1
|
Rogowska-van der Molen MA, Berasategui-Lopez A, Coolen S, Jansen RS, Welte CU. Microbial degradation of plant toxins. Environ Microbiol 2023; 25:2988-3010. [PMID: 37718389 DOI: 10.1111/1462-2920.16507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/05/2023] [Indexed: 09/19/2023]
Abstract
Plants produce a variety of secondary metabolites in response to biotic and abiotic stresses. Although they have many functions, a subclass of toxic secondary metabolites mainly serve plants as deterring agents against herbivores, insects, or pathogens. Microorganisms present in divergent ecological niches, such as soil, water, or insect and rumen gut systems have been found capable of detoxifying these metabolites. As a result of detoxification, microbes gain growth nutrients and benefit their herbivory host via detoxifying symbiosis. Here, we review current knowledge on microbial degradation of toxic alkaloids, glucosinolates, terpenes, and polyphenols with an emphasis on the genes and enzymes involved in breakdown pathways. We highlight that the insect-associated microbes might find application in biotechnology and become targets for an alternative microbial pest control strategy.
Collapse
Affiliation(s)
- Magda A Rogowska-van der Molen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Aileen Berasategui-Lopez
- Department of Microbiology and Biotechnology, University of Tübingen, Tübingen, Baden-Württemberg, Germany
- Amsterdam Institute for Life and Environment, Section Ecology and Evolution, Vrije Universiteit, Amsterdam, The Netherlands
| | - Silvia Coolen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Robert S Jansen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Cornelia U Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| |
Collapse
|
2
|
Ivanova KM, Grishko VV, Ivshina IB. Highly Efficient Biodegradation of Ecotoxic Dehydroabietic Acid by Resting Cells of Rhodococcus rhodochrous IEGM 107. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722100599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
3
|
Msomi NN, Padayachee T, Nzuza N, Syed PR, Kryś JD, Chen W, Gront D, Nelson DR, Syed K. In Silico Analysis of P450s and Their Role in Secondary Metabolism in the Bacterial Class Gammaproteobacteria. Molecules 2021; 26:1538. [PMID: 33799696 PMCID: PMC7998510 DOI: 10.3390/molecules26061538] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/03/2021] [Accepted: 03/08/2021] [Indexed: 12/21/2022] Open
Abstract
The impact of lifestyle on shaping the genome content of an organism is a well-known phenomenon and cytochrome P450 enzymes (CYPs/P450s), heme-thiolate proteins that are ubiquitously present in organisms, are no exception. Recent studies focusing on a few bacterial species such as Streptomyces, Mycobacterium, Cyanobacteria and Firmicutes revealed that the impact of lifestyle affected the P450 repertoire in these species. However, this phenomenon needs to be understood in other bacterial species. We therefore performed genome data mining, annotation, phylogenetic analysis of P450s and their role in secondary metabolism in the bacterial class Gammaproteobacteria. Genome-wide data mining for P450s in 1261 Gammaproteobacterial species belonging to 161 genera revealed that only 169 species belonging to 41 genera have P450s. A total of 277 P450s found in 169 species grouped into 84 P450 families and 105 P450 subfamilies, where 38 new P450 families were found. Only 18% of P450s were found to be involved in secondary metabolism in Gammaproteobacterial species, as observed in Firmicutes as well. The pathogenic or commensal lifestyle of Gammaproteobacterial species influences them to such an extent that they have the lowest number of P450s compared to other bacterial species, indicating the impact of lifestyle on shaping the P450 repertoire. This study is the first report on comprehensive analysis of P450s in Gammaproteobacteria.
Collapse
Affiliation(s)
- Ntombizethu Nokuphiwa Msomi
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.N.M.); (T.P.); (N.N.)
| | - Tiara Padayachee
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.N.M.); (T.P.); (N.N.)
| | - Nomfundo Nzuza
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.N.M.); (T.P.); (N.N.)
| | - Puleng Rosinah Syed
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa;
| | - Justyna Dorota Kryś
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
| | - Wanping Chen
- Department of Molecular Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany;
| | - Dominik Gront
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.N.M.); (T.P.); (N.N.)
