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Fortuna R, Wang W, Mayengbam S, Tuplin EWN, Sampsell K, Sharkey KA, Hart DA, Reimer RA. Effect of prebiotic fiber on physical function and gut microbiota in adults, mostly women, with knee osteoarthritis and obesity: a randomized controlled trial. Eur J Nutr 2024; 63:2149-2161. [PMID: 38713231 DOI: 10.1007/s00394-024-03415-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/18/2024] [Indexed: 05/08/2024]
Abstract
PURPOSE Obesity is a primary risk factor for knee osteoarthritis (OA). Prebiotics enhance beneficial gut microbes and can reduce body fat and inflammation. Our objective was to examine if a 6-month prebiotic intervention improved physical function in adults with knee osteoarthritis and obesity. We also measured knee pain, body composition, quality of life, gut microbiota, inflammatory markers, and serum metabolomics. METHODS Adults (n = 54, mostly women) with co-morbid obesity (BMI > 30 kg/m2) and unilateral/bilateral knee OA were randomly assigned to prebiotic (oligofructose-enriched inulin; 16 g/day; n = 31) or isocaloric placebo (maltodextrin; n = 21) for 6 months. Performance based-tests, knee pain, quality of life, serum metabolomics and inflammatory markers, and fecal microbiota and short-chain fatty acids were assessed. RESULTS Significant between group differences were detected for the change in timed-up-and-go test, 40 m fast paced walk test, and hand grip strength test from baseline that favored prebiotic over placebo. Prebiotic also reduced trunk fat mass (kg) at 6 months and trunk fat (%) at 3 months compared to placebo. There was a trend (p = 0.059) for reduced knee pain at 6 months with prebiotic versus placebo. In gut microbiota analysis, a total of 37 amplicon sequence variants differed between groups. Bifidobacterium abundance was positively correlated with distance walked in the 6-min walk test and hand grip strength. At 6 months, there was a significant separation of serum metabolites between groups with upregulation of phenylalanine and tyrosine metabolism with prebiotic. CONCLUSION Prebiotics may hold promise for conservative management of knee osteoarthritis in adults with obesity and larger trials are warranted. CLINICAL TRIAL REGISTRATION Clinicaltrials.gov/study/NCT04172688.
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Affiliation(s)
- Rafael Fortuna
- Faculty of Kinesiology, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
| | - Weilan Wang
- Faculty of Kinesiology, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
| | - Shyamchand Mayengbam
- Department of Biochemistry, Memorial University of Newfoundland, 45 Artic Ave, St. John's, NL, A1C 5S7, Canada
| | - Erin W Noye Tuplin
- Faculty of Kinesiology, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
| | - Kara Sampsell
- Faculty of Kinesiology, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
| | - Keith A Sharkey
- Department of Physiology and Pharmacology, Cumming School of Medicine, Hotchkiss Brain Institute and Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
| | - David A Hart
- Department of Surgery, and Faculty of Kinesiology, McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada
| | - Raylene A Reimer
- Faculty of Kinesiology, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada.
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada.
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Rodríguez-Castro L, Durán RE, Méndez V, Dorochesi F, Zühlke D, Riedel K, Seeger M. The long-chain flavodoxin FldX1 improves the biodegradation of 4-hydroxyphenylacetate and 3-hydroxyphenylacetate and counteracts the oxidative stress associated to aromatic catabolism in Paraburkholderia xenovorans. Biol Res 2024; 57:12. [PMID: 38561836 PMCID: PMC10983741 DOI: 10.1186/s40659-024-00491-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Bacterial aromatic degradation may cause oxidative stress. The long-chain flavodoxin FldX1 of Paraburkholderia xenovorans LB400 counteracts reactive oxygen species (ROS). The aim of this study was to evaluate the protective role of FldX1 in P. xenovorans LB400 during the degradation of 4-hydroxyphenylacetate (4-HPA) and 3-hydroxyphenylacetate (3-HPA). METHODS The functionality of FldX1 was evaluated in P. xenovorans p2-fldX1 that overexpresses FldX1. The effects of FldX1 on P. xenovorans were studied measuring growth on hydroxyphenylacetates, degradation of 4-HPA and 3-HPA, and ROS formation. The effects of hydroxyphenylacetates (HPAs) on the proteome (LC-MS/MS) and gene expression (qRT-PCR) were quantified. Bioaugmentation with strain p2-fldX1 of 4-HPA-polluted soil was assessed, measuring aromatic degradation (HPLC), 4-HPA-degrading bacteria, and plasmid stability. RESULTS The exposure of P. xenovorans to 4-HPA increased the formation of ROS compared to 3-HPA or glucose. P. xenovorans p2-fldX1 showed an increased growth on 4-HPA and 3-HPA compared to the control strain WT-p2. Strain p2-fldX1 degraded faster 4-HPA and 3-HPA than strain WT-p2. Both WT-p2 and p2-fldX1 cells grown on 4-HPA displayed more changes in the proteome than cells grown on 3-HPA in comparison to glucose-grown cells. Several enzymes involved in ROS detoxification, including AhpC2, AhpF, AhpD3, KatA, Bcp, CpoF1, Prx1 and Prx2, were upregulated by hydroxyphenylacetates. Downregulation of organic hydroperoxide resistance (Ohr) and DpsA proteins was observed. A downregulation of the genes encoding scavenging enzymes (katE and sodB), and gstA and trxB was observed in p2-fldX1 cells, suggesting that FldX1 prevents the antioxidant response. More than 20 membrane proteins, including porins and transporters, showed changes in expression during the growth of both strains on hydroxyphenylacetates. An increased 4-HPA degradation by recombinant strain p2-fldX1 in soil microcosms was observed. In soil, the strain overexpressing the flavodoxin FldX1 showed a lower plasmid loss, compared to WT-p2 strain, suggesting that FldX1 contributes to bacterial fitness. Overall, these results suggest that recombinant strain p2-fldX1 is an attractive bacterium for its application in bioremediation processes of aromatic compounds. CONCLUSIONS The long-chain flavodoxin FldX1 improved the capability of P. xenovorans to degrade 4-HPA in liquid culture and soil microcosms by protecting cells against the degradation-associated oxidative stress.
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Affiliation(s)
- Laura Rodríguez-Castro
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, 2390123, Valparaíso, Chile
| | - Roberto E Durán
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, 2390123, Valparaíso, Chile
- Millenium Nucleus Bioproducts, Genomics and Environmental Genomics (BioGEM), Avenida España 1680, 2390123, Valparaíso, Chile
| | - Valentina Méndez
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, 2390123, Valparaíso, Chile
- Millenium Nucleus Bioproducts, Genomics and Environmental Genomics (BioGEM), Avenida España 1680, 2390123, Valparaíso, Chile
| | - Flavia Dorochesi
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, 2390123, Valparaíso, Chile
| | - Daniela Zühlke
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Strasse 8, 17489, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Strasse 8, 17489, Greifswald, Germany
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, 2390123, Valparaíso, Chile.
- Millenium Nucleus Bioproducts, Genomics and Environmental Genomics (BioGEM), Avenida España 1680, 2390123, Valparaíso, Chile.
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Ning R, Li C, Xia M, Zhang Y, Gan Y, Huang Y, Zhang T, Song H, Zhang S, Guo W. Pseudomonas-associated bacteria play a key role in obtaining nutrition from bamboo for the giant panda ( Ailuropoda melanoleuca). Microbiol Spectr 2024; 12:e0381923. [PMID: 38305171 PMCID: PMC10913395 DOI: 10.1128/spectrum.03819-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 12/28/2023] [Indexed: 02/03/2024] Open
Abstract
Gut microbiota plays a vital role in obtaining nutrition from bamboo for giant pandas. However, low cellulase activity has been observed in the panda's gut. Besides, no specific pathway has been implicated in lignin digestion by gut microbiota of pandas. Therefore, the mechanism by which they obtain nutrients is still controversial. It is necessary to elucidate the precise pathways employed by gut microbiota of pandas to degrade lignin. Here, the metabolic pathways for lignin degradation in pandas were explored by comparing 209 metagenomic sequencing data from wild species with different feeding habits. Lignin degradation central pathways, including beta-ketoadipate and homogentisate pathway, were enriched in the gut of wild bamboo-eating pandas. The gut microbiome of wild bamboo-eating specialists was enriched with genes from pathways implicated in degrading ferulate and p-coumarate into acetyl-CoA and succinyl-CoA, which can potentially provide the raw materials for metabolism in pandas. Specifically, Pseudomonas, as the most dominant gut bacteria genus, was found to be the main bacteria to provide genes involved in lignin or lignin derivative degradation. Herein, three Pseudomonas-associated strains isolated from the feces of wild pandas showed the laccase, lignin peroxidase, and manganese peroxidase activity and extracellular lignin degradation ability in vitro. A potential mechanism for pandas to obtain nutrition from bamboo was proposed based on the results. This study provides novel insights into the adaptive evolution of pandas from the perspective of lignin metabolism. IMPORTANCE Although giant pandas only feed on bamboo, the mechanism of lignin digestion in pandas is unclear. Here, the metabolic pathways for lignin degradation in wild pandas were explored by comparing gut metagenomic from species with different feeding habits. Results showed that lignin degradation central pathways, including beta-ketoadipate and homogentisate pathway, were enriched in the gut of wild bamboo-eating pandas. Genes from pathways involved in degrading ferulate and p-coumarate via beta-ketoadipate pathway were also enriched in bamboo-eating pandas. The final products of the above process, such as acetyl-CoA, can potentially provide the raw materials for metabolism in pandas. Specifically, Pseudomonas, as the most dominant gut bacteria genus, mainly provides genes involved in lignin degradation. Herein, Pseudomonas-associated strains isolated from the feces of pandas could degrade extracellular lignin. These findings suggest that gut microbiome of pandas is crucial in obtaining nutrition from lignin via Pseudomonas, as the main lignin-degrading bacteria.
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Affiliation(s)
- Ruihong Ning
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Caiwu Li
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, China
| | - Maohua Xia
- Beijing Key Laboratory of Captive Wildlife Technology, Beijing Zoo, Beijing, P.R. China
| | - Yu Zhang
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Yunong Gan
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Yan Huang
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, China
| | - Tianyou Zhang
- Chimelong Safari Park in Guangdong Province, Guangzhou, China
| | - Haitao Song
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, China
| | - Siyuan Zhang
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
- The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Wei Guo
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
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Kato H, Takahashi Y, Suzuki H, Ohashi K, Kawashima R, Nakamura K, Sakai K, Hori C, Takasuka TE, Kato M, Shimizu M. Identification and characterization of methoxy- and dimethoxyhydroquinone 1,2-dioxygenase from Phanerochaete chrysosporium. Appl Environ Microbiol 2024; 90:e0175323. [PMID: 38259078 PMCID: PMC10880611 DOI: 10.1128/aem.01753-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
White-rot fungi, such as Phanerochaete chrysosporium, are the most efficient degraders of lignin, a major component of plant biomass. Enzymes produced by these fungi, such as lignin peroxidases and manganese peroxidases, break down lignin polymers into various aromatic compounds based on guaiacyl, syringyl, and hydroxyphenyl units. These intermediates are further degraded, and the aromatic ring is cleaved by 1,2,4-trihydroxybenzene dioxygenases. This study aimed to characterize homogentisate dioxygenase (HGD)-like proteins from P. chrysosporium that are strongly induced by the G-unit fragment of vanillin. We overexpressed two homologous recombinant HGDs, PcHGD1 and PcHGD2, in Escherichia coli. Both PcHGD1 and PcHGD2 catalyzed the ring cleavage in methoxyhydroquinone (MHQ) and dimethoxyhydroquinone (DMHQ). The two enzymes had the highest catalytic efficiency (kcat/Km) for MHQ, and therefore, we named PcHGD1 and PcHGD2 as MHQ dioxygenases 1 and 2 (PcMHQD1 and PcMHQD2), respectively, from P. chrysosporium. This is the first study to identify and characterize MHQ and DMHQ dioxygenase activities in members of the HGD superfamily. These findings highlight the unique and broad substrate spectra of PcHGDs, rendering them attractive candidates for biotechnological applications.IMPORTANCEThis study aimed to elucidate the properties of enzymes responsible for degrading lignin, a dominant natural polymer in terrestrial lignocellulosic biomass. We focused on two homogentisate dioxygenase (HGD) homologs from the white-rot fungus, P. chrysosporium, and investigated their roles in the degradation of lignin-derived aromatic compounds. In the P. chrysosporium genome database, PcMHQD1 and PcMHQD2 were annotated as HGDs that could cleave the aromatic rings of methoxyhydroquinone (MHQ) and dimethoxyhydroquinone (DMHQ) with a preference for MHQ. These findings suggest that MHQD1 and/or MHQD2 play important roles in the degradation of lignin-derived aromatic compounds by P. chrysosporium. The preference of PcMHQDs for MHQ and DMHQ not only highlights their potential for biotechnological applications but also underscores their critical role in understanding lignin degradation by a representative of white-rot fungus, P. chrysosporium.
