP often regulates the function of its protein targets through a unique mechanism that involves a discrete PilZ adaptor protein. However, the molecular mechanism for PilZ protein-mediated protein regulation is unclear. Here, we present the structure of the PilZ adaptor protein MapZ cocrystallized in complex with c-di-GMP and its protein target CheR1, a chemotaxis-regulating methyltransferase in Pseudomonas aeruginosa This cocrystal structure, together with the structure of free CheR1, revealed that the binding of c-di-GMP induces dramatic structural changes in MapZ that are crucial for CheR1 binding. Importantly, we found that restructuring and repositioning of two C-terminal helices enable MapZ to disrupt the CheR1 active site by dislodging a structural domain. The crystallographic observations are reinforced by protein-protein binding and single cell-based flagellar motor switching analyses. Our studies further suggest that the regulation of chemotaxis by c-di-GMP through MapZ orthologs/homologs is widespread in proteobacteria and that the use of allosterically regulated C-terminal motifs could be a common mechanism for PilZ adaptor proteins. Together, the findings provide detailed structural insights into how c-di-GMP controls the activity of an enzyme target indirectly through a PilZ adaptor protein.
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Affiliation(s)
- Xin-Fu Yan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 639798, Singapore
| | - Lingyi Xin
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Jackie Tan Yen
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 639798, Singapore
| | - Yukai Zeng
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, Number 07-01, S138671 Singapore, Singapore
| | - Shengyang Jin
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 639798, Singapore
| | - Qing Wei Cheang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | | | - Keng-Hwee Chiam
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, Number 07-01, S138671 Singapore, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
| | - Yong-Gui Gao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 639798, Singapore; Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Singapore 138673, Singapore.
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29
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Pham TH, Liang ZX, Marcellin E, Turner MS. Replenishing the cyclic-di-AMP pool: regulation of diadenylate cyclase activity in bacteria. Curr Genet 2016; 62:731-738. [PMID: 27074767 DOI: 10.1007/s00294-016-0600-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 03/29/2016] [Accepted: 04/01/2016] [Indexed: 02/08/2023]
Abstract
Bacteria can sense environmental cues and alter their physiology accordingly through the use of signal transduction pathways involving second messenger nucleotides. One broadly conserved second messenger is cyclic-di-AMP (c-di-AMP) which regulates a range of processes including cell wall homeostasis, potassium uptake, DNA repair, fatty acid synthesis, biofilm formation and central metabolism in bacteria. The intracellular pool of c-di-AMP is maintained by the activities of diadenylate cyclase (DAC) and phosphodiesterase (PDE) enzymes, as well as possibly via c-di-AMP export. Whilst extracellular stimuli regulating c-di-AMP levels in bacteria are poorly understood, recent work has identified effector proteins which directly interact and alter the activity of DACs. These include the membrane bound CdaR and the phosphoglucosamine mutase GlmM which both bind directly to the membrane bound CdaA DAC and the recombination protein RadA which binds directly to the DNA binding DisA DAC. The genes encoding these multiprotein complexes are co-localised in many bacteria providing further support for their functional connection. The roles of GlmM in peptidoglycan synthesis and RadA in Holliday junction intermediate processing suggest that c-di-AMP synthesis by DACs will be responsive to these cellular activities. In addition to these modulatory interactions, permanent dysregulation of DAC activity due to suppressor mutations can occur during selection to overcome growth defects, rapid cell lysis and osmosensitivity. DACs have also been investigated as targets for the development of new antibiotics and several small compound inhibitors have recently been identified. This review aims to provide an overview of how c-di-AMP synthesis by DACs can be regulated.
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Affiliation(s)
- Thi Huong Pham
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Mark S Turner
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia.
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, Australia.
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30
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Xu L, Xin L, Zeng Y, Yam JKH, Ding Y, Venkataramani P, Cheang QW, Yang X, Tang X, Zhang LH, Chiam KH, Yang L, Liang ZX. A cyclic di-GMP-binding adaptor protein interacts with a chemotaxis methyltransferase to control flagellar motor switching. Sci Signal 2016; 9:ra102. [PMID: 27811183 DOI: 10.1126/scisignal.aaf7584] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The bacterial messenger cyclic diguanylate monophosphate (c-di-GMP) binds to various effectors, the most common of which are single-domain PilZ proteins. These c-di-GMP effectors control various cellular functions and multicellular behaviors at the transcriptional or posttranslational level. We found that MapZ (methyltransferase-associated PilZ; formerly known as PA4608), a single-domain PilZ protein from the opportunistic pathogen Pseudomonas aeruginosa, directly interacted with the methyltransferase CheR1 and that this interaction was enhanced by c-di-GMP. In vitro assays indicated that, in the presence of c-di-GMP, MapZ inhibited CheR1 from methylating the chemoreceptor PctA, which would be expected to increase its affinity for chemoattractants and promote chemotaxis. MapZ localized to the poles of P. aeruginosa cells, where the flagellar motor and other chemotactic proteins, including PctA and CheR1, are also located. P. aeruginosa cells exhibit a random walk behavior by frequently switching the direction of flagellar rotation in a uniform solution. We showed that binding of c-di-GMP to MapZ decreased the frequency of flagellar motor switching and that MapZ was essential for generating the heterogeneous motility typical of P. aeruginosa cell populations and for efficient surface attachment during biofilm formation. Collectively, the studies revealed that c-di-GMP affects flagellar motor output by regulating the methylation of chemoreceptors through a single-domain PilZ adaptor protein.
