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Liu G, An H, Tang L, Chi Z, Bi Y, Ye Z, Zhao H, Xiang L, Feng N, Mo C, Xu D. Activated DBP degradation and relevant signal transduction path via quorum sensing autoinducers in Streptomyces sp. SH5. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133571. [PMID: 38266588 DOI: 10.1016/j.jhazmat.2024.133571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/07/2023] [Accepted: 01/17/2024] [Indexed: 01/26/2024]
Abstract
Microbe-mediated DBP (dibutyl phthalate) mineralization is acknowledged to be affected by diverse extracellular factors. However, little is known about the regulatory effects from quorum sensing (QS) signals. In this study, extracellularly applied QS signals A-like (hydroxymethyl dihydrofuran) was discovered to significantly enhance DBP degradation efficiency in Streptomyces sp. SH5. Monobutyl phthalate, protocatechuic acid and beta-ketoadipate were discovered as degradation intermediates by HPLC-TOF-MS/MS. Multi-omics analysis revealed the up-regulation of multiple hydrolases, transferases and decarboxylases that potentially contributed to A-like accelerated DBP degradation. Transcription of Orf2708, an orthologue of global transcriptional activator, was significantly induced by A-like. Orf2708 was demonstrated to interact specifically with the promoter of hydrolase orf2879 gene by EMSA, and the overexpression of orf2879 led to an enhanced DBP degradation in SH5. Taken together with the molecular docking studies showing the stability of ligand-receptor complex of A-like and its potential receptor Orf3712, a hierarchical regulatory cascade underlying the QS signal mediated DBP degradation was proposed as A-like/Orf3712 duplex formation, enhanced orf2708 expression and the downstream specific activation of hydrolase Orf2879. Our study presents the first evidence of GBLs-type promoted DBP degradation among bacteria, and the elucidated signal transduction path indicates a universal application potential of this activation strategy.
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Affiliation(s)
- Ganxing Liu
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou 510632, PR China
| | - Hao An
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou 510632, PR China
| | - Lei Tang
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou 510632, PR China
| | - Zhewei Chi
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou 510632, PR China
| | - Yunwen Bi
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou 510632, PR China
| | - Zeqi Ye
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou 510632, PR China
| | - Haiming Zhao
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou 510632, PR China
| | - Lei Xiang
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou 510632, PR China
| | - Naixian Feng
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou 510632, PR China.
| | - Cehui Mo
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou 510632, PR China.
| | - Delin Xu
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou 510632, PR China.
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Gao C, Zeng YH, Li CY, Li L, Cai ZH, Zhou J. Bisphenol A biodegradation by Sphingonomas sp. YK5 is regulated by acyl-homoserine lactone signaling molecules. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 802:149898. [PMID: 34461476 DOI: 10.1016/j.scitotenv.2021.149898] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/11/2021] [Accepted: 08/21/2021] [Indexed: 06/13/2023]
Abstract
Microbial degradation is an effective approach for the removal of Bisphenol A (BPA). During the biodegradation process, quorum sensing (QS) is a phenomenon that enables bacteria to coordinate collective behaviors based on cell density-dependent chemical signals. However, whether the degradation of BPA can be facilitated by this QS system (such as acyl-homoserine lactone, AHL) is unclear. To answer this question, the bifunctional Sphingonomas sp. strain YK5 that had BPA-degrading and AHL-producing properties was used. Biochemical analysis revealed that this bacterial strain mainly produced C8-HSL signals. Gene knockout experiments indicated that the AHL-system (LuxI1/LuxI2) was required for efficient BPA degradation. RT-PCR analyses revealed that the AHL system positively regulated the relative expression of genes (bisdA, CYP450, hapA, ligAB, and proB) involved in BPA degradation. Given that AHL signaling may be a common trait among BPA-degrading microorganisms and AHL system can regulate the degradation activity, manipulation of this system may be a valuable strategy to control BPA biodegradation.
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Affiliation(s)
- Chao Gao
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Yan-Hua Zeng
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Cheng-Yong Li
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong 518114, PR China
| | - Ling Li
- ShenZhen Zhongqi Yihua Enviromental Protection Technology Co. Ltd., Shenzhen, Guangdong 518051, PR China
| | - Zhong-Hua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China.