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Affiliation(s)
- Hiroyuki Kato
- Faculty of Agriculture, Meijo University, Nagoya, Japan
| | | | | | - Keisuke Ohashi
- Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | | | - Koki Nakamura
- Faculty of Agriculture, Meijo University, Nagoya, Japan
| | - Kiyota Sakai
- Faculty of Agriculture, Meijo University, Nagoya, Japan
| | - Chiaki Hori
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
| | | | - Masashi Kato
- Faculty of Agriculture, Meijo University, Nagoya, Japan
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Ke Z, Zhu Q, Zhang M, Gao S, jiang M, Zhou Y, Qiu J, Cheng M, Yan X, Wang J, Hong Q. Unveiling the regulatory mechanisms of salicylate degradation gene cluster cehGHIR4 in Rhizobium sp. strain X9. Appl Environ Microbiol 2023; 89:e0080223. [PMID: 37800922 PMCID: PMC10617420 DOI: 10.1128/aem.00802-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/19/2023] [Indexed: 10/07/2023] Open
Abstract
In a previous study, the novel gene cluster cehGHI was found to be involved in salicylate degradation through the CoA-mediated pathway in Rhizobium sp. strain X9 (Mol Microbiol 116:783-793, 2021). In this study, an IclR family transcriptional regulator CehR4 was identified. In contrast to other regulators involved in salicylate degradation, cehR4 forms one operon with the gentisyl-CoA thioesterase gene cehI, while cehG and cehH (encoding salicylyl-CoA ligase and salicylyl-CoA hydroxylase, respectively) form another operon. cehGH and cehIR4 are divergently transcribed, and their promoters overlap. The results of the electrophoretic mobility shift assay and DNase I footprinting showed that CehR4 binds to the 42-bp motif between genes cehH and cehI, thus regulating transcription of cehGH and cehIR4. The repeat sequences IR1 (5'-TTTATATAAA-3') and IR2 (5'-AATATAGAAA-3') in the motif are key sites for CehR4 binding. The arrangement of cehGH and cehIR4 and the conserved binding motif of CehR4 were also found in other bacterial genera. The results disclose the regulatory mechanism of salicylate degradation through the CoA pathway and expand knowledge about the systems controlled by IclR family transcriptional regulators.IMPORTANCEThe long-term residue of aromatic compounds in the environment has brought great threat to the environment and human health. Microbial degradation plays an important role in the elimination of aromatic compounds in the environment. Salicylate is a common intermediate metabolite in the degradation of various aromatic compounds. Recently, Rhizobium sp. strain X9, capable of degrading the pesticide carbaryl, was isolated from carbaryl-contaminated soil. Salicylate is the intermediate metabolite that appeared during the degradation of carbaryl, and a novel salicylate degradation pathway and the involved gene cluster cehGHIR4 have been identified. This study identified and characterized the IclR transcription regulator CehR4 that represses transcription of cehGHIR4 gene cluster. Additionally, the genetic arrangements of cehGH and cehIR4 and the binding sites of CehR4 were also found in other bacterial genera. This study provides insights into the biodegradation of salicylate and provides an application in the bioremediation of aromatic compound-contaminated environments.
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Affiliation(s)
- Zhijian Ke
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
- School of Biological and Chemical Engineering, Ningbo Tech University, Ningbo, Zhejiang, China
| | - Qian Zhu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Mingliang Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Siyuan Gao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Mingli jiang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yidong Zhou
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Jiguo Qiu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Minggen Cheng
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Xin Yan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jinbo Wang
- School of Biological and Chemical Engineering, Ningbo Tech University, Ningbo, Zhejiang, China
| | - Qing Hong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
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Getino L, Chamizo-Ampudia A, Martín JL, Luengo JM, Barreiro C, Olivera ER. Specific Gene Expression in Pseudomonas Putida U Shows New Alternatives for Cadaverine and Putrescine Catabolism. Genes (Basel) 2023; 14:1897. [PMID: 37895246 PMCID: PMC10606097 DOI: 10.3390/genes14101897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/20/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
Pseudomonas putida strain U can be grown using, as sole carbon sources, the biogenic amines putrescine or cadaverine, as well as their catabolic intermediates, ɣ-aminobutyrate or δ-aminovalerate, respectively. Several paralogs for the genes that encode some of the activities involved in the catabolism of these compounds, such as a putrescine-pyruvate aminotransferase (spuC1 and spuC2 genes) and a ɣ-aminobutyrate aminotransferase (gabT1 and gabT2 genes) have been identified in this bacterium. When the expression pattern of these genes is analyzed by qPCR, it is drastically conditioned by supplying the carbon sources. Thus, spuC1 is upregulated by putrescine, whereas spuC2 seems to be exclusively induced by cadaverine. However, gabT1 increases its expression in response to different polyamines or aminated catabolic derivatives from them (i.e., ɣ-aminobutyrate or δ-aminovalerate), although gabT2 does not change its expression level concerning no-amine unrelated carbon sources (citrate). These results reveal differences between the mechanisms proposed for polyamine catabolism in P. aeruginosa and Escherichia coli concerning P. putida strain U, as well as allow a deeper understanding of the enzymatic systems used by this last strain during polyamine metabolism.
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Affiliation(s)
| | | | | | | | | | - Elías R. Olivera
- Área de Bioquímica y Biología Molecular, Departamento de Biología Molecular, Universidad de León, 24007 León, Spain; (L.G.); (A.C.-A.); (J.L.M.); (J.M.L.); (C.B.)
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Salvà-Serra F, Pérez-Pantoja D, Donoso RA, Jaén-Luchoro D, Fernández-Juárez V, Engström-Jakobsson H, Moore ERB, Lalucat J, Bennasar-Figueras A. Comparative genomics of Stutzerimonas balearica ( Pseudomonas balearica): diversity, habitats, and biodegradation of aromatic compounds. Front Microbiol 2023; 14:1159176. [PMID: 37275147 PMCID: PMC10234333 DOI: 10.3389/fmicb.2023.1159176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 04/13/2023] [Indexed: 06/07/2023] Open
Abstract
Stutzerimonas balearica (Pseudomonas balearica) has been found principally in oil-polluted environments. The capability of S. balearica to thrive from the degradation of pollutant compounds makes it a species of interest for potential bioremediation applications. However, little has been reported about the diversity of S. balearica. In this study, genome sequences of S. balearica strains from different origins were analyzed, revealing that it is a diverse species with an open pan-genome that will continue revealing new genes and functionalities as the genomes of more strains are sequenced. The nucleotide signatures and intra- and inter-species variation of the 16S rRNA genes of S. balearica were reevaluated. A strategy of screening 16S rRNA gene sequences in public databases enabled the detection of 158 additional strains, of which only 23% were described as S. balearica. The species was detected from a wide range of environments, although mostly from aquatic and polluted environments, predominantly related to petroleum oil. Genomic and phenotypic analyses confirmed that S. balearica possesses varied inherent capabilities for aromatic compounds degradation. This study increases the knowledge of the biology and diversity of S. balearica and will serve as a basis for future work with the species.
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Affiliation(s)
- Francisco Salvà-Serra
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Raúl A. Donoso
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Víctor Fernández-Juárez
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Hedvig Engström-Jakobsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Edward R. B. Moore
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jorge Lalucat
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Antoni Bennasar-Figueras
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
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AIDmut-Seq: a Three-Step Method for Detecting Protein-DNA Binding Specificity. Microbiol Spectr 2023; 11:e0378322. [PMID: 36533916 PMCID: PMC9927353 DOI: 10.1128/spectrum.03783-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Transcriptional factors (TFs) and their regulons make up the gene regulatory networks. Here, we developed a method based on TF-directed activation-induced cytidine deaminase (AID) mutagenesis in combination with genome sequencing, called AIDmut-Seq, to detect TF targets on the genome. AIDmut-Seq involves only three simple steps, including the expression of the AID-TF fusion protein, whole-genome sequencing, and single nucleotide polymorphism (SNP) profiling, making it easy for junior and interdisciplinary researchers to use. Using AIDmut-Seq for the major quorum sensing regulator LasR in Pseudomonas aeruginosa, we confirmed that a few TF-guided C-T (or G-A) conversions occurred near their binding boxes on the genome, and a number of previously characterized and uncharacterized LasR-binding sites were detected. Further verification of AIDmut-Seq using various transcriptional regulators demonstrated its high efficiency for most transcriptional activators (FleQ, ErdR, GacA, ExsA). We confirmed the binding of LasR, FleQ, and ErdR to 100%, 50%, and 86% of their newly identified promoters by using in vitro protein-DNA binding assay. And real-time RT-PCR data validated the intracellular activity of these TFs to regulate the transcription of those newly found target promoters. However, AIDmut-Seq exhibited low efficiency for some small transcriptional repressors such as RsaL and AmrZ, with possible reasons involving fusion-induced TF dysfunction as well as low transcription rates of target promoters. Although there are false-positive and false-negative results in the AIDmut-Seq data, preliminary results have demonstrated the value of AIDmut-Seq to act as a complementary tool for existing methods. IMPORTANCE Protein-DNA interactions (PDI) play a central role in gene regulatory networks (GRNs). However, current techniques for studying genome-wide PDI usually involve complex experimental procedures, which prevent their broad use by scientific researchers. In this study, we provide a in vivo method called AIDmut-Seq. AIDmut-Seq involves only three simple steps that are easy to operate for researchers with basic skills in molecular biology. The efficiency of AIDmut-Seq was tested and confirmed using multiple transcription factors in Pseudomonas aeruginosa. Although there are still some defects regarding false-positive and false-negative results, AIDmut-Seq will be a good choice in the early stage of PDI study.
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Dell'Anno F, Joaquim van Zyl L, Trindade M, Buschi E, Cannavacciuolo A, Pepi M, Sansone C, Brunet C, Ianora A, de Pascale D, Golyshin PN, Dell'Anno A, Rastelli E. Microbiome enrichment from contaminated marine sediments unveils novel bacterial strains for petroleum hydrocarbon and heavy metal bioremediation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 317:120772. [PMID: 36455775 DOI: 10.1016/j.envpol.2022.120772] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/24/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
Petroleum hydrocarbons and heavy metals are some of the most widespread contaminants affecting marine ecosystems, urgently needing effective and sustainable remediation solutions. Microbial-based bioremediation is gaining increasing interest as an effective, economically and environmentally sustainable strategy. Here, we hypothesized that the heavily polluted coastal area facing the Sarno River mouth, which discharges >3 tons of polycyclic aromatic hydrocarbons (PAHs) and ∼15 tons of heavy metals (HMs) into the sea annually, hosts unique microbiomes including marine bacteria useful for PAHs and HMs bioremediation. We thus enriched the microbiome of marine sediments, contextually selecting for HM-resistant bacteria. The enriched mixed bacterial culture was subjected to whole-DNA sequencing, metagenome-assembled-genomes (MAGs) annotation, and further sub-culturing to obtain the major bacterial species as pure strains. We obtained two novel isolates corresponding to the two most abundant MAGs (Alcanivorax xenomutans strain-SRM1 and Halomonas alkaliantarctica strain-SRM2), and tested their ability to degrade PAHs and remove HMs. Both strains exhibited high PAHs degradation (60-100%) and HMs removal (21-100%) yield, and we described in detail >60 genes in their MAGs to unveil the possible genetic basis for such abilities. Most promising yields (∼100%) were obtained towards naphthalene, pyrene and lead. We propose these novel bacterial strains and related genetic repertoire to be further exploited for effective bioremediation of marine environments contaminated with both PAHs and HMs.
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Affiliation(s)
- Filippo Dell'Anno
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy.
| | - Leonardo Joaquim van Zyl
- Department of Biotechnology, Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, 7535, Cape Town, South Africa.
| | - Marla Trindade
- Department of Biotechnology, Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, 7535, Cape Town, South Africa.
| | - Emanuela Buschi
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Fano Marine Centre, Viale Adriatico 1-N, 61032, Fano, Italy.
| | - Antonio Cannavacciuolo
- Department of Integrative Marine Ecology, Stazione Zoologica "Anton Dohrn", Fano Marine Centre, Viale Adriatico 1-N, 61032, Fano, Italy.
| | - Milva Pepi
- Department of Integrative Marine Ecology, Stazione Zoologica "Anton Dohrn", Fano Marine Centre, Viale Adriatico 1-N, 61032, Fano, Italy.
| | - Clementina Sansone
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy.
| | - Christophe Brunet
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy.
| | - Adrianna Ianora
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy.
| | - Donatella de Pascale
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy.
| | - Peter N Golyshin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Gwynedd LL57 2UW, UK.
| | - Antonio Dell'Anno
- Department of Life and Environmental Sciences, Università Politecnica Delle Marche, Via Brecce Bianche, 60131, Ancona, Italy.
| | - Eugenio Rastelli
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Fano Marine Centre, Viale Adriatico 1-N, 61032, Fano, Italy.
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Park H, Toogood HS, Chen G, Scrutton NS. Co-production of biofuel, bioplastics and biochemicals during extended fermentation of Halomonas bluephagenesis. Microb Biotechnol 2022; 16:307-321. [PMID: 36353812 PMCID: PMC9871518 DOI: 10.1111/1751-7915.14158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 09/29/2022] [Indexed: 11/12/2022] Open
Abstract
Halomonas bluephagenesis TD1.0 was engineered to produce the biofuel propane, bioplastic poly-3-hydroxybutyrate (PHB), and biochemicals mandelate and hydroxymandelate in a single, semi-continuous batch fermentation under non-sterile conditions. Multi-product separation was achieved by segregation of the headspace gas (propane), fermentation broth ([hydroxy]mandelate) and cellular biomass (PHB). Engineering was performed by incorporating the genes encoding fatty acid photodecarboxylase (CvFAP) and hydroxymandelic acid synthase (SyHMAS) into a H. bluephagenesis hmgCAB cassette knockout to channel flux towards (hydroxy)mandelate. Design of Experiment strategies were coupled with fermentation trials to simultaneously optimize each product. Propane and mandelate titres were the highest reported for H. bluephagenesis (62 g/gDCW and 71 ± 10 mg/L respectively) with PHB titres (69% g/gDCW) comparable to other published studies. This proof-of-concept achievement of four easily separated products within one fermentation is a novel achievement probing the versatility of biotechnology, further elevating H. bluephagenesis as a Next Generation Industrial Biotechnology (NGIB) chassis by producing highly valued products at a reduced cost.