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Affiliation(s)
- Linghui Xu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.,Guangdong Innovative and Entrepreneurial Research Team of Sociomicrobiology Basic Science and Frontier Technology, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Lingyi Xin
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Yukai Zeng
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Singapore 138671, Singapore
| | - Joey Kuok Hoong Yam
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.,Interdisciplinary Graduate School, Nanyang Technological University, Singapore 637551, Singapore
| | - Yichen Ding
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.,Interdisciplinary Graduate School, Nanyang Technological University, Singapore 637551, Singapore
| | - Prabhadevi Venkataramani
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Qing Wei Cheang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Xiaobei Yang
- Guangdong Innovative and Entrepreneurial Research Team of Sociomicrobiology Basic Science and Frontier Technology, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Xuhua Tang
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Lian-Hui Zhang
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China
| | - Keng-Hwee Chiam
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Singapore 138671, Singapore
| | - Liang Yang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore. .,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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31
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Han X, Chakrabortti A, Zhu J, Liang ZX, Li J. Sequencing and functional annotation of the whole genome of the filamentous fungus Aspergillus westerdijkiae. BMC Genomics 2016; 17:633. [PMID: 27527502 PMCID: PMC4986183 DOI: 10.1186/s12864-016-2974-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/28/2016] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Aspergillus westerdijkiae produces ochratoxin A (OTA) in Aspergillus section Circumdati. It is responsible for the contamination of agricultural crops, fruits, and food commodities, as its secondary metabolite OTA poses a potential threat to animals and humans. As a member of the filamentous fungi family, its capacity for enzymatic catalysis and secondary metabolite production is valuable in industrial production and medicine. To understand the genetic factors underlying its pathogenicity, enzymatic degradation, and secondary metabolism, we analysed the whole genome of A. westerdijkiae and compared it with eight other sequenced Aspergillus species. RESULTS We sequenced the complete genome of A. westerdijkiae and assembled approximately 36 Mb of its genomic DNA, in which we identified 10,861 putative protein-coding genes. We constructed a phylogenetic tree of A. westerdijkiae and eight other sequenced Aspergillus species and found that the sister group of A. westerdijkiae was the A. oryzae - A. flavus clade. By searching the associated databases, we identified 716 cytochrome P450 enzymes, 633 carbohydrate-active enzymes, and 377 proteases. By combining comparative analysis with Kyoto Encyclopaedia of Genes and Genomes (KEGG), Conserved Domains Database (CDD), and Pfam annotations, we predicted 228 potential carbohydrate-active enzymes related to plant polysaccharide degradation (PPD). We found a large number of secondary biosynthetic gene clusters, which suggested that A. westerdijkiae had a remarkable capacity to produce secondary metabolites. Furthermore, we obtained two more reliable and integrated gene sequences containing the reported portions of OTA biosynthesis and identified their respective secondary metabolite clusters. We also systematically annotated these two hybrid t1pks-nrps gene clusters involved in OTA biosynthesis. These two clusters were separate in the genome, and one of them encoded a couple of GH3 and AA3 enzyme genes involved in sucrose and glucose metabolism. CONCLUSIONS The genomic information obtained in this study is valuable for understanding the life cycle and pathogenicity of A. westerdijkiae. We identified numerous enzyme genes that are potentially involved in host invasion and pathogenicity, and we provided a preliminary prediction for each putative secondary metabolite (SM) gene cluster. In particular, for the OTA-related SM gene clusters, we delivered their components with domain and pathway annotations. This study sets the stage for experimental verification of the biosynthetic and regulatory mechanisms of OTA and for the discovery of new secondary metabolites.
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Affiliation(s)
- Xiaolong Han
- State Key Laboratory of Organ Failure Research, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Alolika Chakrabortti
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, Republic of Singapore
| | - Jindong Zhu
- State Key Laboratory of Organ Failure Research, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, Republic of Singapore.
| | - Jinming Li
- State Key Laboratory of Organ Failure Research, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China.
