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Qi Q, Ghaly TM, Penesyan A, Rajabal V, Stacey JA, Tetu SG, Gillings MR. Uncovering Bacterial Hosts of Class 1 Integrons in an Urban Coastal Aquatic Environment with a Single-Cell Fusion-Polymerase Chain Reaction Technology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:4870-4879. [PMID: 36912846 DOI: 10.1021/acs.est.2c09739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Horizontal gene transfer (HGT) is a key driver of bacterial evolution via transmission of genetic materials across taxa. Class 1 integrons are genetic elements that correlate strongly with anthropogenic pollution and contribute to the spread of antimicrobial resistance (AMR) genes via HGT. Despite their significance to human health, there is a shortage of robust, culture-free surveillance technologies for identifying uncultivated environmental taxa that harbor class 1 integrons. We developed a modified version of epicPCR (emulsion, paired isolation, and concatenation polymerase chain reaction (PCR)) that links class 1 integrons amplified from single bacterial cells to taxonomic markers from the same cells in emulsified aqueous droplets. Using this single-cell genomic approach and Nanopore sequencing, we successfully assigned class 1 integron gene cassette arrays containing mostly AMR genes to their hosts in coastal water samples that were affected by pollution. Our work presents the first application of epicPCR for targeting variable, multigene loci of interest. We also identified the Rhizobacter genus as novel hosts of class 1 integrons. These findings establish epicPCR as a powerful tool for linking taxa to class 1 integrons in environmental bacterial communities and offer the potential to direct mitigation efforts toward hotspots of class 1 integron-mediated dissemination of AMR.
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Affiliation(s)
- Qin Qi
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
| | - Timothy M Ghaly
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
| | - Anahit Penesyan
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| | - Vaheesan Rajabal
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| | - Jeremy Ac Stacey
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
| | - Sasha G Tetu
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| | - Michael R Gillings
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
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Son HF, Joo S, Seo H, Sagong HY, Lee SH, Hong H, Kim KJ. Structural bioinformatics-based protein engineering of thermo-stable PETase from Ideonella sakaiensis. Enzyme Microb Technol 2020; 141:109656. [PMID: 33051015 DOI: 10.1016/j.enzmictec.2020.109656] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 10/23/2022]
Abstract
Poly(ethylene terephthalate) (PET), a widely used plastic around the world, causes various environmental and health problems. Several groups have been extensively conducting research to solve these problems through enzymatic degradation of PET at high temperatures around 70 °C. Recently, Ideonella sakaiensis, a bacterium that degrades PET at mild temperatures, has been newly identified, and further protein engineering studies on the PET degrading enzyme from the organism (IsPETase) have also been conducted to overcome the low thermal stability of the enzyme. In this study, we performed structural bioinformatics-based protein engineering of IsPETase to optimize the substrate binding site of the enzyme and developed two variants, IsPETaseS242T and IsPETaseN246D, with higher enzymatic activity at both 25 and 37 °C compared with IsPETaseWT. We also developed the IsPETaseS121E/D186H/S242T/N246D variant by integrating the S242 T and N246D mutations into the previously reported IsPETaseS121E/D186H/R208A variant. At the 37 °C incubation, the quadruple variant maintained the PET degradation activity for 20 days, unlike IsPETaseWT that lost its activity within a day. Consequently, this study exhibited 58-fold increase in the activity compared with IsPETaseWT.
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Affiliation(s)
- Hyeoncheol Francis Son
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566, Republic of Korea
| | - Seongjoon Joo
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566, Republic of Korea
| | - Hogyun Seo
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566, Republic of Korea
| | - Hye-Young Sagong
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566, Republic of Korea
| | - Seul Hoo Lee
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566, Republic of Korea
| | - Hwaseok Hong
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566, Republic of Korea.