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Affiliation(s)
- Helen Park
- EPSRC/BBSRC Future Biomanufacturing Research Hub, EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and School of ChemistryThe University of ManchesterManchesterUK,Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua‐Peking Center for Life SciencesTsinghua UniversityBeijingChina
| | - Helen S. Toogood
- EPSRC/BBSRC Future Biomanufacturing Research Hub, EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and School of ChemistryThe University of ManchesterManchesterUK
| | - Guo‐Qiang Chen
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua‐Peking Center for Life SciencesTsinghua UniversityBeijingChina
| | - Nigel S. Scrutton
- EPSRC/BBSRC Future Biomanufacturing Research Hub, EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and School of ChemistryThe University of ManchesterManchesterUK
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Wirth NT, Gurdo N, Krink N, Vidal-Verdú À, Donati S, Férnandez-Cabezón L, Wulff T, Nikel PI. A synthetic C2 auxotroph of Pseudomonas putida for evolutionary engineering of alternative sugar catabolic routes. Metab Eng 2022; 74:83-97. [PMID: 36155822 DOI: 10.1016/j.ymben.2022.09.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/17/2022] [Accepted: 09/17/2022] [Indexed: 11/30/2022]
Abstract
Acetyl-coenzyme A (AcCoA) is a metabolic hub in virtually all living cells, serving as both a key precursor of essential biomass components and a metabolic sink for catabolic pathways for a large variety of substrates. Owing to this dual role, tight growth-production coupling schemes can be implemented around the AcCoA node. Building on this concept, a synthetic C2 auxotrophy was implemented in the platform bacterium Pseudomonas putida through an in silico-informed engineering approach. A growth-coupling strategy, driven by AcCoA demand, allowed for direct selection of an alternative sugar assimilation route-the phosphoketolase (PKT) shunt from bifidobacteria. Adaptive laboratory evolution forced the synthetic P. putida auxotroph to rewire its metabolic network to restore C2 prototrophy via the PKT shunt. Large-scale structural chromosome rearrangements were identified as possible mechanisms for adjusting the network-wide proteome profile, resulting in improved PKT-dependent growth phenotypes. 13C-based metabolic flux analysis revealed an even split between the native Entner-Doudoroff pathway and the synthetic PKT bypass for glucose processing, leading to enhanced carbon conservation. These results demonstrate that the P. putida metabolism can be radically rewired to incorporate a synthetic C2 metabolism, creating novel network connectivities and highlighting the importance of unconventional engineering strategies to support efficient microbial production.
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Affiliation(s)
- Nicolas T Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Nicolás Gurdo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Nicolas Krink
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Àngela Vidal-Verdú
- Institute for Integrative Systems Biology I2SysBio (Universitat de València-CSIC), Calle del Catedràtic Agustin Escardino Benlloch 9, 46980, Paterna, Spain
| | - Stefano Donati
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Lorena Férnandez-Cabezón
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Tune Wulff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark.
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Mashabela MD, Tugizimana F, Steenkamp PA, Piater LA, Dubery IA, Mhlongo MI. Untargeted metabolite profiling to elucidate rhizosphere and leaf metabolome changes of wheat cultivars (Triticum aestivum L.) treated with the plant growth-promoting rhizobacteria Paenibacillus alvei (T22) and Bacillus subtilis. Front Microbiol 2022; 13:971836. [PMID: 36090115 PMCID: PMC9453603 DOI: 10.3389/fmicb.2022.971836] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 07/25/2022] [Indexed: 11/21/2022] Open
Abstract
The rhizosphere is a highly complex and biochemically diverse environment that facilitates plant–microbe and microbe–microbe interactions, and this region is found between plant roots and the bulk soil. Several studies have reported plant root exudation and metabolite secretion by rhizosphere-inhabiting microbes, suggesting that these metabolites play a vital role in plant–microbe interactions. However, the biochemical constellation of the rhizosphere soil is yet to be fully elucidated and thus remains extremely elusive. In this regard, the effects of plant growth-promoting rhizobacteria (PGPR)–plant interactions on the rhizosphere chemistry and above ground tissues are not fully understood. The current study applies an untargeted metabolomics approach to profile the rhizosphere exo-metabolome of wheat cultivars generated from seed inoculated (bio-primed) with Paenibacillus (T22) and Bacillus subtilis strains and to elucidate the effects of PGPR treatment on the metabolism of above-ground tissues. Chemometrics and molecular networking tools were used to process, mine and interpret the acquired mass spectrometry (MS) data. Global metabolome profiling of the rhizosphere soil of PGPR-bio-primed plants revealed differential accumulation of compounds from several classes of metabolites including phenylpropanoids, organic acids, lipids, organoheterocyclic compounds, and benzenoids. Of these, some have been reported to function in plant–microbe interactions, chemotaxis, biocontrol, and plant growth promotion. Metabolic perturbations associated with the primary and secondary metabolism were observed from the profiled leaf tissue of PGPR-bio-primed plants, suggesting a distal metabolic reprograming induced by PGPR seed bio-priming. These observations gave insights into the hypothetical framework which suggests that PGPR seed bio-priming can induce metabolic changes in plants leading to induced systemic response for adaptation to biotic and abiotic stress. Thus, this study contributes knowledge to ongoing efforts to decipher the rhizosphere metabolome and mechanistic nature of biochemical plant–microbe interactions, which could lead to metabolome engineering strategies for improved plant growth, priming for defense and sustainable agriculture.
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Affiliation(s)
- Manamele D. Mashabela
- Research Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Fidele Tugizimana
- Research Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
- International Research and Development Division, Omnia Group, Ltd., Johannesburg, South Africa
| | - Paul A. Steenkamp
- Research Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Lizelle A. Piater
- Research Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Ian A. Dubery
- Research Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Msizi I. Mhlongo
- Research Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
- *Correspondence: Msizi I. Mhlongo,
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Wang H, Lei P, Liu B, Zhu J, He Q, Chen L, He J. Mutations of Asn321 and Glu322 Improve Resistance of 4-Hydroxyphenylpyruvate Dioxygenase SpHPPDm to Topramezone. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:9703-9710. [PMID: 35856450 DOI: 10.1021/acs.jafc.2c02327] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
As a highly efficient 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide, topramezone is an ideal target for herbicide-resistant genetic engineering. In this study, two mutants, K-19 (N321Y) and K-63 (Q166R/E322V), with topramezone resistance increased by 205.3 and 58.5%, respectively, were screened from the random mutation library of SpHPPDm, a topramezone-resistant HPPD mutant that we previously obtained. Sites N321 and E322 were identified as key sites for increased topramezone resistance by single-site mutation analysis. A mutant KB-145 (N321Y/E322K) was further obtained by saturation mutation at sites N321 and E322. The topramezone resistance of KB-145 increased by 955.3% compared to mutant SpHPPDm. In conclusion, this study identifies two new sites that significantly affect the topramezone resistance of SpHPPDm, which provides new insights into the molecular mechanism of herbicide resistance of HPPD, and the acquired mutants have great application potential in the construction of herbicide-resistant crops.
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Affiliation(s)
- Haiyan Wang
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Peng Lei
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Bin Liu
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Jianchun Zhu
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Qin He
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Le Chen
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Science, Nanjing, Jiangsu 210014, People's Republic of China
| | - Jian He
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
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Wei W, Li J, Liu F, Wu M, Xiong K, He Q, Zhang B, Deng Y, Li Y. Alteration of intestinal microecology by oral antibiotics promotes oral squamous cell carcinoma development. Mol Immunol 2022; 149:94-106. [PMID: 35803000 DOI: 10.1016/j.molimm.2022.06.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/01/2022] [Accepted: 06/27/2022] [Indexed: 02/07/2023]
Abstract
Oral antibiotics can influence cancers and immunotherapy by interfering with the intestinal microbiota. However, the association between oral antibiotics and oral squamous cell carcinoma (OSCC) as well as the mechanisms underlying the effects of oral antibiotics on OSCC remain unclear. Here, we found that oral antibiotics cocktail (4Abx) promoted the tumor development and shifted the microbiota, decreasing the abundance of probiotic bacteria, and altered microbial metabolism in the gut of OSCC mice, increasing tyrosine and decreasing glutamate levels. In vitro experiments showed that tyrosine upregulated the PD-1 expression in T cells, SCC7 cell proliferation, and necroptosis expression. IL-10 expression level in CD11c+ cells was reduced by glutamate. Furthermore, the expression of the necroptosis-related proteins, including receptor-interacting protein kinase 1 (RIPK1), RIPK3, and mixed lineage kinase domain-like (MLKL), was higher in the OSCC mice treated with 4Abx. Supplementation with glutamate or healthy mouse feces by gavage alleviated the tumor-promoting effect of 4Abx with restored balance of microbial metabolism. Overall, we identified the detrimental role of oral antibiotics in promoting OSCC development through altered intestinal microbiota, microbial metabolism, and immune dysbiosis, implying the need for antibiotic stewardship in OSCC treatment.
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Affiliation(s)
- Wei Wei
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Jia Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Fan Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China; Nursing department, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Miaomiao Wu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Kaixin Xiong
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Qing He
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Bo Zhang
- Department of Stomatology, Minda Hospital of Hubei Minzu University, Enshi 445000, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yan Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China.
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Breisch J, Schumm C, Poehlein A, Daniel R, Averhoff B. The carnitine degradation pathway of Acinetobacter baumannii and its role in virulence. Environ Microbiol 2022; 24:4437-4448. [PMID: 35652489 DOI: 10.1111/1462-2920.16075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/10/2022] [Accepted: 05/16/2022] [Indexed: 11/30/2022]
Abstract
The opportunistic human pathogen Acinetobacter baumannii can grow with carnitine but its metabolism, regulation and role in virulence remained elusive. Recently, we identified a carnitine transporter encoded by a gene closely associated with potential carnitine degradation genes. Among those is a gene coding for a putative d-malate dehydrogenase (Mdh). Deletion of the mdh gene led to a loss of growth with carnitine but not l-malate; growth with d-malate was strongly reduced. Therefore, it is hypothesized that d-malate is formed during carnitine oxidation and further oxidized to CO2 and pyruvate and, that not, as previously suggested, l-malate is the product and funnelled directly into the TCA cycle. Mutant analyses revealed that the hydrolase in this cluster funnels acetylcarnitine into the degradation pathway by deacetylation. A transcriptional regulator CarR bound in a concentration-dependent manner to the intergenic region between the mdh gene, the first gene of the carnitine catabolic operon and the carR gene in the presence and absence of carnitine. Both carnitine and d-malate induced CarR-dependent expression of the carnitine operon. Infection studies with Galleria mellonella larvae demonstrated a strong increase in virulence by addition of carnitine indicating that carnitine degradation plays a pivotal role in virulence of A. baumannii.
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Affiliation(s)
- Jennifer Breisch
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Clemens Schumm
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Beate Averhoff
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
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Orlandi VT, Martegani E, Giaroni C, Baj A, Bolognese F. Bacterial pigments: A colorful palette reservoir for biotechnological applications. Biotechnol Appl Biochem 2022; 69:981-1001. [PMID: 33870552 PMCID: PMC9544673 DOI: 10.1002/bab.2170] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 04/09/2021] [Indexed: 12/12/2022]
Abstract
Synthetic derivatives are currently used instead of pigments in many applicative fields, from food to feed, from pharmaceutical to diagnostic, from agronomy to industry. Progress in organic chemistry allowed to obtain rather cheap compounds covering the whole color spectrum. However, several concerns arise from this chemical approach, as it is mainly based on nonrenewable resources such as fossil oil, and the toxicity or carcinogenic properties of products and/or precursors may be harmful for personnel involved in the productive processes. In this scenario, microorganisms and their pigments represent a colorful world to discover and reconsider. Each living bacterial strain may be a source of secondary metabolites with peculiar functions. The aim of this review is to link the physiological role of bacterial pigments with their potential use in different biotechnological fields. This enormous potential supports the big challenge for the development of strategies useful to identify, produce, and purify the right pigment for the desired application. At the end of this ideal journey through the world of bacterial pigments, the attention will be focused on melanin compounds, whose production relies upon different techniques ranging from natural producers, heterologous hosts, or isolated enzymes. In a green workflow, the microorganisms represent the starting and final point of pigment production.
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Affiliation(s)
| | - Eleonora Martegani
- Department of Biotechnologies and Life SciencesUniversity of InsubriaVareseItaly
| | - Cristina Giaroni
- Department of Medicine and SurgeryUniversity of InsubriaVareseItaly
| | - Andreina Baj
- Department of Medicine and SurgeryUniversity of InsubriaVareseItaly
| | - Fabrizio Bolognese
- Department of Biotechnologies and Life SciencesUniversity of InsubriaVareseItaly
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Abstract
Here, the choice of the first coordination shell of the metal center is analyzed from the perspective of charge maintenance in a binary enzyme-substrate complex and an O2-bound ternary complex in the nonheme iron oxygenases. Comparing homogentisate 1,2-dioxygenase and gentisate dioxygenase highlights the significance of charge maintenance after substrate binding as an important factor that drives the reaction coordinate. We then extend the charge analysis to several common types of nonheme iron oxygenases containing either a 2-His-1-carboxylate facial triad or a 3-His or 4-His ligand motif, including extradiol and intradiol ring-cleavage dioxygenases, thiol dioxygenases, α-ketoglutarate-dependent oxygenases, and carotenoid cleavage oxygenases. After forming the productive enzyme-substrate complex, the overall charge of the iron complex at the 0, +1, or +2 state is maintained in the remaining catalytic steps. Hence, maintaining a constant charge is crucial to promote the reaction of the iron center beginning from the formation of the Michaelis or ternary complex. The charge compensation to the iron ion is tuned not only by protein-derived carboxylate ligands but also by substrates. Overall, these analyses indicate that charge maintenance at the iron center is significant when all the necessary components form a productive complex. This charge maintenance concept may apply to most oxygen-activating metalloenzymes systems that do not draw electrons and protons step-by-step from a separate reactant, such as NADH, via a reductase. The charge maintenance perception may also be useful in proposing catalytic pathways or designing prototypical reactions using artificial or engineered enzymes for biotechnological applications.
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Affiliation(s)
- Ephrahime S. Traore
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Aimin Liu
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
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Ghimire N, Kim B, Lee CM, Oh TJ. Comparative genome analysis among Variovorax species and genome guided aromatic compound degradation analysis emphasizing 4-hydroxybenzoate degradation in Variovorax sp. PAMC26660. BMC Genomics 2022; 23:375. [PMID: 35585492 PMCID: PMC9115942 DOI: 10.1186/s12864-022-08589-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/25/2022] [Indexed: 11/29/2022] Open
Abstract
Background While the genus Variovorax is known for its aromatic compound metabolism, no detailed study of the peripheral and central pathways of aromatic compound degradation has yet been reported. Variovorax sp. PAMC26660 is a lichen-associated bacterium isolated from Antarctica. The work presents the genome-based elucidation of peripheral and central catabolic pathways of aromatic compound degradation genes in Variovorax sp. PAMC26660. Additionally, the accessory, core and unique genes were identified among Variovorax species using the pan genome analysis tool. A detailed analysis of the genes related to xenobiotic metabolism revealed the potential roles of Variovorax sp. PAMC26660 and other species in bioremediation. Results TYGS analysis, dDDH, phylogenetic placement and average nucleotide identity (ANI) analysis identified the strain as Variovorax sp. Cell morphology was assessed using scanning electron microscopy (SEM). On analysis of the core, accessory, and unique genes, xenobiotic metabolism accounted only for the accessory and unique genes. On detailed analysis of the aromatic compound catabolic genes, peripheral pathway related to 4-hydroxybenzoate (4-HB) degradation was found among all species while phenylacetate and tyrosine degradation pathways were present in most of the species including PAMC26660. Likewise, central catabolic pathways, like protocatechuate, gentisate, homogentisate, and phenylacetyl-CoA, were also present. The peripheral pathway for 4-HB degradation was functionally tested using PAMC26660, which resulted in the growth using it as a sole source of carbon. Conclusions Computational tools for genome and pan genome analysis are important to understand the behavior of an organism. Xenobiotic metabolism-related genes, that only account for the accessory and unique genes infer evolution through events like lateral gene transfer, mutation and gene rearrangement. 4-HB, an aromatic compound present among lichen species is utilized by lichen-associated Variovorax sp. PAMC26660 as the sole source of carbon. The strain holds genes and pathways for its utilization. Overall, this study outlines the importance of Variovorax in bioremediation and presents the genomic information of the species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08589-3.