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China.
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32
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Xu L, Venkataramani P, Ding Y, Liu Y, Deng Y, Yong GL, Xin L, Ye R, Zhang L, Yang L, Liang ZX. A Cyclic di-GMP-binding Adaptor Protein Interacts with Histidine Kinase to Regulate Two-component Signaling. J Biol Chem 2016; 291:16112-23. [PMID: 27231351 DOI: 10.1074/jbc.m116.730887] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 11/06/2022] Open
Abstract
The bacterial messenger cyclic di-GMP (c-di-GMP) binds to a diverse range of effectors to exert its biological effect. Despite the fact that free-standing PilZ proteins are by far the most prevalent c-di-GMP effectors known to date, their physiological function and mechanism of action remain largely unknown. Here we report that the free-standing PilZ protein PA2799 from the opportunistic pathogen Pseudomonas aeruginosa interacts directly with the hybrid histidine kinase SagS. We show that PA2799 (named as HapZ: histidine kinase associated PilZ) binds directly to the phosphoreceiver (REC) domain of SagS, and that the SagS-HapZ interaction is further enhanced at elevated c-di-GMP concentration. We demonstrate that binding of HapZ to SagS inhibits the phosphotransfer between SagS and the downstream protein HptB in a c-di-GMP-dependent manner. In accordance with the role of SagS as a motile-sessile switch and biofilm growth factor, we show that HapZ impacts surface attachment and biofilm formation most likely by regulating the expression of a large number of genes. The observations suggest a previously unknown mechanism whereby c-di-GMP mediates two-component signaling through a PilZ adaptor protein.
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Affiliation(s)
- Linghui Xu
- From the School of Biological Sciences and Guangdong Innovative and Entrepreneurial Research Team of Sociomicrobiology Basic Science and Frontier Technology and
| | | | - Yichen Ding
- From the School of Biological Sciences and Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 and
| | - Yang Liu
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 and
| | - Yinyue Deng
- Guangdong Innovative and Entrepreneurial Research Team of Sociomicrobiology Basic Science and Frontier Technology and
| | | | - Lingyi Xin
- From the School of Biological Sciences and
| | - Ruijuan Ye
- From the School of Biological Sciences and
| | - Lianhui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Liang Yang
- From the School of Biological Sciences and Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 and
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33
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Abstract
The development of rotary nanomotors is an essential step towards intelligent nanomachines and nanorobots. In this article, we review the concept, design, working mechanisms, and applications of state-of-the-art rotary nanomotors made from synthetic nanoentities. The rotary nanomotors are categorized according to the energy sources employed to drive the rotary motion, including biochemical, optical, magnetic, and electric fields. The unique advantages and limitations for each type of rotary nanomachines are discussed. The advances of rotary nanomotors is pivotal for realizing dream nanomachines for myriad applications including microfluidics, biodiagnosis, nano-surgery, and biosubstance delivery.
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Affiliation(s)
- Kwanoh Kim
- Department of Mechanical Engineering, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Jianhe Guo
- Materials Science and Engineering Program, Texas Materials Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - Z X Liang
- Materials Science and Engineering Program, Texas Materials Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - F Q Zhu
- NovaMinds, LLC, 9535 Ketona Cv., Austin, TX 78759, USA
| | - D L Fan
- Department of Mechanical Engineering, The University of Texas at Austin, Austin, TX 78712, USA. and Materials Science and Engineering Program, Texas Materials Institute, The University of Texas at Austin, Austin, TX 78712, USA
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34
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Zhu Y, Pham TH, Nhiep THN, Vu NMT, Marcellin E, Chakrabortti A, Wang Y, Waanders J, Lo R, Huston WM, Bansal N, Nielsen LK, Liang ZX, Turner MS. Cyclic-di-AMP synthesis by the diadenylate cyclase CdaA is modulated by the peptidoglycan biosynthesis enzyme GlmM in Lactococcus lactis. Mol Microbiol 2015; 99:1015-27. [PMID: 26585449 DOI: 10.1111/mmi.13281] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2015] [Indexed: 12/28/2022]
Abstract
The second messenger cyclic-di-adenosine monophosphate (c-di-AMP) plays important roles in growth, virulence, cell wall homeostasis, potassium transport and affects resistance to antibiotics, heat and osmotic stress. Most Firmicutes contain only one c-di-AMP synthesizing diadenylate cyclase (CdaA); however, little is known about signals and effectors controlling CdaA activity and c-di-AMP levels. In this study, a genetic screen was employed to identify components which affect the c-di-AMP level in Lactococcus. We characterized suppressor mutations that restored osmoresistance to spontaneous c-di-AMP phosphodiesterase gdpP mutants, which contain high c-di-AMP levels. Loss-of-function and gain-of-function mutations were identified in the cdaA and gdpP genes, respectively, which led to lower c-di-AMP levels. A mutation was also identified in the phosphoglucosamine mutase gene glmM, which is commonly located within the cdaA operon in bacteria. The glmM I154F mutation resulted in a lowering of the c-di-AMP level and a reduction in the key peptidoglycan precursor UDP-N-acetylglucosamine in L. lactis. C-di-AMP synthesis by CdaA was shown to be inhibited by GlmM(I154F) more than GlmM and GlmM(I154F) was found to bind more strongly to CdaA than GlmM. These findings identify GlmM as a c-di-AMP level modulating protein and provide a direct connection between c-di-AMP synthesis and peptidoglycan biosynthesis.