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Thomas SG, Abajorga M, Glover MA, Wengert PC, Parthasarathy A, Savka MA, Wadsworth CB, Shipman PA, Hudson AO. Aeromonas hydrophila RIT668 and Citrobacter portucalensis RIT669-Potential Zoonotic Pathogens Isolated from Spotted Turtles. Microorganisms 2020; 8:microorganisms8111805. [PMID: 33212916 PMCID: PMC7698337 DOI: 10.3390/microorganisms8111805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/06/2020] [Accepted: 11/13/2020] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance (AMR) is one of the biggest challenges of the 21st century, and biofilm formation enables bacteria to resist antibiotic at much higher concentrations than planktonic cells. Earlier, we showed that the Gram-negative Aeromonas hydrophila RIT668 and Citrobacter portucalensis RIT669 (closely related to C. freundii NBRC 12681) from infected spotted turtles (Clemmys guttata), formed biofilms and upregulated toxin expression on plastic surfaces, and were predicted to possess multiple antibiotic resistance genes. Here, we show that they each resist several antibiotics in the planktonic phase, but were susceptible to neomycin, and high concentrations of tetracycline and cotrimoxazole. The susceptibility of their biofilms to neomycin and cotrimoxazole was tested using the Calgary device. For A. hydrophila, the minimum inhibitory concentration (MIC) = 500-1000, and the minimum biofilm eradication concentration (MBEC) > 1000 μg/mL, using cotrimoxazole, and MIC = 32.3-62.5, and MBEC > 1000 μg/mL, using neomycin. For C. freundii MIC = 7.8-15.6, and, MBEC > 1000 μg/mL, using cotrimoxazole, and MIC = 7.8, and MBEC > 1000 μg/mL, using neomycin. Both A. hydrophila and C. portucalensis activated an acyl homoserine lactone (AHL) dependent biosensor, suggesting that quorum sensing could mediate biofilm formation. Their multidrug resistance in the planktonic form, and weak biofilm eradication even with neomycin and cotrimoxazole, indicate that A. hydrophila and C. portucalensis are potential zoonotic pathogens, with risks for patients living with implants.
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Zeng YH, Cai ZH, Zhu JM, Du XP, Zhou J. Two hierarchical LuxR-LuxI type quorum sensing systems in Novosphingobium activate microcystin degradation through transcriptional regulation of the mlr pathway. WATER RESEARCH 2020; 183:116092. [PMID: 32622230 DOI: 10.1016/j.watres.2020.116092] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 06/11/2023]
Abstract
Microcystins (MCs) are the most common cyanotoxins produced by harmful cyanobacterial blooms and pose an increasing global threat to human health and ecosystems. Microbial degradation represents an efficient and sustainable approach for the removal of MCs. Although the enzymatic pathway for biodegradation of MCs has been characterized, the regulatory mechanisms underlying the degradation processes remain unclear. Quorum sensing (QS) is a cell-density-dependent regulatory mechanism that enables bacteria to orchestrate collective behaviors. The acyl-homoserine lactone (AHL)-mediated QS system regulates the biodegradation of many organic pollutants. However, it is not known whether this QS system is involved in the degradation of MCs. This study aimed to fill this knowledge gap. In this study, the proportion of culturable AHL-producers increased significantly after enrichment of MCs, and AHL-based QS systems were present in all genome-sequenced MC-degrading strains, supporting the hypothesis that QS participates in the degradation of MCs. Two bifunctional Novosphingobium strains (with MC-degrading and AHL-producing abilities) were isolated using a novel primer pair targeting mlrA, the marker gene of mlr degradation pathway. Biochemical and genetic analysis revealed that the MC-degrading bacterium Novosphingobium sp. ERW19 encodes two hierarchical regulatory QS systems designated novR1/novI1 and novR2/novI2. Gene knockout and complementation experiments indicated that both systems were required for efficient degradation of MCs. Transcriptomic analyses revealed that the QS systems positively regulate degradation of MCs through transcriptional activation of MC-degrading genes, especially mlrA. Given that QS may be a common trait within mlr pathway-dependent MC-degrading bacterial strains and the degradation activity is directly regulated by QS, manipulation of the QS systems may be a promising strategy to control biodegradation of MCs.
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Affiliation(s)
- Yan-Hua Zeng
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China
| | - Zhong-Hua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China
| | - Jian-Ming Zhu
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China
| | - Xiao-Peng Du
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China
| | - Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China.
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Gan HM, Austin CM. Nanopore long reads enable the first complete genome assembly of a Malaysian Vibrio parahaemolyticus isolate bearing the pVa plasmid associated with acute hepatopancreatic necrosis disease. F1000Res 2019. [DOI: 10.12688/f1000research.21570.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Background: The genome of Vibrio parahaemolyticus MVP1, isolated from a Malaysian aquaculture farm with shrimp acute hepatopancreatic necrosis disease (AHPND), was previously sequenced using Illumina MiSeq and assembled de novo, producing a relatively fragmented assembly. Despite identifying the binary toxin genes in the MVP1 draft genome that were linked to AHPND, the toxin genes were localized on a very small contig precluding proper analysis of gene neighbourhood. Methods: The genome of MVP1 was sequenced on Nanopore MinION to obtain long reads to improve genome contiguity. De novo genome assembly was performed using long-read only assembler followed by genome polishing and hybrid assembler. Results: Long-read assembly produced three complete circular MVP1 contigs: chromosome 1, chromosome 2 and the pVa plasmid encoding pirABvp binary toxin genes. Polishing of the long-read assembly with Illumina short reads was necessary to remove indel errors. Complete assembly of the pVa plasmid could not be achieved using Illumina reads due to identical repetitive elements flanking the binary toxin genes leading to multiple contigs. These regions were fully spanned by the Nanopore long-reads resulting in a single contig. Alignment of Illumina reads to the complete genome assembly indicated there is sequencing bias as read depth was lowest in low-GC genomic regions. Comparative genomic analysis revealed a gene cluster coding for additional insecticidal toxins in chromosome 2 of MVP1 that may further contribute to host pathogenesis pending functional validation. Scanning of publicly available V. parahaemolyticus genomes revealed the presence of a single AinS-family quorum-sensing system that can be targeted for future microbial management. Conclusions: We generated the first chromosome-scale genome assembly of a Malaysian pirABVp-bearing V. parahaemolyticus isolate. Structural variations identified from comparative genomic analysis provide new insights into the genomic features of V. parahaemolyticus MVP1 that may be associated with host colonization and pathogenicity.