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Affiliation(s)
- Nisha Ghimire
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, 31460, Korea
| | - Byeollee Kim
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, 31460, Korea
| | - Chang-Muk Lee
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 55365, Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, 31460, Korea. .,Genome-based BioIT Convergence Institute, Asan, 31460, Korea. .,Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, 31460, South Korea.
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Yue SJ, Huang P, Li S, Cai YY, Wang W, Zhang XH, Nikel PI, Hu HB. Developing a CRISPR-assisted base-editing system for genome engineering of Pseudomonas chlororaphis. Microb Biotechnol 2022; 15:2324-2336. [PMID: 35575623 PMCID: PMC9437888 DOI: 10.1111/1751-7915.14075] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/29/2022] [Accepted: 05/02/2022] [Indexed: 12/01/2022] Open
Abstract
Pseudomonas chlororaphis is a non‐pathogenic, plant growth‐promoting rhizobacterium that secretes phenazine compounds with broad‐spectrum antibiotic activity. Currently available genome‐editing methods for P. chlororaphis are based on homologous recombination (HR)‐dependent allelic exchange, which requires both exogenous DNA repair proteins (e.g. λ‐Red–like systems) and endogenous functions (e.g. RecA) for HR and/or providing donor DNA templates. In general, these procedures are time‐consuming, laborious and inefficient. Here, we established a CRISPR‐assisted base‐editing (CBE) system based on the fusion of a rat cytidine deaminase (rAPOBEC1), enhanced‐specificity Cas9 nickase (eSpCas9ppD10A) and uracil DNA glycosylase inhibitor (UGI). This CBE system converts C:G into T:A without DNA strands breaks or any donor DNA template. By engineering a premature STOP codon in target spacers, the hmgA and phzO genes of P. chlororaphis were successfully interrupted at high efficiency. The phzO‐inactivated strain obtained by base editing exhibited identical phenotypic features as compared with a mutant obtained by HR‐based allelic exchange. The use of this CBE system was extended to other P. chlororaphis strains (subspecies LX24 and HT66) and also to P. fluorescens 10586, with an equally high editing efficiency. The wide applicability of this CBE method will accelerate bacterial physiology research and metabolic engineering of non‐traditional bacterial hosts.
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Affiliation(s)
- Sheng-Jie Yue
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Peng Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Song Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yu-Yuan Cai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xue-Hong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, 2800, Denmark
| | - Hong-Bo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,National Experimental Teaching Center for Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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Lorquin F, Piccerelle P, Orneto C, Robin M, Lorquin J. New insights and advances on pyomelanin production: from microbial synthesis to applications. J Ind Microbiol Biotechnol 2022; 49:6575554. [PMID: 35482661 PMCID: PMC9338888 DOI: 10.1093/jimb/kuac013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/21/2022] [Indexed: 11/14/2022]
Abstract
Pyomelanin is a brown-black phenolic polymer and results from the oxidation of homogentisic acid (HGA) in the L-tyrosine pathway. As part of the research for natural and active ingredients issued from realistic bioprocesses, this work re-evaluates the HGA pigment and makes an updated inventory of its syntheses, microbial pathways, and properties, with tracks and recent advances for its large-scale production. The mechanism of the HGA polymerization is also well documented. In alkaptonuria, pyomelanin formation leads to connective tissue damages and arthritis, most probably due to the ROS issued from HGA oxidation. While UV radiation on human melanin may generate degradation products, pyomelanin is not photodegradable, is hyperthermostable, and has other properties better than the L-Dopa melanin. This review aims to raise awareness about the potential of this pigment for various applications, not only for skin coloring and protection but also for other cells, materials, and as a promising (semi)conductor for bioelectronics and energy.
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Affiliation(s)
- Faustine Lorquin
- Aix-Marseille Université, Mediterranean Institute of Oceanology (MIO), 163 avenue de Luminy, 13288 Marseille Cedex 9, France.,Aix-Marseille Université, Mediterranean Institute of Marine and Terrestrial Biodiversity and Ecology (IMBE), 27 boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Philippe Piccerelle
- Aix-Marseille Université, Mediterranean Institute of Marine and Terrestrial Biodiversity and Ecology (IMBE), 27 boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Caroline Orneto
- Aix-Marseille Université, Mediterranean Institute of Marine and Terrestrial Biodiversity and Ecology (IMBE), 27 boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Maxime Robin
- Aix-Marseille Université, Mediterranean Institute of Marine and Terrestrial Biodiversity and Ecology (IMBE), 27 boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Jean Lorquin
- Aix-Marseille Université, Mediterranean Institute of Oceanology (MIO), 163 avenue de Luminy, 13288 Marseille Cedex 9, France
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21
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Abdullah, Wang P, Han T, Liu W, Ren W, Wu Y, Xiao Y. Adenine Base Editing System for Pseudomonas and Prediction Workflow for Protein Dysfunction via ABE. ACS Synth Biol 2022; 11:1650-1657. [PMID: 35389616 DOI: 10.1021/acssynbio.2c00066] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pseudomonas is a large genus that inhabits diverse environments due to its distinct metabolic versatility. Its applications range from environmental to industrial biotechnology. Molecular tools that allow precise and efficient genetic manipulation are required to understand and harness its full potential. Here, we report the development of a highly efficient adenine base editing system, i.e., dxABE-PS, for Pseudomonas species. The system allows A:T → G:C transition with up to 100% efficiency along a broad target spectrum because we use xCas9 3.7, which recognizes NG PAM. To enhance the dxABE-PS utility, we develop a prediction workflow for protein dysfunction using ABE, namely, DABE-CSP (dysfunction via ABE through CRISPOR-SIFT prediction). We applied DABE-CSP to inactivate several genes in Pseudomonas putida KT2440 to accumulate a nylon precursor, i.e., muconic acid from catechol with 100% yield. Moreover, we expanded the ABE to non-model Pseudomonas species by developing an nxABE system for P. chengduensisDY56-96, isolated from sediment samples from the seamount area in the West Pacific Ocean. Taken together, the establishment of the ABE systems along with DABE-CSP will fast-track research on Pseudomonas species.
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Affiliation(s)
- Abdullah
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan RD. Minhang District, Shanghai 200240, China
| | - Pujie Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan RD. Minhang District, Shanghai 200240, China
| | - Tongren Han
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan RD. Minhang District, Shanghai 200240, China
| | - Wei Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan RD. Minhang District, Shanghai 200240, China
| | - Wenting Ren
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China
| | - Yuehong Wu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China
| | - Yi Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan RD. Minhang District, Shanghai 200240, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, 800 Dongchuan RD. Minhang District, Shanghai 200240, China
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22
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Liu Y, Xie N, Yu B. De Novo Biosynthesis of D- p-Hydroxyphenylglycine by a Designed Cofactor Self-Sufficient Route and Co-culture Strategy. ACS Synth Biol 2022; 11:1361-1372. [PMID: 35244401 DOI: 10.1021/acssynbio.2c00007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
d-p-Hydroxyphenylglycine (D-HPG) is an important intermediate for the synthesis of β-lactam antibiotics with an annual market demand of thousands of tons. Currently, the main production processes are via chemical approaches. Although enzymatic conversion has been investigated for D-HPG production, synthesis of the substrate DL-hydroxyphenylhydantoin is still chemically based, which suffers from high pollution and harsh reaction conditions. In this study, one cofactor self-sufficient route for D-HPG production from l-phenylalanine was newly designed and the artificial pathway was functionalized by selecting suitable enzymes and adjusting their expressions in strain Pseudomonas putida KT2440. Notably, a new R-mandelate dehydrogenase from Lactococcus lactis with relatively high activity under pH neutral conditions was successfully mined to demonstrate the biosynthetic pathway in vivo. The performance of the engineered P. putida strain was further increased by enhancing cellular NAD availability and blocking l-phenylalanine consumption. Coupled with the l-phenylalanine producer, Escherichia coli strain ATCC 31884, a stable and interactive co-culture process was also developed by engineering a "cross-link auxotrophic" system to produce D-HPG directly from glucose. Thus, this study is the first approach for the de novo biosynthesis of D-HPG by engineering a non-natural pathway and lays the foundation for further improving the efficiency of D-HPG production via a green and sustainable route.
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Affiliation(s)
- Yang Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nengzhong Xie
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Biomass Engineering Technology Research Center, Guangxi Key Laboratory of Bio-refinery, Guangxi Academy of Sciences, Nanning 530007, China
| | - Bo Yu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Chen S, Fan L, Song J, Zhang H, Doucette C, Hughes T, Campbell L. Quantitative proteomic analysis of Neosartorya pseudofischeri ascospores subjected to heat treatment. J Proteomics 2022; 252:104446. [PMID: 34883268 DOI: 10.1016/j.jprot.2021.104446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 10/19/2022]
Abstract
Neosartorya pseudofischeri, a heat- resistant fungus, was isolated from contaminated blueberry juice in our laboratory. To obtain a better understanding of the cellular process of heat- resistant fungus, a quantitative proteomic investigation employing stable isotope labeling by peptide demethylation was conducted on changes in intracellular proteins of N. pseudofischeri ascospores subjected to heat treatment at 93 °C for 0, 1 or 8 min. In total, 811 proteins were identified and quantified. Using the normalized ratio of protein abundance, proteins that changed more than two- fold after heat treatment were identified as significantly increased or decreased proteins and grouped into four clusters based on their quantitative changes. Decreased proteins were found mainly involved in the central carbon metabolism, heat stress responses, reactive oxygen intermediates elimination and translation events. A group of proteins in relation to toxicant degradation and antibiotic neutralization linking to environmental adaptability and tolerance of heat- resistant, was also identified. These findings provide insights into protein changes of N. pseudofischeri ascospores and lay foundations for further investigations on heat- resistant molds using targeted quantitative approaches. SIGNIFICANCE OF THE RESEARCH: Heat- resistant fungi can survive pasteurization processes, and subsequently germinate and grow to cause spoilage of food products, leading to significant economic losses for the food industry and potential health risk for the consumers. To obtain a better understanding of the cellular process of heat- resistant fungi, a quantitative proteomic approach employing stable isotope labeling by peptide demethylation has been used to investigate the intracellular protein changes of N. pseudofischeri ascospores isolated from blueberry juice and subjected to heat treatment. 150 significantly changed proteins were grouped into four clusters based on their quantitative changes. The significant decrease in protein abundance in response to heat treatment revealed possible mechanism that N. pseudofischeri ascospores could survive the heat treatment. This is the first proteomic profile report for N. pseudofischeri. These findings provide insights into protein changes of N. pseudofischeri and lay foundations for further investigations on heat- resistant fungi using targeted quantitative approaches to evaluate the efficiency of thermal treatment for processed food products.
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Affiliation(s)
- Si Chen
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, China; Laboratory of aquatic product processing and quality safety, Marine Fisheries Research Institute of Zhejiang Province, Zhejiang, China
| | - Lihua Fan
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, 32 Main Street, Kentville, NS B4N 1J5, Canada.
| | - Jun Song
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, 32 Main Street, Kentville, NS B4N 1J5, Canada
| | - Hong Zhang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, China.
| | - Craig Doucette
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, 32 Main Street, Kentville, NS B4N 1J5, Canada
| | - Timothy Hughes
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, 32 Main Street, Kentville, NS B4N 1J5, Canada
| | - Leslie Campbell
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, 32 Main Street, Kentville, NS B4N 1J5, Canada
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Breisch J, Huber LS, Kraiczy P, Hubloher J, Averhoff B. The ß-ketoadipate pathway of Acinetobacter baumannii is involved in complement resistance and affects resistance against aromatic antibiotics. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:170-178. [PMID: 35023294 DOI: 10.1111/1758-2229.13042] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
Acinetobacter baumannii can thrive on a broad range of substrates such as sugars, alcohols, lipids, amino acids and aromatic compounds. The latter three are abundant in the human host and are potential candidates as carbon sources for the metabolic adaptation of A. baumannii to the human host. In this study we determined the biodegradative activities of A. baumannii AYE with monocyclic aromatic compounds. Deletion of genes encoding the key enzymes of the ß-ketoadipate pathway, the protocatechuate-3,4-dioxygenase (ΔpcaHG) and the catechol-1,2-dioxygenase (ΔcatA), led to a complete loss of growth on benzoate and p-hydroxybenzoate, suggesting that these substrates are metabolized via the two distinct branches (pca and cat) of this pathway. Furthermore, we investigated the potential role of these gene products in host adaptation by analyzing the capability of the mutants to resist complement-mediated killing. These studies revealed that the mutants exhibit a decreased complement resistance, but a dramatic increase in survival in normal human serum in the presence of p-hydroxybenzoate or protocatechuate. These results indicate that the ß-ketoadipate pathway plays a role in adaptation of A. baumannii to the human host. Moreover, the single and double mutants exhibited increased antibiotic resistances indicating a link between the two dioxygenases and antibiotic resistance.