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Affiliation(s)
- Yan Zhu
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Thi Huong Pham
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia.,University of Science and Technology, The University of Danang, Da Nang, Vietnam
| | - Thi Hanh Nguyen Nhiep
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Ngoc Minh Thu Vu
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
| | - Alolika Chakrabortti
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yuanliang Wang
- College of Food Science and Technology, Hunan Agricultural University, Changsha, Hunan Province, China
| | - Jennifer Waanders
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Raquel Lo
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Wilhelmina M Huston
- School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Nidhi Bansal
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Mark S Turner
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia.,Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
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35
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Chin KH, Liang JM, Yang JG, Shih MS, Tu ZL, Wang YC, Sun XH, Hu NJ, Liang ZX, Dow JM, Ryan RP, Chou SH. Structural Insights into the Distinct Binding Mode of Cyclic Di-AMP with SaCpaA_RCK. Biochemistry 2015; 54:4936-51. [PMID: 26171638 DOI: 10.1021/acs.biochem.5b00633] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Cyclic di-AMP (c-di-AMP) is a relatively new member of the family of bacterial cyclic dinucleotide second messengers. It has attracted significant attention in recent years because of the abundant roles it plays in a variety of Gram-positive bacteria. The structural features that allow diverse bacterial proteins to bind c-di-AMP are not fully understood. Here we report the biophysical and structural studies of c-di-AMP in complex with a bacterial cation-proton antiporter (CpaA) RCK (regulator of the conductance of K(+)) protein from Staphylococcus aureus (Sa). The crystal structure of the SaCpaA_RCK C-terminal domain (CTD) in complex with c-di-AMP was determined to a resolution of 1.81 Å. This structure revealed two well-liganded water molecules, each interacting with one of the adenine bases by a unique H2Olp-π interaction to stabilize the complex. Sequence blasting using the SaCpaA_RCK primary sequence against the bacterial genome database returned many CpaA analogues, and alignment of these sequences revealed that the active site residues are all well-conserved, indicating a universal c-di-AMP binding mode for CpaA_RCK. A proteoliposome activity assay using the full-length SaCpaA membrane protein indicated that c-di-AMP binding alters its antiporter activity by approximately 40%. A comparison of this structure to all other reported c-di-AMP-receptor complex structures revealed that c-di-AMP binds to receptors in either a "U-shape" or "V-shape" mode. The two adenine rings are stabilized in the inner interaction zone by a variety of CH-π, cation-π, backbone-π, or H2Olp-π interaction, but more commonly in the outer interaction zone by hydrophobic CH-π or π-π interaction. The structures determined to date provide an understanding of the mechanisms by which a single c-di-AMP can interact with a variety of receptor proteins, and how c-di-AMP binds receptor proteins in a special way different from that of c-di-GMP.
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Affiliation(s)
- Ko-Hsin Chin
- †National Chung Hsing University Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Juin-Ming Liang
- ‡Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Jauo-Guey Yang
- ‡Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Min-Shao Shih
- ‡Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Zhi-Le Tu
- ‡Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Yu-Chuang Wang
- ‡Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Xing-Han Sun
- ‡Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Nien-Jen Hu
- ‡Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Zhao-Xun Liang
- §School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - J Maxwell Dow
- ∥School of Microbiology, Biosciences Institute, University College Cork, Cork, Ireland
| | - Robert P Ryan
- ⊥Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, U.K
| | - Shan-Ho Chou
- †National Chung Hsing University Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan, ROC.,‡Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC
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36
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Abstract
The cyclic dinucleotide c-di-GMP has emerged in the last decade as a prevalent intracellular messenger that orchestrates the transition between the motile and sessile lifestyles of many bacterial species. The motile-to-sessile transition is often associated with the formation of extracellular matrix-encased biofilm, an organized community of bacterial cells that often contributes to antibiotic resistance and host-pathogen interaction. It is increasingly clear that c-di-GMP controls motility, biofilm formation and bacterial pathogenicity partially through regulating the production of exopolysaccharides (EPS) and small-molecule secondary metabolites. This review summarizes our current understanding of the regulation of EPS biosynthesis by c-di-GMP in a diversity of bacterial species and highlights the emerging role of c-di-GMP in the biosynthesis of small-molecule secondary metabolites.