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Kasai D. Poly( cis-1,4-isoprene)-cleavage enzymes from natural rubber-utilizing bacteria. Biosci Biotechnol Biochem 2020; 84:1089-1097. [PMID: 32114907 DOI: 10.1080/09168451.2020.1733927] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Natural rubber and synthetic poly(cis-1,4-isoprene) are used industrially in the world. Microbial utilization for the isoprene rubbers has been reported in gram-positive and gram-negative bacteria. Poly(cis-1,4-isoprene)-cleavage enzymes that are secreted by rubber-utilizing bacteria cleave the poly(cis-1,4-isoprene) chain to generate low-molecular-weight oligo(cis-1,4-isoprene) derivatives containing aldehyde and ketone groups. The resulting products are converted to the compounds including carboxyl groups, which could then be further catabolized through β-oxidation pathway. One of poly(cis-1,4-isoprene)-cleavage enzymes is latex-clearing protein (Lcp) that was found in gram-positive rubber degraders including Streptomyces, Gordonia, Rhodococcus, and Nocardia species. The other one is rubber oxygenase A and B (RoxA/RoxB) which have been identified from gram-negative rubber degraders such as Steroidobacter cummioxidans and Rhizobacter gummiphilus. Recently, the transcriptional regulation mechanisms for Lcp-coding genes in gram-positive bacteria have been characterized. Here, the current knowledge of genes and enzymes for the isoprene rubber catabolism were summarized.
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Affiliation(s)
- Daisuke Kasai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
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Birke J, Jendrossek D. Solimonas fluminis has an active latex-clearing protein. Appl Microbiol Biotechnol 2019; 103:8229-8239. [PMID: 31485689 DOI: 10.1007/s00253-019-10085-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/26/2019] [Accepted: 08/05/2019] [Indexed: 11/26/2022]
Abstract
The utilization of rubber (poly (cis-1,4-isoprene)) by rubber-degrading bacteria depends on the synthesis of rubber oxygenases that cleave the polymer extracellularly to low molecular weight products that can be taken up and used as a carbon source. All so far described Gram-negative rubber-degrading species use two related ≈ 70 kDa rubber oxygenases (RoxA and RoxB) for the primary attack of rubber while all described Gram-positive rubber-degrading strains use RoxA/RoxB-unrelated latex-clearing proteins (Lcps, ≈ 40 kDa) as rubber oxygenase(s). In this study, we identified an lcp orthologue in a Gram-negative species (Solimonas fluminis). We cloned and heterologously expressed the lcp gene of S. fluminis HR-BB, purified the corresponding Lcp protein (LcpHR-BB) from recombinant Escherichia coli, and biochemically characterised the LcpHR-BB activity. LcpHR-BB cleaved polyisoprene to a mixture of C20 and higher oligoisoprenoids at a specific activity of 1.5 U/mg. Furthermore, spectroscopic investigation identified LcpHR-BB as a b-haem-containing protein with an oxidised, fivefold coordinated (open) haem centre. To the best of our knowledge, this is the first report that Gram-negative bacteria can have an active rubber oxygenase of the Lcp type.
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Affiliation(s)
- Jakob Birke
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Strasse 35, 88400, Biberach, Germany
| | - Dieter Jendrossek
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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First report of cis-1,4-polyisoprene degradation by Gordonia paraffinivorans. Braz J Microbiol 2019; 50:1051-1062. [PMID: 31440991 DOI: 10.1007/s42770-019-00143-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 08/14/2019] [Indexed: 12/25/2022] Open
Abstract
The use of rubber has increased over the years, leading to a series of environmental problems due to its indefinite decomposition time. Bioremediation employing microorganisms have drawn an increasing interest and originated several studies of microbial rubber degradation. Genome sequencing and in silico analysis demonstrated that G. paraffinivorans MTZ041 isolate encodes the lcp gene (Latex Clearing Protein), responsible for expressing an enzyme that performs the first step in the assimilation of synthetic and natural rubber. Growth curves and scanning electron microscopy (SEM) were conducted for MTZ041 in natural (NR) and synthetic rubber (IR) as sole carbon source during 11 weeks. After 80 days, robust growth was observed and SEM analysis revealed the presence of bacilli and the formation of biofilm-like structures on natural and synthetic rubber. This is the first report of a G. paraffinivorans rubber degrader. Given the complexity of this substrate and the relative small number of microorganisms with this ability, the description and characterization of MTZ041 is of great importance on bioremediation processes of rubber products.
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