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Affiliation(s)
- Jennifer Breisch
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Lisa Sophie Huber
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Peter Kraiczy
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Josephine Hubloher
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Beate Averhoff
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
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Wang H, Liu B, Lei P, Zhu J, Chen L, He Q, He J. Improving the herbicide resistance of 4-hydroxyphenylpyruvate dioxygenase SpHPPD by directed evolution. Enzyme Microb Technol 2021; 154:109964. [PMID: 34902641 DOI: 10.1016/j.enzmictec.2021.109964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 11/27/2021] [Accepted: 12/06/2021] [Indexed: 11/03/2022]
Abstract
Topramezone, a highly efficient 4-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibitor herbicide, is an ideal target for herbicide-resistant genetic engineering. However, there is still a lack of HPPD gene that is highly resistant to topramezone. In previous studies, we obtained a topramezone-resistant HPPD (SpHPPDm) gene from Sphingobium sp. TPM-19, however, its resistance strength still could not meet the requirements for construction of herbicide-resistant crop. In this study, random mutagenesis (error-prone PCR) was employed to improve the topramezone resistance of SpHPPDm. Two mutants with improved resistance, K-28 (E322R) and K-113 (K249R, G327C), were screened from the random mutation library of SpHPPDm. The catalytic efficiency (kcat/Km) of mutants K-28 and K-113 only slightly decreased by approximately 2%. The half-maximal inhibitory concentration (IC50) of topramezone increased by 58.5% and 195.5% for mutants K-28 and K-113, respectively. Furthermore, mutant K-113 also showed significantly improved resistance to mesotrione and DKN (the active ingredient of isoxaflutole) with the IC50 increasing by 60.3% and 167.5%, respectively; while mutant K-28 only showed increased resistance to mesotrione with IC50 increasing by 77.6%, but reduced resistance to DKN with IC50 declining by 20.9%. Site-directed mutation assays revealed that G327C, but not K249R, contributed to topramezone resistance in mutant K-113. This study provides genetic resources for the genetic engineering of HPPD-inhibitor-resistant crops and a basis for further research on HPPD resistance mechanisms.
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Affiliation(s)
- Haiyan Wang
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Bin Liu
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Peng Lei
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Jianchun Zhu
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Le Chen
- Excellence and innovation center, Jiangsu Academy of Agricultural Science, Nanjing 210014, China.
| | - Qin He
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
| | - Jian He
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
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Jiang L, Jeon D, Kim J, Lee CW, Peng Y, Seo J, Lee JH, Paik JH, Kim CY, Lee J. Pyomelanin-Producing Brevundimonas vitisensis sp. nov., Isolated From Grape ( Vitis vinifera L.). Front Microbiol 2021; 12:733612. [PMID: 34721332 PMCID: PMC8551962 DOI: 10.3389/fmicb.2021.733612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/23/2021] [Indexed: 11/13/2022] Open
Abstract
A novel endophytic bacterial strain, designated GR-TSA-9T, was isolated from surface-sterilized grape (Vitis vinifera L.). 16S rRNA gene sequence analyses showed that the isolate was grouped within the genus Brevundimonas, displaying the highest similarity with Brevundimonas lenta DS-18T (97.9%) and Brevundimonas kwangchunensis KSL-102T (97.8%) and less than 97.5% similarity with other members of Brevundimonas. The strain GR-TSA-9T was a gram negative, rod shaped, facultatively anaerobic, catalase and oxidase positive, and motile bacterium. Its growth occurred at 10–37°C (optimally 25–30°C), at pH 7.0–8.0, and in NaCl 0–1% (optimally 0%). It contained ubiquinone-10 as a respiratory quinone, and the major cellular fatty acids (>10% of the total) were C16:0 (14.2%) and summed feature 8 (C18:1ω7c and/or C18:1ω6c, 65.6%). The polar lipids present in the strain were phosphoglycolipids, phosphatidylglycerol, 1,2-di-O-acyl-3-O-[d-glucopyranosyl-(1→4)-α-d-glucopyranuronosyl]glycerol, and unidentified lipids (L1, L2, and L4). The strain had one 2,976,716bp circular chromosome with a G+C content of 66.4%. The digital DNA–DNA hybridization value between strain GR-TSA-9T and B. lenta DS-18T was 20.9%, while the average nucleotide identity value was 76.7%. In addition, the dDDH and ANI values to other members in this genus, whose genome sequences are available, are less than 21.1 and 77.6%. Genome annotation predicted the presence of some gene clusters related to tyrosine degradation and pyomelanin formation. Strain GR-TSA-9T produced a brown melanin-like pigment in the presence of L-tyrosine-containing media. The highest pigment production (0.19g/L) was observed in tryptic soy broth with 1.0mg/ml L-tyrosine at 25°C for 6days of culture. Biophysical characterization by ultraviolet (UV)–visible spectroscopy, Fourier-transform infrared spectroscopy, and electrospray ionization mass spectrometry confirmed that the pigment was pyomelanin. Additionally, melanized GR-TSA-9T cells could protect the cells against UVC exposure. The phylogenetic, genomic, phenotypic, and chemotaxonomic features indicated that strain GR-TSA-9T represents a novel melanin-producing species of Brevundimonas. The type strain was GR-TSA-9T (KCTC 82386T=CGMCC 1.18820T).
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Affiliation(s)
- Lingmin Jiang
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, South Korea
| | - Doeun Jeon
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, South Korea
| | - Jueun Kim
- Department of Chemistry, Chonnam National University, Gwangju, South Korea
| | - Chul Won Lee
- Department of Chemistry, Chonnam National University, Gwangju, South Korea
| | - Yuxin Peng
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, South Korea
| | - Jiyoon Seo
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, South Korea
| | - Ju Huck Lee
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, South Korea
| | - Jin Hyub Paik
- International Biological Material Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Cha Young Kim
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, South Korea
| | - Jiyoung Lee
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, South Korea
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Davoodi J, Majidi S, Jahani M, Tayarani-Najaran Z, Golmohammadzadeh S, Kamali H. Implementation of design of experiments for optimization of forced degradation conditions and development of a stability-indicating high-performance liquid chromatography method for sepiwhite. J Sep Sci 2021; 44:4299-4312. [PMID: 34669262 DOI: 10.1002/jssc.202100388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 09/21/2021] [Accepted: 10/04/2021] [Indexed: 12/21/2022]
Abstract
Sepiwhite is a novel anti-pigmenting agent that is derived from fatty acid and phenylalanine and used for hyperpigmentation induced by light exposure or inflammation. In this study, a simple and validated high-performance liquid chromatography method for the quantitation of sepiwhite was developed. Optimized forced degradation of sepiwhite at thermal, acid/base, photolysis, oxidative, and heavy metal ions conditions were evaluated and the effect of each of them on production of specific 10%-30% degradants was studied by the approach of design of experiments. Sepiwhite accelerated study was conducted and toxicity of sepiwhite at each condition was tested. An optimized high-performance liquid chromatography method was validated by a face-centered central composition design. Ten different degradants were identified from sepiwhite and degradation behavior under different conditions was studied. Sepiwhite and its degradant products show no cytotoxicity. This optimized high-performance liquid chromatography method can be applied for quality control assay and sepiwhite degradation behavior may be considered in the manufacturing of sepiwhite products.
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Affiliation(s)
- Javid Davoodi
- Department of Pharmaceutics, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sina Majidi
- Student Research Committee, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maryam Jahani
- Department of Pharmaceutical Control, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Tayarani-Najaran
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Shiva Golmohammadzadeh
- Department of Pharmaceutics, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.,Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hossein Kamali
- Department of Pharmaceutics, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.,Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
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28
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Kuroda K, Narihiro T, Nobu MK, Tobo A, Yamauchi M, Yamada M. Ecogenomics Reveals Microbial Metabolic Networks in a Psychrophilic Methanogenic Bioreactor Treating Soy Sauce Production Wastewater. Microbes Environ 2021; 36. [PMID: 34588388 PMCID: PMC8674449 DOI: 10.1264/jsme2.me21045] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
An ecogenomic analysis of the methanogenic microbial community in a laboratory-scale up-flow anaerobic sludge blanket (UASB) reactor treating soy sauce-processing wastewater revealed a synergistic metabolic network. Granular sludge samples were collected from the UASB reactor operated under psychrophilic (20°C) conditions with a COD removal rate >75%. A 16S rRNA gene amplicon sequencing-based microbial community analysis classified the major microbial taxa as Methanothrix, Methanobacterium, Pelotomaculaceae, Syntrophomonadaceae, Solidesulfovibrio, and members of the phyla Synergistota and Bacteroidota. Draft genomes of dominant microbial populations were recovered by metagenomic shotgun sequencing. Metagenomic- and metatranscriptomic-assisted metabolic reconstructions indicated that Synergistota- and Bacteroidota-related organisms play major roles in the degradation of amino acids. A metagenomic bin of the uncultured Bacteroidales 4484-276 clade encodes genes for proteins that may function in the catabolism of phenylalanine and tyrosine under microaerobic conditions. Syntrophomonadaceae and Pelotomaculaceae oxidize fatty acid byproducts presumably derived from the degradation of amino acids in syntrophic association with aceticlastic and hydrogenotrophic methanogen populations. Solidesulfovibrio organisms are responsible for the reduction of sulfite and may support the activity of hydrogenotrophic methanogens and other microbial populations by providing hydrogen and ammonia using nitrogen fixation-related proteins. Overall, functionally diverse anaerobic organisms unite to form a metabolic network that performs the complete degradation of amino acids in the psychrophilic methanogenic microbiota.
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Affiliation(s)
- Kyohei Kuroda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Atsushi Tobo
- Department of Urban Environmental Design and Engineering, National Institute of Technology, Kagoshima College
| | - Masahito Yamauchi
- Department of Urban Environmental Design and Engineering, National Institute of Technology, Kagoshima College
| | - Masayoshi Yamada
- Department of Urban Environmental Design and Engineering, National Institute of Technology, Kagoshima College
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29
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Wright RJ, Bosch R, Langille MGI, Gibson MI, Christie-Oleza JA. A multi-OMIC characterisation of biodegradation and microbial community succession within the PET plastisphere. MICROBIOME 2021; 9:141. [PMID: 34154652 PMCID: PMC8215760 DOI: 10.1186/s40168-021-01054-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/19/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Plastics now pollute marine environments across the globe. On entering these environments, plastics are rapidly colonised by a diverse community of microorganisms termed the plastisphere. Members of the plastisphere have a myriad of diverse functions typically found in any biofilm but, additionally, a number of marine plastisphere studies have claimed the presence of plastic-biodegrading organisms, although with little mechanistic verification. Here, we obtained a microbial community from marine plastic debris and analysed the community succession across 6 weeks of incubation with different polyethylene terephthalate (PET) products as the sole carbon source, and further characterised the mechanisms involved in PET degradation by two bacterial isolates from the plastisphere. RESULTS We found that all communities differed significantly from the inoculum and were dominated by Gammaproteobacteria, i.e. Alteromonadaceae and Thalassospiraceae at early time points, Alcanivoraceae at later time points and Vibrionaceae throughout. The large number of encoded enzymes involved in PET degradation found in predicted metagenomes and the observation of polymer oxidation by FTIR analyses both suggested PET degradation was occurring. However, we were unable to detect intermediates of PET hydrolysis with metabolomic analyses, which may be attributed to their rapid depletion by the complex community. To further confirm the PET biodegrading potential within the plastisphere of marine plastic debris, we used a combined proteogenomic and metabolomic approach to characterise amorphous PET degradation by two novel marine isolates, Thioclava sp. BHET1 and Bacillus sp. BHET2. The identification of PET hydrolytic intermediates by metabolomics confirmed that both isolates were able to degrade PET. High-throughput proteomics revealed that whilst Thioclava sp. BHET1 used the degradation pathway identified in terrestrial environment counterparts, these were absent in Bacillus sp. BHET2, indicating that either the enzymes used by this bacterium share little homology with those characterised previously, or that this bacterium uses a novel pathway for PET degradation. CONCLUSIONS Overall, the results of our multi-OMIC characterisation of PET degradation provide a significant step forwards in our understanding of marine plastic degradation by bacterial isolates and communities and evidences the biodegrading potential extant in the plastisphere of marine plastic debris. Video abstract.
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Affiliation(s)
- Robyn J. Wright
- School of Life Sciences, University of Warwick, Coventry, UK
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - Rafael Bosch
- University of the Balearic Islands, Palma, Spain
- IMEDEA (CSIC-UIB), Esporles, Spain
| | - Morgan G. I. Langille
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - Matthew I. Gibson
- Department of Chemistry, University of Warwick, Coventry, UK
- Medical School, University of Warwick, Coventry, UK
| | - Joseph A. Christie-Oleza
- School of Life Sciences, University of Warwick, Coventry, UK
- University of the Balearic Islands, Palma, Spain
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30
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Suvorova IA, Gelfand MS. Comparative Analysis of the IclR-Family of Bacterial Transcription Factors and Their DNA-Binding Motifs: Structure, Positioning, Co-Evolution, Regulon Content. Front Microbiol 2021; 12:675815. [PMID: 34177859 PMCID: PMC8222616 DOI: 10.3389/fmicb.2021.675815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/14/2021] [Indexed: 11/13/2022] Open
Abstract
The IclR-family is a large group of transcription factors (TFs) regulating various biological processes in diverse bacteria. Using comparative genomics techniques, we have identified binding motifs of IclR-family TFs, reconstructed regulons and analyzed their content, finding co-occurrences between the regulated COGs (clusters of orthologous genes), useful for future functional characterizations of TFs and their regulated genes. We describe two main types of IclR-family motifs, similar in sequence but different in the arrangement of the half-sites (boxes), with GKTYCRYW3-4RYGRAMC and TGRAACAN1-2TGTTYCA consensuses, and also predict that TFs in 32 orthologous groups have binding sites comprised of three boxes with alternating direction, which implies two possible alternative modes of dimerization of TFs. We identified trends in site positioning relative to the translational gene start, and show that TFs in 94 orthologous groups bind tandem sites with 18-22 nucleotides between their centers. We predict protein-DNA contacts via the correlation analysis of nucleotides in binding sites and amino acids of the DNA-binding domain of TFs, and show that the majority of interacting positions and predicted contacts are similar for both types of motifs and conform well both to available experimental data and to general protein-DNA interaction trends.