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Affiliation(s)
- Zhao-Xun Liang
- Division of Structural Biology & Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore 637551.
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37
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Ribeiro AJM, Yang L, Ramos MJ, Fernandes PA, Liang ZX, Hirao H. Insight into Enzymatic Nitrile Reduction: QM/MM Study of the Catalytic Mechanism of QueF Nitrile Reductase. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00528] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- António J. M. Ribeiro
- UCIBIO,
REQUIMTE, Departamento de Quı́mica e Bioquı́mica,
Faculdade de Ciências, Universidade do Porto, Rua do Campo
Alegre s/n, 4169-007 Porto, Portugal
| | - Lifeng Yang
- Division of Structural Biology & Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Maria J. Ramos
- UCIBIO,
REQUIMTE, Departamento de Quı́mica e Bioquı́mica,
Faculdade de Ciências, Universidade do Porto, Rua do Campo
Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- UCIBIO,
REQUIMTE, Departamento de Quı́mica e Bioquı́mica,
Faculdade de Ciências, Universidade do Porto, Rua do Campo
Alegre s/n, 4169-007 Porto, Portugal
| | - Zhao-Xun Liang
- Division of Structural Biology & Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Hajime Hirao
- Division
of Chemistry and Biological Chemistry, School of Physical and Mathematical
Sciences, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
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38
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Deepthi A, Liew CW, Liang ZX, Swaminathan K, Lescar J. Structure of a diguanylate cyclase from Thermotoga maritima: insights into activation, feedback inhibition and thermostability. PLoS One 2014; 9:e110912. [PMID: 25360685 PMCID: PMC4215984 DOI: 10.1371/journal.pone.0110912] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [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: 07/19/2014] [Accepted: 09/24/2014] [Indexed: 01/02/2023] Open
Abstract
Large-scale production of bis-3′-5′-cyclic-di-GMP (c-di-GMP) would facilitate biological studies of numerous bacterial signaling pathways and phenotypes controlled by this second messenger molecule, such as virulence and biofilm formation. C-di-GMP constitutes also a potentially interesting molecule as a vaccine adjuvant. Even though chemical synthesis of c-di-GMP can be done, the yields are incompatible with mass-production. tDGC, a stand-alone diguanylate cyclase (DGC or GGDEF domain) from Thermotoga maritima, enables the robust enzymatic production of large quantities of c-di-GMP. To understand the structural correlates of tDGC thermostability, its catalytic mechanism and feedback inhibition, we determined structures of an active-like dimeric conformation with both active (A) sites facing each other and of an inactive dimeric conformation, locked by c-di-GMP bound at the inhibitory (I) site. We also report the structure of a single mutant of tDGC, with the R158A mutation at the I-site, abolishing product inhibition and unproductive dimerization. A comparison with structurally characterized DGC homologues from mesophiles reveals the presence of a higher number of salt bridges in the hyperthermophile enzyme tDGC. Denaturation experiments of mutants disrupting in turn each of the salt bridges unique to tDGC identified three salt-bridges critical to confer thermostability.
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Affiliation(s)
- Angeline Deepthi
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Chong Wai Liew
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | | | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; Centre d' Immunologie et des Maladies Infectieuses, Centre Hospitalier Universitaire Pitié-Salpêtrière Faculté de Médecine Pierre et Marie Curie, Paris, France
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39
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Soehano I, Yang L, Ding F, Sun H, Low ZJ, Liu X, Liang ZX. Insights into the programmed ketoreduction of partially reducing polyketide synthases: stereo- and substrate-specificity of the ketoreductase domain. Org Biomol Chem 2014; 12:8542-9. [DOI: 10.1039/c4ob01777c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Evidence are provided to support that partially reducing polyketide synthases achieve programmed ketoreduction by differential recognition of polyketide intermediates.
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Affiliation(s)
- Ishin Soehano
- School of Biological Sciences Nanyang Technological University
- , Singapore
| | - Lifeng Yang
- School of Biological Sciences Nanyang Technological University
- , Singapore
| | - Feiqing Ding
- School of Mathematics and Physics
- Nanyang Technological University
- , Singapore
| | - Huihua Sun
- School of Biological Sciences Nanyang Technological University
- , Singapore
| | - Zhen Jie Low
- School of Biological Sciences Nanyang Technological University
- , Singapore
| | - Xuewei Liu
- School of Mathematics and Physics
- Nanyang Technological University
- , Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences Nanyang Technological University
- , Singapore
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40
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Abstract
The review highlights the recent progress and challenges in developing a family of nitrile reductases as biocatalysts for nitrile-to-amine transformation.