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Gan HM, Szegedi E, Fersi R, Chebil S, Kovács L, Kawaguchi A, Hudson AO, Burr TJ, Savka MA. Insight Into the Microbial Co-occurrence and Diversity of 73 Grapevine ( Vitis vinifera) Crown Galls Collected Across the Northern Hemisphere. Front Microbiol 2019; 10:1896. [PMID: 31456792 PMCID: PMC6700373 DOI: 10.3389/fmicb.2019.01896] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 07/31/2019] [Indexed: 12/15/2022] Open
Abstract
Crown gall (CG) is a globally distributed and economically important disease of grapevine and other important crop plants. The causal agent of CG is Agrobacterium or Allorhizobium strains that harbor a tumor-inducing plasmid (pTi). The microbial community within the CG tumor has not been widely elucidated and it is not known if certain members of this microbial community promote or inhibit CG. This study investigated the microbiotas of grapevine CG tumor tissues from seven infected vineyards located in Hungary, Japan, Tunisia, and the United States. Heavy co-amplification of grapevine chloroplast and mitochondrial ribosomal RNA genes was observed with the widely used Illumina V3-V4 16S rRNA gene primers, requiring the design of a new reverse primer to enrich for bacterial 16S rRNA from CG tumors. The operational taxonomic unit (OTU) clustering approach is not suitable for CG microbiota analysis as it collapsed several ecologically distinct Agrobacterium species into a single OTU due to low interspecies genetic divergence. The CG microbial community assemblages were significantly different across sampling sites (ANOSIM global R = 0.63, p-value = 0.001) with evidence of site-specific differentially abundant ASVs. The presence of Allorhizobium vitis in the CG microbiota is almost always accompanied by Xanthomonas and Novosphingobium, the latter may promote the spread of pTi plasmid by way of acyl-homoserine lactone signal production, whereas the former may take advantage of the presence of substrates associated with plant cell wall growth and repair. The technical and biological insights gained from this study will contribute to the understanding of complex interaction between the grapevine and its microbial community and may facilitate better management of CG disease in the future.
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Affiliation(s)
- Han Ming Gan
- Deakin Genomics Centre, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
- School of Science, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Ernõ Szegedi
- National Agricultural Research and Innovation Centre, Research Institute for Viticulture and Enology, Kecskemét, Hungary
| | - Rabeb Fersi
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cédria, Hammam-Lif, Tunisia
| | - Samir Chebil
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cédria, Hammam-Lif, Tunisia
| | - László Kovács
- Department of Biology, Missouri State University, Springfield, MO, United States
| | - Akira Kawaguchi
- Western Region Agricultural Research Center, National Agricultural and Food Research Organization, Fukuyama, Japan
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Thomas J. Burr
- Section of Plant Pathology, School of Integrative Plant Sciences, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
| | - Michael A. Savka
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
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Parthasarathy A, Gan HM, Wong NH, Savka MA, Steiner KK, Henry KR, Hudson AO. Isolation and genomic characterization of six endophytic bacteria isolated from Saccharum sp (sugarcane): Insights into antibiotic, secondary metabolite and quorum sensing metabolism. J Genomics 2018; 6:117-121. [PMID: 30310525 PMCID: PMC6170322 DOI: 10.7150/jgen.28335] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 09/05/2018] [Indexed: 11/05/2022] Open
Abstract
Six endophytic bacteria were isolated from Saccharum sp (sugarcane) grown in the parish of Westmoreland on the island of Jamaica located in the West Indies. Whole genome sequence and annotation of the six bacteria show that three were from the genus Pseudomonas and the other three were from the genera Pantoea, Pseudocitrobacter, and Enterobacter. A scan of each genome using the antibiotics and secondary metabolite analysis shell (antiSMASH4.0) webserver showed evidence that the bacteria were able to produce a variety of secondary metabolites. In addition, we were able to show that one of the organisms, Enterobacter sp RIT418 produces N-acyl-homoserine lactones (AHLs), which is indicative of cell-cell communication via quorum sensing (QS).
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Affiliation(s)
- Anutthaman Parthasarathy
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA
| | - Han Ming Gan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
| | - Narayan H Wong
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA
| | - Michael A Savka
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA
| | - KayLee K Steiner
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA
| | - Kurtis R Henry
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA
| | - André O Hudson
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA
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