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Affiliation(s)
- Inna A Suvorova
- Institute for Information Transmission Problems of Russian Academy of Sciences (The Kharkevich Institute), Moscow, Russia
| | - Mikhail S Gelfand
- Institute for Information Transmission Problems of Russian Academy of Sciences (The Kharkevich Institute), Moscow, Russia.,Skolkovo Institute of Science and Technology, Moscow, Russia
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31
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d'Ischia M, Manini P, Martins Z, Remusat L, O'D Alexander CM, Puzzarini C, Barone V, Saladino R. Insoluble organic matter in chondrites: Archetypal melanin-like PAH-based multifunctionality at the origin of life? Phys Life Rev 2021; 37:65-93. [PMID: 33774429 DOI: 10.1016/j.plrev.2021.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 03/12/2021] [Indexed: 12/11/2022]
Abstract
An interdisciplinary review of the chemical literature that points to a unifying scenario for the origin of life, referred to as the Primordial Multifunctional organic Entity (PriME) scenario, is provided herein. In the PriME scenario it is suggested that the Insoluble Organic Matter (IOM) in carbonaceous chondrites, as well as interplanetary dust particles from meteorites and comets may have played an important role in the three most critical processes involved in the origin of life, namely 1) metabolism, via a) the provision and accumulation of molecules that are the building blocks of life, b) catalysis (e.g., by templation), and c) protection of developing life molecules against radiation by excited state deactivation; 2) compartmentalization, via adsorption of compounds on the exposed organic surfaces in fractured meteorites, and 3) replication, via deaggregation, desorption and related physical phenomena. This scenario is based on the hitherto overlooked structural and physicochemical similarities between the IOM and the dark, insoluble, multifunctional melanin polymers found in bacteria and fungi and associated with the ability of these microorganisms to survive extreme conditions, including ionizing radiation. The underlying conceptual link between these two materials is strengthened by the fact that primary precursors of bacterial and fungal melanins (collectively referred to herein as allomelanins) are hydroxylated aromatic compounds like homogentisic acid and 1,8-dihydroxynaphthalene, and that similar hydroxylated aromatic compounds, including hydroxynaphthalenes, figure prominently among possible components of the organic materials on dust grains and ices in the interstellar matter, and may be involved in the formation of IOM in meteorites. Inspired by this rationale, a vis-à-vis review of the properties of IOM from various chondrites and non-nitrogenous allomelanin pigments from bacteria and fungi is provided herein. The unrecognized similarities between these materials may pave the way for a novel scenario at the origin of life, in which IOM-related complex organic polymers delivered to the early Earth are proposed to serve as PriME and were preserved and transformed in those primitive forms of life that shared the ability to synthesize melanin polymers playing an important role in the critical processes underlying the establishment of terrestrial eukaryotes.
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Affiliation(s)
- Marco d'Ischia
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126 Naples, Italy.
| | - Paola Manini
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126 Naples, Italy
| | - Zita Martins
- Centro de Química Estrutural and Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Laurent Remusat
- Institut de minéralogie, de physique des matériaux et de cosmochimie, UMR CNRS 7590, Sorbonne Université, Muséum National d'Histoire Naturelle, 61 rue Buffon, 75005 Paris, France
| | - Conel M O'D Alexander
- Earth and Planets Laboratory, Carnegie Institution for Science, 5241 Broad Branch Road, NW Washington, DC 20015-1305, USA
| | - Cristina Puzzarini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, Bologna, I-40126, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa, I-56126, Italy
| | - Raffaele Saladino
- Biological and Ecological Sciences Department (DEB), University of Tuscia, Via S. Camillo de Lellis 01100 Viterbo, Italy
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Dhyani R, Shankar K, Bhatt A, Jain S, Hussain A, Navani NK. Homogentisic Acid-Based Whole-Cell Biosensor for Detection of Alkaptonuria Disease. Anal Chem 2021; 93:4521-4527. [PMID: 33655752 DOI: 10.1021/acs.analchem.0c04914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Clinicians require simple quantitative tools for the detection of homogentisic acid in alkaptonuria patients, a rare inherited disorder of amino acid metabolism. In this study, we report a whole-cell biosensor for homogentisic acid to detect alkaptonuria disease through the expression of green fluorescence protein. The assay system utilizes a promoter sequence (hmgA) isolated from the Pseudomonas aeruginosa genome. To increase the sensitivity, the sensor module harboring phmgA::GFP was further transformed into various transposon mutants debilitated in steps involved in the metabolism of phenylalanine and tyrosine via homogentisic acid as a central intermediate. The proposed biosensor was further checked for analytical features such as sensitivity, selectivity, linearity, and precision for the quantification of homogentisic acid in spiked urine samples. The limit of detection for the developed biosensor was calculated to be 3.9 μM, which is comparable to that of the various analytical techniques currently in use. The sensor construct showed no interference from all of the amino acids and its homolog molecules. The accuracy and precision of the proposed biosensor were validated using high-performance liquid chromatography (HPLC) with satisfactory results.
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Affiliation(s)
- Rajat Dhyani
- Chemical Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Krishna Shankar
- Chemical Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Ankita Bhatt
- Chemical Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Shubham Jain
- Chemical Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Ajmal Hussain
- Chemical Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Naveen Kumar Navani
- Chemical Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
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Lopez-Echartea E, Suman J, Smrhova T, Ridl J, Pajer P, Strejcek M, Uhlik O. Genomic analysis of dibenzofuran-degrading Pseudomonas veronii strain Pvy reveals its biodegradative versatility. G3-GENES GENOMES GENETICS 2021; 11:6029021. [PMID: 33693598 PMCID: PMC8022969 DOI: 10.1093/g3journal/jkaa030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 11/30/2020] [Indexed: 11/30/2022]
Abstract
Certain industrial chemicals accumulate in the environment due to their recalcitrant properties. Bioremediation uses the capability of some environmental bacteria to break down these chemicals and attenuate the pollution. One such bacterial strain, designated Pvy, was isolated from sediment samples from a lagoon in Romania located near an oil refinery due to its capacity to degrade dibenzofuran (DF). The genome sequence of the Pvy strain was obtained using an Oxford Nanopore MiniION platform. According to the consensus 16S rRNA gene sequence that was compiled from six 16S rRNA gene copies contained in the genome and orthologous average nucleotide identity (OrthoANI) calculation, the Pvy strain was identified as Pseudomonas veronii, which confirmed the identification obtained with the aid of MALDI-TOF mass spectrometry and MALDI BioTyper. The genome was analyzed with respect to enzymes responsible for the overall biodegradative versatility of the strain. The Pvy strain was able to derive carbon from naphthalene (NP) and several aromatic compounds of natural origin, including salicylic, protocatechuic, p-hydroxybenzoic, trans-cinnamic, vanillic, and indoleacetic acids or vanillin, and was shown to degrade but not utilize DF. In total seven loci were found in the Pvy genome, which enables the strain to participate in the degradation of these aromatic compounds. Our experimental data also indicate that the transcription of the NP-dioxygenase α-subunit gene (ndoB), carried by the plasmid of the Pvy strain, is inducible by DF. These features make the Pvy strain a potential candidate for various bioremediation applications.
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Affiliation(s)
- Eglantina Lopez-Echartea
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic
| | - Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic
| | - Tereza Smrhova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic
| | - Jakub Ridl
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 40 Prague, Czech Republic.,Division of Animal Evolutionary Biology, Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, 128 44 Prague, Czech Republic
| | - Petr Pajer
- Military Health Institute, Ministry of Defence of the Czech Republic, U Vojenske nemocnice 1200, 169 02 Prague 6, Czech Republic
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic
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34
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Neuckermans J, Lequeue S, Mertens A, Branson S, Schwaneberg U, De Kock J. High-throughput quantification of ochronotic pigment formation in Escherichia coli to evaluate the potency of human 4-hydroxyphenylpyruvate dioxygenase inhibitors in multi-well format. MethodsX 2020; 8:101181. [PMID: 33365261 PMCID: PMC7749435 DOI: 10.1016/j.mex.2020.101181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/30/2020] [Accepted: 12/08/2020] [Indexed: 02/06/2023] Open
Abstract
4-hydroxyphenylpyruvate dioxygenase (HPD) is a key enzyme in the catabolism of tyrosine and therefore of great importance as a drug target to treat tyrosine-related inherited metabolic disorders (TIMD). Inhibition of this enzyme is therapeutically applied to prevent accumulation of toxic metabolites in TIMD patients. Nowadays an ex-herbicide, nitisinone, is used for this purpose and many more inhibitors are being explored and need to be tested. Here, we describe a colorimetric bacterial whole-cell screening system that allows quantifying the inhibitory effects of new human HPD inhibitors in a high-throughput and robust fashion. For this high-throughput screening (HTS) system we rely on the capability of recombinant E. coli that express human HPD, to generate a brown ochronotic pigment after the addition of tyrosine, whereafter this brown pigment can be quantified in a very specific and sensitive way by spectrophotometric analysis. Altogether, this robust and simple HTS screening system can be described as non-harmful, non-laborious and cost-effective with the aim to identify and evaluate novel therapeutic human HPD inhibitors for the treatment of TIMD.This robust high-throughput screening system enables rapid identification and evaluation of potential inhibitors of human 4-hydroxyphenylpyruvate dioxygenase. Simple and fast colorimetric quantification of the formation of ochronotic pigment.
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Affiliation(s)
- Jessie Neuckermans
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Sien Lequeue
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Alan Mertens
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Steven Branson
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Joery De Kock
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium
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35
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Manzo G, Hind CK, Ferguson PM, Amison RT, Hodgson-Casson AC, Ciazynska KA, Weller BJ, Clarke M, Lam C, Man RCH, Shaughnessy BGO, Clifford M, Bui TT, Drake AF, Atkinson RA, Lam JKW, Pitchford SC, Page CP, Phoenix DA, Lorenz CD, Sutton JM, Mason AJ. A pleurocidin analogue with greater conformational flexibility, enhanced antimicrobial potency and in vivo therapeutic efficacy. Commun Biol 2020; 3:697. [PMID: 33247193 PMCID: PMC7699649 DOI: 10.1038/s42003-020-01420-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 10/22/2020] [Indexed: 01/08/2023] Open
Abstract
Antimicrobial peptides (AMPs) are a potential alternative to classical antibiotics that are yet to achieve a therapeutic breakthrough for treatment of systemic infections. The antibacterial potency of pleurocidin, an AMP from Winter Flounder, is linked to its ability to cross bacterial plasma membranes and seek intracellular targets while also causing membrane damage. Here we describe modification strategies that generate pleurocidin analogues with substantially improved, broad spectrum, antibacterial properties, which are effective in murine models of bacterial lung infection. Increasing peptide-lipid intermolecular hydrogen bonding capabilities enhances conformational flexibility, associated with membrane translocation, but also membrane damage and potency, most notably against Gram-positive bacteria. This negates their ability to metabolically adapt to the AMP threat. An analogue comprising D-amino acids was well tolerated at an intravenous dose of 15 mg/kg and similarly effective as vancomycin in reducing EMRSA-15 lung CFU. This highlights the therapeutic potential of systemically delivered, bactericidal AMPs.
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Affiliation(s)
- Giorgia Manzo
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Charlotte K Hind
- Technology Development Group, National Infection Service, Public Health England, Salisbury, UK
| | - Philip M Ferguson
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Richard T Amison
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
- Sackler Institute of Pulmonary Pharmacology, King's College London, London, UK
| | - Alice C Hodgson-Casson
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Katarzyna A Ciazynska
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Bethany J Weller
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Maria Clarke
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Carolyn Lam
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Rico C H Man
- Department of Pharmacology and Pharmacy, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Blaze G O' Shaughnessy
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
- Sackler Institute of Pulmonary Pharmacology, King's College London, London, UK
| | - Melanie Clifford
- Technology Development Group, National Infection Service, Public Health England, Salisbury, UK
| | - Tam T Bui
- Centre for Biomolecular Spectroscopy and Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, London, SE1 1UL, UK
| | - Alex F Drake
- Centre for Biomolecular Spectroscopy and Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, London, SE1 1UL, UK
| | - R Andrew Atkinson
- Centre for Biomolecular Spectroscopy and Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, London, SE1 1UL, UK
| | - Jenny K W Lam
- Department of Pharmacology and Pharmacy, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Simon C Pitchford
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
- Sackler Institute of Pulmonary Pharmacology, King's College London, London, UK
| | - Clive P Page
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
- Sackler Institute of Pulmonary Pharmacology, King's College London, London, UK
| | - David A Phoenix
- School of Applied Science, London South Bank University, 103 Borough Road, London, SE1 0AA, UK
| | | | - J Mark Sutton
- Technology Development Group, National Infection Service, Public Health England, Salisbury, UK.
| | - A James Mason
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK.
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Fonseca É, Freitas F, Caldart R, Morgado S, Vicente AC. Pyomelanin biosynthetic pathway in pigment-producer strains from the pandemic Acinetobacter baumannii IC-5. Mem Inst Oswaldo Cruz 2020; 115:e200371. [PMID: 33174904 PMCID: PMC7646211 DOI: 10.1590/0074-02760200371] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/16/2020] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Acinetobacter baumannii outbreaks have been associated with pandemic International Clones (ICs), but the virulence factors involved with their pathogenicity are sparsely understood. Pigment production has been linked with bacterial pathogenicity, however, this phenotype is rarely observed in A. baumannii. OBJECTIVES This study aimed to characterise the reddish-brown pigment produced by A. baumannii strains, and to determine its biosynthetic pathway by genomic approaches. METHODS Pigment characterisation and antimicrobial susceptibility were conducted by phenotypic tests. The clonal relationship was obtained by pulsed field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). The genome of an A. baumannii was obtained for characterisation of genes involved with pigment production. FINDINGS The pyomelanin was the pigment produced by A. baumannii. Strains were extensively drug resistant and belonged to the IC-5/ST79. The pyomelanin biosynthetic pathway was determined and presented a particular architecture concerning the peripheral (tyrB, phhB and hpd) and central (hmgB, hmgC and hmgR) metabolic pathway genes. The identification of a distant HmgA homologue, probably without dioxygenase activity, could explain pyomelanin production. Virulence determinants involved with adherence (csuA/BABCDE and a T5bSS-carrying genomic island), and iron uptake (basABCDEFGHIJ, bauABCDEF and barAB) were characterised. MAIN CONCLUSION There is a biosynthetic pathway compatible with the pyomelanin production observed in persistent A. baumannii IC-5 strains.