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Affiliation(s)
- Lifeng Yang
- Division of Structural Biology & Biochemistry
- School of Biological Sciences
- Nanyang Technological University
- , Singapore 637551
| | - Siew Lee Koh
- Division of Structural Biology & Biochemistry
- School of Biological Sciences
- Nanyang Technological University
- , Singapore 637551
| | | | - Zhao-Xun Liang
- Division of Structural Biology & Biochemistry
- School of Biological Sciences
- Nanyang Technological University
- , Singapore 637551
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41
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Wigren E, Liang ZX, Römling U. Finally! The structural secrets of a HD-GYP phosphodiesterase revealed. Mol Microbiol 2013; 91:1-5. [PMID: 24236493 DOI: 10.1111/mmi.12463] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2013] [Indexed: 12/22/2022]
Abstract
The major sessility-motility lifestyle change and additional fundamental aspects of bacterial physiology, behaviour and morphology are regulated by the secondary messenger cyclic di-GMP (c-di-GMP). Although the c-di-GMP metabolizing enzymes and many receptors have been readily characterized upon discovery, the HD-GYP domain c-di-GMP phosphodiesterase family remained underinvestigated. In this issue of Molecular Microbiology, Bellini et al. provide an important step towards functional and structural characterization of the previously neglected HD-GYP domain family by resolving the crystal structure of PmGH, a catalytically active family member from the thermophilic bacterium Persephonella marina. The crystal structure revealed a novel tri-nuclear catalytic iron centre involved in c-di-GMP binding and catalysis and provides the structural basis to subsequently characterize in detail the catalytic mechanism of hydrolysis of c-di-GMP to GMP by HD-GYP domains.
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Affiliation(s)
- Edvard Wigren
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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42
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Ahmad I, Wigren E, Le Guyon S, Vekkeli S, Blanka A, El Mouali Y, Anwar N, Chuah ML, Lünsdorf H, Frank R, Rhen M, Liang ZX, Lindqvist Y, Römling U. The EAL-like protein STM1697 regulates virulence phenotypes, motility and biofilm formation in Salmonella typhimurium. Mol Microbiol 2013; 90:1216-32. [PMID: 24127899 DOI: 10.1111/mmi.12428] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2013] [Indexed: 11/30/2022]
Abstract
The ubiquitous second messenger c-di-GMP regulates the switching of bacterial lifestyles from motility to sessility and acute to chronic virulence to adjust bacterial fitness to altered environmental conditions. Conventionally, EAL proteins being c-di-GMP phosphodiesterases promote motility and acute virulence phenotypes such as invasion into epithelial cells and inhibit biofilm formation. We report here that in contradiction, the EAL-like protein STM1697 of Salmonella typhimurium suppresses motility, invasion into HT-29 epithelial cell line and secretion of the type three secretion system 1 effector protein SipA, whereas it promotes rdar biofilm formation and CsgD expression. STM1697 can, however, functionally replace the EAL-like protein STM1344 and vice versa, whereby both proteins neither degrade nor bind c-di-GMP. Like STM1344, STM1697 suppresses the transcription of class 2 and class 3 flagella regulon genes by binding to FlhD, a component of the master regulator of the flagella regulon FlhD4 C2 and act additively under numerous conditions. Interestingly, the interaction interface of STM1697 with FlhD2 is distinct from its paralogue STM1344. We predict that the stand alone EAL domain proteins STM1697 and STM1344 belong to a subclass of EAL domain proteins in S. typhimurium, which are all involved in motility, biofilm and virulence regulation through interaction with proteins that regulate flagella function.
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Affiliation(s)
- Irfan Ahmad
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177, Stockholm, Sweden
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43
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Chin KH, Tu ZL, Su YC, Yu YJ, Chen HC, Lo YC, Chen CP, Barber GN, Chuah MLC, Liang ZX, Chou SH. Novel c-di-GMP recognition modes of the mouse innate immune adaptor protein STING. Corrigendum. Acta Crystallogr D Biol Cryst 2013. [DOI: 10.1107/s0907444913012158] [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] [Indexed: 11/11/2022]
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44
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Tan E, Rao F, Pasunooti S, Pham TH, Soehano I, Turner MS, Liew CW, Lescar J, Pervushin K, Liang ZX. Solution structure of the PAS domain of a thermophilic YybT protein homolog reveals a potential ligand-binding site. J Biol Chem 2013; 288:11949-59. [PMID: 23504327 DOI: 10.1074/jbc.m112.437764] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Bacillus subtilis protein YybT (or GdpP) and its homologs were recently established as stress signaling proteins that exert their biological effect by degrading the bacterial messenger cyclic di-AMP. YybT homologs contain a small Per-ARNT-Sim (PAS) domain (~80 amino acids) that can bind b-type heme with 1:1 stoichiometry despite the small size of the domain and the lack of a conserved heme iron-coordinating residue. We determined the solution structure of the PAS domain of GtYybT from Geobacillus thermodenitrificans by NMR spectroscopy to further probe its function. The solution structure confirms that PASGtYybT adopts the characteristic PAS fold composed of a five-stranded antiparallel β sheet and a few short α-helices. One α-helix and three central β-strands of PASGtYybT are noticeably shorter than those of the typical PAS domains. Despite the small size of the protein domain, a hydrophobic pocket is formed by the side chains of nonpolar residues stemming from the β-strands and α-helices. A set of residues in the vicinity of the pocket and in the C-terminal region at the dimeric interface exhibits perturbed NMR parameters in the presence of heme or zinc protoporphyrin. Together, the results unveil a compact PAS domain with a potential ligand-binding pocket and reinforce the view that the PASYybT domains function as regulatory domains in the modulation of cellular cyclic di-AMP concentration.
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Affiliation(s)
- Edward Tan
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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Chin KH, Tu ZL, Su YC, Yu YJ, Chen HC, Lo YC, Chen CP, Barber GN, Chuah MLC, Liang ZX, Chou SH. Novel c-di-GMP recognition modes of the mouse innate immune adaptor protein STING. Acta Crystallogr D Biol Crystallogr 2013; 69:352-66. [PMID: 23519410 DOI: 10.1107/s0907444912047269] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 11/16/2012] [Indexed: 12/26/2022]
Abstract
The mammalian ER protein STING (stimulator of interferon genes; also known as MITA, ERIS, MPYS or TMEM173) is an adaptor protein that links the detection of cytosolic dsDNA to the activation of TANK-binding kinase 1 (TBK1) and its downstream transcription factor interferon regulatory factor 3 (IFN3). Recently, STING itself has been found to be the direct receptor of bacterial c-di-GMP, and crystal structures of several human STING C-terminal domain (STING-CTD) dimers in the apo form or in complex with c-di-GMP have been published. Here, a novel set of structures of mouse STING-CTD (mSTING(137-344)) in apo and complex forms determined from crystals obtained under different crystallization conditions are reported. These novel closed-form structures exhibited considerable differences from previously reported open-form human STING-CTD structures. The novel mSTING structures feature extensive interactions between the two monomers, a unique asymmetric c-di-GMP molecule with one guanine base in an unusual syn conformation that is well accommodated in the dimeric interface with many direct specific interactions and two unexpected equivalent secondary peripheral c-di-GMP binding sites. Replacement of the amino acids crucial for specific c-di-GMP binding in mSTING significantly changes the ITC titration profiles and reduces the IFN-β reporter luciferase activity. Taken together, these results reveal a more stable c-di-GMP binding mode of STING proteins that could serve as a template for rational drug design to stimulate interferon production by mammalian cells.
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Affiliation(s)
- Ko-Hsin Chin
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
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Lim J, Sun H, Fan JS, Hameed IF, Lescar J, Liang ZX, Yang D. Rigidifying acyl carrier protein domain in iterative type I PKS CalE8 does not affect its function. Biophys J 2013; 103:1037-44. [PMID: 23009853 DOI: 10.1016/j.bpj.2012.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 07/31/2012] [Accepted: 08/02/2012] [Indexed: 10/27/2022] Open
Abstract
Acyl carrier protein (ACP) domains shuttle acyl intermediates among the catalytic domains of multidomain type I fatty acid synthase and polyketide synthase (PKS) systems. It is believed that the unique function of ACPs is associated with their dynamic property, but it remains to be fully elucidated what type of protein dynamics is critical for the shuttling domain. Using NMR techniques, we found that the ACP domain of iterative type I PKS CalE8 from Micromonospora echinospora is highly dynamic on the millisecond-second timescale. Introduction of an interhelical disulfide linkage in the ACP domain suppresses the dynamics on the millisecond-second timescale and reduces the mobility on the picosecond-nanosecond timescale. We demonstrate that the full-length PKS is fully functional upon rigidification of the ACP domain, suggesting that although the flexibility of the disordered terminal linkers may be important for the function of the ACP domain, the internal dynamics of the helical regions is not critical for that function.