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Affiliation(s)
- Érica Fonseca
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genética Molecular de Microrganismos, Rio de Janeiro, RJ, Brasil
| | - Fernanda Freitas
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genética Molecular de Microrganismos, Rio de Janeiro, RJ, Brasil
| | | | - Sérgio Morgado
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genética Molecular de Microrganismos, Rio de Janeiro, RJ, Brasil
| | - Ana Carolina Vicente
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genética Molecular de Microrganismos, Rio de Janeiro, RJ, Brasil
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Yeshi K, Creek DJ, Anderson D, Ritmejerytė E, Becker L, Loukas A, Wangchuk P. Metabolomes and Lipidomes of the Infective Stages of the Gastrointestinal nematodes, Nippostrongylus brasiliensis and Trichuris muris. Metabolites 2020; 10:metabo10110446. [PMID: 33171998 PMCID: PMC7694664 DOI: 10.3390/metabo10110446] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/01/2020] [Accepted: 11/03/2020] [Indexed: 02/08/2023] Open
Abstract
Soil-transmitted helminths, including hookworms and whipworms, infect billions of people worldwide. Their capacity to penetrate and migrate through their hosts’ tissues is influenced by the suite of molecules produced by the infective developmental stages. To facilitate a better understanding of the immunobiology and pathogenicity of human hookworms and whipworms, we investigated the metabolomes of the infective stage of Nippostrongylus brasiliensis third-stage larvae (L3) which penetrate the skin and Trichuris muris eggs which are orally ingested, using untargeted liquid chromatography-mass spectrometry (LC-MS). We identified 55 polar metabolites through Metabolomics Standard Initiative level-1 (MSI-I) identification from N. brasiliensis and T. muris infective stages, out of which seven were unique to excretory/secretory products (ESPs) of N. brasiliensis L3. Amino acids were a principal constituent (33 amino acids). Additionally, we identified 350 putative lipids, out of which 28 (all known lipids) were unique to N. brasiliensis L3 somatic extract and four to T. muris embryonated egg somatic extract. Glycerophospholipids and glycerolipids were the major lipid groups. The catalogue of metabolites identified in this study shed light on the biology, and possible therapeutic and diagnostic targets for the treatment of these critical infectious pathogens. Moreover, with the growing body of literature on the therapeutic utility of helminth ESPs for treating inflammatory diseases, a role for metabolites is likely but has received little attention thus far.
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Affiliation(s)
- Karma Yeshi
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Building E4, McGregor Rd, Smithfield, Cairns, QLD 4878, Australia; (E.R.); (L.B.); (A.L.)
- Correspondence: (K.Y.); (P.W.)
| | - Darren J. Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia; (D.J.C.); (D.A.)
| | - Dovile Anderson
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia; (D.J.C.); (D.A.)
| | - Edita Ritmejerytė
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Building E4, McGregor Rd, Smithfield, Cairns, QLD 4878, Australia; (E.R.); (L.B.); (A.L.)
| | - Luke Becker
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Building E4, McGregor Rd, Smithfield, Cairns, QLD 4878, Australia; (E.R.); (L.B.); (A.L.)
| | - Alex Loukas
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Building E4, McGregor Rd, Smithfield, Cairns, QLD 4878, Australia; (E.R.); (L.B.); (A.L.)
| | - Phurpa Wangchuk
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Building E4, McGregor Rd, Smithfield, Cairns, QLD 4878, Australia; (E.R.); (L.B.); (A.L.)
- Correspondence: (K.Y.); (P.W.)
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Liu B, Wang H, Zhang K, Zhu J, He Q, He J. Improved Herbicide Resistance of 4-Hydroxyphenylpyruvate Dioxygenase from Sphingobium sp. TPM-19 through Directed Evolution. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:12365-12374. [PMID: 33105985 DOI: 10.1021/acs.jafc.0c05785] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
4-Hydroxyphenylpyruvate dioxygenase (HPPD) has attracted extensive interest as a promising target for the genetic engineering of herbicide-resistant crops. However, naturally occurring HPPDs are generally very sensitive to HPPD inhibitors. In this study, random mutagenesis was performed to increase the HPPD inhibitors' resistance of Sphingobium sp. HPPD (SpHPPD). Two mutants, Q258M and Y333F, with improved resistance were obtained. Subsequently, a double-mutant (Q258M/Y333F) was generated through combined mutation. Q258M/Y333F exhibited the highest resistance to four HPPD inhibitors [topramezone, mesotrione, tembotrione, and diketonitrile (DKN)]. The enzyme fitness of Q258M/Y333F to topramezone, mesotrione, tembotrione, and DKN was increased by 4.0-, 4.1-, 4.2-, and 3.2-folds, respectively, in comparison with that of the wild-type. Molecular modeling and docking revealed that Q258M mutation leads to the decrease of enzyme-inhibitor-binding strength by breaking the hydrogen bond between the enzyme and the inhibitor, and Y333F mutation changes the conformational balance of the C-terminal helix H11, which hinders the binding of the inhibitor to the enzyme and thus would contribute to improved herbicide resistance. This study helps to further elucidate the structural basis for herbicide resistance and provides better genetic resources for the genetic engineering of herbicide-resistant crops.
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Affiliation(s)
- Bin Liu
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095 Jiangsu, P. R. China
| | - Haiyan Wang
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095 Jiangsu, P. R. China
| | - Kaiyun Zhang
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095 Jiangsu, P. R. China
| | - Jianchun Zhu
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095 Jiangsu, P. R. China
| | - Qin He
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095 Jiangsu, P. R. China
| | - Jian He
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095 Jiangsu, P. R. China
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The Syringate O-Demethylase Gene of Sphingobium sp. Strain SYK-6 Is Regulated by DesX, while Other Vanillate and Syringate Catabolism Genes Are Regulated by DesR. Appl Environ Microbiol 2020; 86:AEM.01712-20. [PMID: 32917754 DOI: 10.1128/aem.01712-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 09/02/2020] [Indexed: 12/26/2022] Open
Abstract
Syringate and vanillate are the major metabolites of lignin biodegradation. In Sphingobium sp. strain SYK-6, syringate is O demethylated to gallate by consecutive reactions catalyzed by DesA and LigM, and vanillate is O demethylated to protocatechuate by a reaction catalyzed by LigM. The gallate ring is cleaved by DesB, and protocatechuate is catabolized via the protocatechuate 4,5-cleavage pathway. The transcriptions of desA, ligM, and desB are induced by syringate and vanillate, while those of ligM and desB are negatively regulated by the MarR-type transcriptional regulator DesR, which is not involved in desA regulation. Here, we clarified the regulatory system for desA transcription by analyzing the IclR-type transcriptional regulator desX, located downstream of desA Quantitative reverse transcription (RT)-PCR analyses of a desX mutant indicated that the transcription of desA was negatively regulated by DesX. In contrast, DesX was not involved in the regulation of ligM and desB The ferulate catabolism genes (ferBA), under the control of a MarR-type transcriptional regulator, FerC, are located upstream of desA RT-PCR analyses suggested that the ferB-ferA-SLG_25010-desA gene cluster consists of the ferBA operon and the SLG_25010-desA operon. Promoter assays revealed that a syringate- and vanillate-inducible promoter is located upstream of SLG_25010. Purified DesX bound to this promoter region, which overlaps an 18-bp inverted-repeat sequence that appears to be essential for the DNA binding of DesX. Syringate and vanillate inhibited the DNA binding of DesX, indicating that the compounds are effector molecules of DesX.IMPORTANCE Syringate is a major degradation product in the microbial and chemical degradation of syringyl lignin. Along with other low-molecular-weight aromatic compounds, syringate is produced by chemical lignin depolymerization. Converting this mixture into value-added chemicals using bacterial metabolism (i.e., biological funneling) is a promising option for lignin valorization. To construct an efficient microbial lignin conversion system, it is necessary to identify and characterize the genes involved in the uptake and catabolism of lignin-derived aromatic compounds and to elucidate their transcriptional regulation. In this study, we found that the transcription of desA, encoding syringate O-demethylase in SYK-6, is regulated by an IclR-type transcriptional regulator, DesX. The findings of this study, combined with our previous results on desR (encoding a MarR transcriptional regulator that controls the transcription of ligM and desB), provide an overall picture of the transcriptional-regulatory systems for syringate and vanillate catabolism in SYK-6.
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Schwanemann T, Otto M, Wierckx N, Wynands B. Pseudomonasas Versatile Aromatics Cell Factory. Biotechnol J 2020; 15:e1900569. [DOI: 10.1002/biot.201900569] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/08/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Tobias Schwanemann
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology Forschungszentrum Jülich, GmbH 52425 Jülich Germany
| | - Maike Otto
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology Forschungszentrum Jülich, GmbH 52425 Jülich Germany
| | - Nick Wierckx
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology Forschungszentrum Jülich, GmbH 52425 Jülich Germany
| | - Benedikt Wynands
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology Forschungszentrum Jülich, GmbH 52425 Jülich Germany
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Sheng M, Liu B, Xu J, Peng Q, Zhang L, Chen K, He J. Cloning of a novel topramezone-resistant 4-hydroxyphenylpyruvate dioxygenase gene and improvement of its resistance through pressure acclimation. Enzyme Microb Technol 2020; 140:109642. [DOI: 10.1016/j.enzmictec.2020.109642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 07/07/2020] [Accepted: 08/04/2020] [Indexed: 10/23/2022]
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Mitra M, Nguyen KMAK, Box TW, Gilpin JS, Hamby SR, Berry TL, Duckett EH. Isolation and characterization of a novel bacterial strain from a Tris-Acetate-Phosphate agar medium plate of the green micro-alga Chlamydomonas reinhardtii that can utilize common environmental pollutants as a carbon source. F1000Res 2020; 9:656. [PMID: 32855811 PMCID: PMC7425125 DOI: 10.12688/f1000research.24680.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/19/2020] [Indexed: 12/28/2022] Open
Abstract
Background:Chlamydomonas reinhardtii, a green micro-alga can be grown at the lab heterotrophically or photo-heterotrophically in Tris-Phosphate-Acetate (TAP) medium which contains acetate as the sole carbon source. When grown in TAP medium,
Chlamydomonas can utilize the exogenous acetate in the medium for gluconeogenesis using the glyoxylate cycle, which is also present in many bacteria and higher plants. A novel bacterial strain, LMJ, was isolated from a contaminated TAP medium plate of
Chlamydomonas. We present our work on the isolation and physiological and biochemical characterizations of LMJ. Methods: Several microbiological tests were conducted to characterize LMJ, including its sensitivity to four antibiotics. We amplified and sequenced partially the 16S rRNA gene of LMJ. We tested if LMJ can utilize cyclic alkanes, aromatic hydrocarbons, poly-hydroxyalkanoates, and fresh and combusted car motor oil as the sole carbon source on Tris-Phosphate (TP) agar medium plates for growth. Results: LMJ is a gram-negative rod, oxidase-positive, mesophilic, non-enteric, pigmented, salt-sensitive bacterium. LMJ can ferment glucose, is starch hydrolysis-negative, and is very sensitive to penicillin and chloramphenicol. Preliminary spectrophotometric analyses indicate LMJ produces pyomelanin. NCBI-BLAST analyses of the partial 16S rRNA gene sequence of LMJ showed that it matched to that of an uncultured bacterium clone LIB091_C05_1243. The nearest genus relative of LMJ is an
Acidovorax sp. strain. LMJ was able to use alkane hydrocarbons, fresh and combusted car motor oil, poly-hydroxybutyrate, phenanthrene, naphthalene, benzoic acid and phenyl acetate as the sole carbon source for growth on TP-agar medium plates. Conclusions: LMJ has 99.14% sequence identity with the
Acidovorax sp. strain A16OP12 whose genome has not been sequenced yet. LMJ’s ability to use chemicals that are common environmental pollutants makes it a promising candidate for further investigation for its use in bioremediation and, provides us with an incentive to sequence its genome.
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Affiliation(s)
- Mautusi Mitra
- Department of Biology, University of West Georgia, Carrollton, Georgia, 30118, USA
| | - Kevin Manoap-Anh-Khoa Nguyen
- Department of Biology, University of West Georgia, Carrollton, Georgia, 30118, USA.,Department of Mechanical Engineering, Kennesaw State University, Marietta, Georgia, 30060, USA
| | - Taylor Wayland Box
- Department of Biology, University of West Georgia, Carrollton, Georgia, 30118, USA
| | - Jesse Scott Gilpin
- Department of Biology, University of West Georgia, Carrollton, Georgia, 30118, USA
| | - Seth Ryan Hamby
- Department of Biology, University of West Georgia, Carrollton, Georgia, 30118, USA
| | - Taylor Lynne Berry
- Carrollton High School, Carrollton, Georgia, 30117, USA.,Department of Chemistry and Biochemistry, University of North Georgia, Dahlonega, Georgia, 30597, USA
| | - Erin Harper Duckett
- Department of Biology, University of West Georgia, Carrollton, Georgia, 30118, USA
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Sun J, Lu LB, Liang TX, Yang LR, Wu JP. CRISPR-Assisted Multiplex Base Editing System in Pseudomonas putida KT2440. Front Bioeng Biotechnol 2020; 8:905. [PMID: 32850749 PMCID: PMC7413065 DOI: 10.3389/fbioe.2020.00905] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/14/2020] [Indexed: 12/25/2022] Open
Abstract
Pseudomonas putida (P. putida) KT2440 is a paradigmatic environmental-bacterium that possesses significant potential in synthetic biology, metabolic engineering and biodegradation applications. However, most genome editing methods of P. putida KT2440 depend on heterologous repair proteins and the provision of donor DNA templates, which is laborious and inefficient. In this report, an efficient cytosine base editing system was established by using cytidine deaminase (APOBEC1), enhanced specificity Cas9 nickase (eSpCas9ppD10A) and the uracil DNA glycosylase inhibitor (UGI). This constructed base editor converts C-G into T-A in the absence of DNA strands breaks and donor DNA templates. By introducing a premature stop codon in target spacers, we successfully applied this system for gene inactivation with an efficiency of 25–100% in various Pseudomonas species, including P. putida KT2440, P. aeruginosa PAO1, P. fluorescens Pf-5 and P. entomophila L48. We engineered an eSpCas9ppD10A-NG variant with a NG protospacer adjacent motif to expand base editing candidate sites. By modifying the APOBEC1 domain, we successfully narrowed the editable window to increase gene inactivation efficiency in cytidine-rich spacers. Additionally, multiplex base editing in double and triple loci was achieved with mutation efficiencies of 90–100% and 25–35%, respectively. Taken together, the establishment of a fast, convenient and universal base editing system will accelerate the pace of future research undertaken with P. putida KT2440 and other Pseudomonas species.
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Affiliation(s)
- Jun Sun
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Li-Bing Lu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Tian-Xin Liang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Li-Rong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Jian-Ping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
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Sun H, Yang J, Lin X, Li C, He Y, Cai Z, Zhang G, Song H. De Novo High-Titer Production of Delta-Tocotrienol in Recombinant Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:7710-7717. [PMID: 32580548 DOI: 10.1021/acs.jafc.0c00294] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Delta-tocotrienol as a vitamin E isomer has received much attention because of its diverse biomedical applications. Microbial biosynthesis of delta-tocotrienol is a promising strategy for its economic and environmental advantages. Here, we accomplished complete biosynthesis of delta-tocotrienol in Saccharomyces cerevisiae from glucose. We first constructed and incorporated a heterologous pathway into the genome of S. cerevisiae by incorporating the genes hpd (from Pseudomonas putida KT2440), hpt (from Synechocystis sp. PCC 6803), and vte1 (from Arabidopsis thaliana) for the biosynthesis of delta-tocotrienol. We further enhanced the biosynthesis of the precursor geranylgeranyl diphosphate by overexpressing the thmg1 and ggppssa (from Sulfolobus acidocaldarius) genes, leading to a production titer of delta-tocotrienol of 1.39 ± 0.01 mg/L. Finally, we optimized the fermentation medium using the response surface methodology, enabling a high-titer production of delta-tocotrienol (3.56 ± 0.25 mg/L), ∼2.6-fold of that of the initial culture medium. Fed-batch fermentation in a 2 L fermenter was further used to enhance the production titer of delta-tocotrienol (4.10 ± 0.10 mg/L). To the best of our knowledge, this is the first report on the de novo biosynthesis of delta-tocotrienol in S. cerevisiae, and the highest titer obtained for microbial production of delta-tocotrienol.
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Affiliation(s)
- Hong Sun
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Jingli Yang
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Xue Lin
- College of Food Science and Technology, Hainan University, Haikou 570228, P. R. China
| | - Congfa Li
- College of Food Science and Technology, Hainan University, Haikou 570228, P. R. China
| | - Yongjin He
- Chifeng Pharmaceutical Company Limited, Chifeng, Inner Mongolia 024000, P. R. China
| | - Zhigang Cai
- Chifeng Pharmaceutical Company Limited, Chifeng, Inner Mongolia 024000, P. R. China
| | - Guoyin Zhang
- Chifeng Pharmaceutical Company Limited, Chifeng, Inner Mongolia 024000, P. R. China
| | - Hao Song
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
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Evaluation of chromosomal insertion loci in the Pseudomonas putida KT2440 genome for predictable biosystems design. Metab Eng Commun 2020; 11:e00139. [PMID: 32775199 PMCID: PMC7398981 DOI: 10.1016/j.mec.2020.e00139] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/02/2020] [Accepted: 07/15/2020] [Indexed: 01/27/2023] Open
Abstract
The development of Pseudomonas strains for industrial production of fuels and chemicals will require the integration of heterologous genes and pathways into the chromosome. Finding the most appropriate integration site to maximize strain performance is an essential part of the strain design process. We characterized seven chromosomal loci in Pseudomonas putida KT2440 for integration of a fluorescent protein expression construct. Insertion in five of the loci did not affect growth rate, but fluorescence varied by up to 27-fold. Three sites displaying a diversity of phenotypes with the fluorescent reporter were also chosen for the integration of a gene encoding a muconate importer. Depending on the integration locus, expression of the importer varied by approximately 3-fold and produced significant phenotypic differences. This work demonstrates the impact of the integration location on host viability, gene expression, and overall strain performance. Pseudomonas putida KT2440 chromosomal loci were characterized as potential insertion targets for heterologous genes. Integration location had a significant effect on heterologous protein expression and host phenotype. The identification of an appropriate chromosomal insertion location is essential to optimize genetic engineering design.
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García-Estrada C, Martín JF, Cueto L, Barreiro C. Omics Approaches Applied to Penicillium chrysogenum and Penicillin Production: Revealing the Secrets of Improved Productivity. Genes (Basel) 2020; 11:E712. [PMID: 32604893 PMCID: PMC7348727 DOI: 10.3390/genes11060712] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/07/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022] Open
Abstract
Penicillin biosynthesis by Penicillium chrysogenum is one of the best-characterized biological processes from the genetic, molecular, biochemical, and subcellular points of view. Several omics studies have been carried out in this filamentous fungus during the last decade, which have contributed to gathering a deep knowledge about the molecular mechanisms underlying improved productivity in industrial strains. The information provided by these studies is extremely useful for enhancing the production of penicillin or other bioactive secondary metabolites by means of Biotechnology or Synthetic Biology.
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Affiliation(s)
- Carlos García-Estrada
- INBIOTEC (Instituto de Biotecnología de León). Avda. Real 1—Parque Científico de León, 24006 León, Spain; (L.C.); (C.B.)
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - Juan F. Martín
- Área de Microbiología, Departamento de Biología Molecular, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain;
| | - Laura Cueto
- INBIOTEC (Instituto de Biotecnología de León). Avda. Real 1—Parque Científico de León, 24006 León, Spain; (L.C.); (C.B.)
| | - Carlos Barreiro
- INBIOTEC (Instituto de Biotecnología de León). Avda. Real 1—Parque Científico de León, 24006 León, Spain; (L.C.); (C.B.)
- Departamento de Biología Molecular, Universidad de León, Campus de Ponferrada, Avda. Astorga s/n, 24401 Ponferrada, Spain
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Granja-Travez RS, Persinoti GF, Squina FM, Bugg TDH. Functional genomic analysis of bacterial lignin degraders: diversity in mechanisms of lignin oxidation and metabolism. Appl Microbiol Biotechnol 2020; 104:3305-3320. [PMID: 32088760 DOI: 10.1007/s00253-019-10318-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/06/2019] [Accepted: 12/13/2019] [Indexed: 02/07/2023]
Abstract
Although several bacterial lignin-oxidising enzymes have been discovered in recent years, it is not yet clear whether different lignin-degrading bacteria use similar mechanisms for lignin oxidation and degradation of lignin fragments. Genome sequences of 13 bacterial lignin-oxidising bacteria, including new genome sequences for Microbacterium phyllosphaerae and Agrobacterium sp., were analysed for the presence of lignin-oxidising enzymes and aromatic degradation gene clusters that could be used to metabolise the products of lignin degradation. Ten bacterial genomes contain DyP-type peroxidases, and ten bacterial strains contain putative multi-copper oxidases (MCOs), both known to have activity for lignin oxidation. Only one strain lacks both MCOs and DyP-type peroxidase genes. Eleven bacterial genomes contain aromatic degradation gene clusters, of which ten contain the central β-ketoadipate pathway, with variable numbers and types of degradation clusters for other aromatic substrates. Hence, there appear to be diverse metabolic strategies used for lignin oxidation in bacteria, while the β-ketoadipate pathway appears to be the most common route for aromatic metabolism in lignin-degrading bacteria.
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Affiliation(s)
- Rommel Santiago Granja-Travez
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.,Facultad de Ciencias de la Ingeniería e Industrias, Universidad UTE, Quito, Ecuador
| | | | - Fabio M Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil
| | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
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48
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Liu B, Peng Q, Sheng M, Ni H, Xiao X, Tao Q, He Q, He J. Isolation and Characterization of a Topramezone-Resistant 4-Hydroxyphenylpyruvate Dioxygenase from Sphingobium sp. TPM-19. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:1022-1029. [PMID: 31884791 DOI: 10.1021/acs.jafc.9b06871] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Topramezone is a 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor. Due to its broad-spectrum, high efficiency, and low toxicity, topramezone is a candidate herbicide for the construction of genetically modified (GM) herbicide-resistant crops. In the present study, we screened a topramezone-resistant isolate Sphingobium sp. TPM-19 and cloned a topramezone-resistant HPPD gene (SphppD) from this isolate. SpHPPD shared the highest similarity (53%) with an HPPD from Vibrio vulnificus CMCP6. SpHPPD was synthesized in Escherichia coli BL21(DE3) and purified to homogeneity using Co2+-affinity chromatography. SpHPPD was found to be a monomer. The Km and kcat of SpHPPD for 4-hydroxyphenylpyruvate (4-HPP) were 82.8 μM and 15.0 s-1, respectively. SpHPPD showed high resistance to topramezone with half maximal inhibitory concentration (IC50) and Ki values of 5.2 and 2.5 μM, respectively. Additionally, SpHPPD also showed high resistance to isoxaflutole (DKN) (IC50: 8.7 μM; Ki: 6.0 μM) and mesotrione (IC50: 4.2 μM; Ki: 1.3 μM) and moderate resistance to tembotrione (IC50: 2.5 μM; Ki: 1.0 μM). The introduction of the SphppD gene into Arabidopsis thaliana enhanced obvious resistance against topramezone. In conclusion, this study provides a novel topramezone-resistant HPPD gene for the genetic engineering of GM herbicide-resistant crops.
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Affiliation(s)
- Bin Liu
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences , Nanjing Agricultural University , Nanjing 210095 , Jiangsu , P. R. China
| | - Qian Peng
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences , Nanjing Agricultural University , Nanjing 210095 , Jiangsu , P. R. China
| | - Mengyao Sheng
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences , Nanjing Agricultural University , Nanjing 210095 , Jiangsu , P. R. China
| | - Haiyan Ni
- College of Life Science , Jiangxi Normal University , Nanchang 330022 , Jiangxi , China
| | - Xiang Xiao
- DBN Biotech Center, Beijing DBN Technology Group Co., Ltd. , Beijing 100193 , P. R. China
| | - Qing Tao
- DBN Biotech Center, Beijing DBN Technology Group Co., Ltd. , Beijing 100193 , P. R. China
| | - Qin He
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences , Nanjing Agricultural University , Nanjing 210095 , Jiangsu , P. R. China
| | - Jian He
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences , Nanjing Agricultural University , Nanjing 210095 , Jiangsu , P. R. China
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49
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Pavan ME, López NI, Pettinari MJ. Melanin biosynthesis in bacteria, regulation and production perspectives. Appl Microbiol Biotechnol 2019; 104:1357-1370. [PMID: 31811318 DOI: 10.1007/s00253-019-10245-y] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/25/2019] [Accepted: 11/04/2019] [Indexed: 12/26/2022]
Abstract
The production of black pigments in bacteria was discovered more than a century ago and related to tyrosine metabolism. However, their diverse biological roles and the control of melanin synthesis in different bacteria have only recently been investigated. The broad distribution of these pigments suggests that they have an important role in a variety of organisms. Melanins protect microorganisms from many environmental stress conditions, ranging from ultraviolet radiation and toxic heavy metals to oxidative stress. Melanins can also affect bacterial interactions with other organisms and are important in pathogenesis and survival in many environments. Bacteria produce several types of melanin through dedicated pathways or as a result of enzymatic imbalances in altered metabolic routes. The control of the melanin synthesis in bacteria involves metabolic and transcriptional regulation, but many aspects remain still largely unknown. The diverse properties of melanins have spurred a large number of applications, and recent efforts have been done to produce the pigment at biotechnologically relevant scales.
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Affiliation(s)
- María Elisa Pavan
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Nancy I López
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina. .,IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - M Julia Pettinari
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina. .,IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
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50
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Hong H, Seo H, Park W, Kim KJ. Sequence, structure and function-based classification of the broadly conserved FAH superfamily reveals two distinct fumarylpyruvate hydrolase subfamilies. Environ Microbiol 2019; 22:270-285. [PMID: 31657110 DOI: 10.1111/1462-2920.14844] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/21/2019] [Accepted: 10/23/2019] [Indexed: 11/30/2022]
Abstract
Fumarylacetoacetate hydrolase (FAH) superfamily proteins are found ubiquitously in microbial pathways involved in the catabolism of aromatic substances. Although extensive bioinformatic data on these proteins have been acquired, confusion caused by problems with the annotation of these proteins hinders research into determining their physiological functions. Here we classify 606 FAH superfamily proteins using a maximum likelihood (ML) phylogenetic tree, comparative gene-neighbourhood patterns and in vitro enzyme assays. The FAH superfamily proteins used for the analyses are divided into five distinct subfamilies, and two of them, FPH-A and FPH-B, contain the majority of the proteins of undefined function. These subfamilies include clusters designated FPH-I and FPH-II, respectively, which include two distinct types of fumarylpyruvate hydrolase (FPH), an enzyme involved in the final step of the gentisate pathway. We determined the crystal structures of these FPH enzymes at 2.0 Å resolutions and investigate the substrate binding mode by which these types of enzymes can accommodate fumarylpyruvate as a substrate. Consequentially, we identify the molecular signatures of the two types of FPH enzymes among the broadly conserved FAH superfamily proteins. Our studies allowed us to predict the relationship of unknown FAH superfamily proteins using their sequence information.
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Affiliation(s)
- Hwaseok Hong
- Structural and Molecular Biology Laboratory, School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 702701, Republic of Korea.,KNU Institute for Microorganisms, Kyungpook National University, Daegu, 702701, Republic of Korea
| | - Hogyun Seo
- Structural and Molecular Biology Laboratory, School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 702701, Republic of Korea.,KNU Institute for Microorganisms, Kyungpook National University, Daegu, 702701, Republic of Korea
| | - Woojin Park
- Structural and Molecular Biology Laboratory, School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 702701, Republic of Korea.,KNU Institute for Microorganisms, Kyungpook National University, Daegu, 702701, Republic of Korea
| | - Kyung-Jin Kim
- Structural and Molecular Biology Laboratory, School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 702701, Republic of Korea.,KNU Institute for Microorganisms, Kyungpook National University, Daegu, 702701, Republic of Korea
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