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Affiliation(s)
- Jackwee Lim
- Department of Biological Sciences, National University of Singapore, Singapore
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Ho CL, Chong KSJ, Oppong JA, Chuah MLC, Tan SM, Liang ZX. Visualizing the perturbation of cellular cyclic di-GMP levels in bacterial cells. J Am Chem Soc 2013; 135:566-9. [PMID: 23289502 DOI: 10.1021/ja310497x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyclic di-GMP (c-di-GMP) has emerged as a prominent intracellular messenger that coordinates biofilm formation and pathogenicity in many bacterial species. Developing genetically encoded biosensors for c-di-GMP will help us understand how bacterial cells respond to environmental changes via the modulation of cellular c-di-GMP levels. Here we report the design of two genetically encoded c-di-GMP fluorescent biosensors with complementary dynamic ranges. By using the biosensors, we found that several compounds known to promote biofilm dispersal trigger a decline in c-di-GMP levels in Escherichia coli cells. In contrast, cellular c-di-GMP levels were elevated when the bacterial cells were treated with subinhibitory concentrations of biofilm-promoting antibiotics. The biosensors also revealed that E. coli cells engulfed by macrophages exhibit lower c-di-GMP levels, most likely as a response to the enormous pressures of survival during phagocytosis.
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Affiliation(s)
- Chun Loong Ho
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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Wang YC, Chin KH, Chuah MLC, Liang ZX, Chou SH. Crystallization and preliminary X-ray diffraction studies of Xanthomonas campestris PNPase in the presence of c-di-GMP. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1247-50. [PMID: 23027759 DOI: 10.1107/s1744309112036202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 08/18/2012] [Indexed: 11/11/2022]
Abstract
Bacterial polynucleotide phosphorylase (PNPase) is a 3'-5' processive exoribonuclease that participates in mRNA turnover and quality control of rRNA precursors in many bacterial species. It also associates with the RNase E scaffold and other components to form a multi-enzyme RNA degradasome machinery that performs a wider regulatory role in degradation, quality control and maturation of mRNA and noncoding RNA. Several crystal structures of bacterial PNPases, as well as some biological activity studies, have been published. However, how the enzymatic activity of PNPase is regulated is less well understood. Recently, Escherichia coli PNPase was found to be a direct c-di-GMP binding target, raising the possibility that c-di-GMP may participate in the regulation of RNA processing. Here, the successful cloning, purification and crystallization of S1-domain-truncated Xanthomonas campestris PNPase (XcPNPaseΔS1) in the presence of c-di-GMP are reported. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 132.76, b = 128.38, c = 133.01 Å, γ = 93.3°, and diffracted to a resolution of 2.00 Å.
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Affiliation(s)
- Yu-Chuan Wang
- Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan
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Su YC, Tu ZL, Yang CY, Chin KH, Chuah MLC, Liang ZX, Chou SH. Crystallization studies of the murine c-di-GMP sensor protein STING. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:906-10. [PMID: 22869119 DOI: 10.1107/s1744309112024372] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 05/28/2012] [Indexed: 11/10/2022]
Abstract
The innate immune response is the first defence system against pathogenic microorganisms, and cytosolic detection of pathogen-derived DNA is believed to be one of the major mechanisms of interferon production. Recently, the mammalian ER membrane protein STING (stimulator of IFN genes; also known as MITA, ERIS, MPYS and TMEM173) has been found to be the master regulator linking the detection of cytosolic DNA to TANK-binding kinase 1 (TBK1) and its downstream transcription factor IFN regulatory factor 3 (IRF3). In addition, STING itself was soon discovered to be a direct sensor of bacterial cyclic dinucleotides such as c-di-GMP or c-di-AMP. However, structural studies of apo STING and its complexes with these cyclic dinucleotides and with other cognate binding proteins are essential in order to fully understand the roles played by STING in these crucial signalling pathways. In this manuscript, the successful crystallization of the C-terminal domain of murine STING (STING-CTD; residues 138-344) is reported. Native and SeMet-labelled crystals were obtained and diffracted to moderate resolutions of 2.39 and 2.2 Å, respectively.
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Affiliation(s)
- Yi-Che Su
- Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan
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Sun H, Ho CL, Ding F, Soehano I, Liu XW, Liang ZX. Synthesis of (R)-Mellein by a Partially Reducing Iterative Polyketide Synthase. J Am Chem Soc 2012; 134:11924-7. [DOI: 10.1021/ja304905e] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Huihua Sun
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive,
Singapore 637551
| | - Chun Loong Ho
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive,
Singapore 637551
| | - Feiqing Ding
- School
of Mathematics and Physics, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Ishin Soehano
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive,
Singapore 637551
| | - Xue-Wei Liu
- School
of Mathematics and Physics, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive,
Singapore 637551
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