| |
Collapse
|
4
|
Luchnikova NA, Ivanova KM, Tarasova EV, Grishko VV, Ivshina IB. Microbial Conversion of Toxic Resin Acids. Molecules 2019; 24:molecules24224121. [PMID: 31739575 PMCID: PMC6891630 DOI: 10.3390/molecules24224121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/07/2019] [Accepted: 11/13/2019] [Indexed: 12/03/2022] Open
Abstract
Organic wood extractives—resin acids—significantly contribute to an increase in the toxicity level of pulp and paper industry effluents. Entering open ecosystems, resin acids accumulate and have toxic effects on living organisms, which can lead to the ecological imbalance. Among the most effective methods applied to neutralize these ecotoxicants is enzymatic detoxification using microorganisms. A fundamental interest in the in-depth study of the oxidation mechanisms of resin acids and the search for their key biodegraders is increasing every year. Compounds from this group receive attention because of the need to develop highly effective procedures of resin acid removal from pulp and paper effluents and also the possibility to obtain their derivatives with pronounced pharmacological effects. Over the past fifteen years, this is the first report analyzing the data on distribution, the impacts on living organisms, and the microbial transformation of resin acids. Using the example of dehydroabietic acid—the dominant compound of resin acids in effluents—the review discusses the features of interactions between microorganisms and this pollutant and also highlights the pathways and main products of resin acid bioconversion.
Collapse
Affiliation(s)
- Natalia A. Luchnikova
- Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, 614081 Perm, Russia; (N.A.L.); (K.M.I.); (E.V.T.)
- Department of Microbiology and Immunology, Perm State National Research University, 614990 Perm, Russia
| | - Kseniya M. Ivanova
- Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, 614081 Perm, Russia; (N.A.L.); (K.M.I.); (E.V.T.)
- Department of Microbiology and Immunology, Perm State National Research University, 614990 Perm, Russia
| | - Ekaterina V. Tarasova
- Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, 614081 Perm, Russia; (N.A.L.); (K.M.I.); (E.V.T.)
- Department of Microbiology and Immunology, Perm State National Research University, 614990 Perm, Russia
| | - Victoria V. Grishko
- Institute of Technical Chemistry, Ural Branch of the Russian Academy of Sciences, 614013 Perm, Russia;
| | - Irina B. Ivshina
- Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, 614081 Perm, Russia; (N.A.L.); (K.M.I.); (E.V.T.)
- Department of Microbiology and Immunology, Perm State National Research University, 614990 Perm, Russia
- Correspondence: ; Tel.: +7-342-2808114
| |
Collapse
|
5
|
Greule A, Stok JE, De Voss JJ, Cryle MJ. Unrivalled diversity: the many roles and reactions of bacterial cytochromes P450 in secondary metabolism. Nat Prod Rep 2019; 35:757-791. [PMID: 29667657 DOI: 10.1039/c7np00063d] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covering: 2000 up to 2018 The cytochromes P450 (P450s) are a superfamily of heme-containing monooxygenases that perform diverse catalytic roles in many species, including bacteria. The P450 superfamily is widely known for the hydroxylation of unactivated C-H bonds, but the diversity of reactions that P450s can perform vastly exceeds this undoubtedly impressive chemical transformation. Within bacteria, P450s play important roles in many biosynthetic and biodegradative processes that span a wide range of secondary metabolite pathways and present diverse chemical transformations. In this review, we aim to provide an overview of the range of chemical transformations that P450 enzymes can catalyse within bacterial secondary metabolism, with the intention to provide an important resource to aid in understanding of the potential roles of P450 enzymes within newly identified bacterial biosynthetic pathways.
Collapse
Affiliation(s)
- Anja Greule
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia. and EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Jeanette E Stok
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia. and EMBL Australia, Monash University, Clayton, Victoria 3800, Australia and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.
| |
Collapse
|
6
|
Berasategui A, Salem H, Paetz C, Santoro M, Gershenzon J, Kaltenpoth M, Schmidt A. Gut microbiota of the pine weevil degrades conifer diterpenes and increases insect fitness. Mol Ecol 2017; 26:4099-4110. [DOI: 10.1111/mec.14186] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/02/2017] [Accepted: 05/05/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Aileen Berasategui
- Biochemistry Department; Max Planck Institute for Chemical Ecology; Jena Germany
- Insect Symbiosis Research Group; Max Planck Institute for Chemical Ecology; Jena Germany
| | - Hassan Salem
- Insect Symbiosis Research Group; Max Planck Institute for Chemical Ecology; Jena Germany
- Department of Biology; Emory University; Atlanta GA USA
| | - Christian Paetz
- NMR Department; Max Planck Institute for Chemical Ecology; Jena Germany
| | - Maricel Santoro
- Biochemistry Department; Max Planck Institute for Chemical Ecology; Jena Germany
- Departamento de Biología Molecular; Universidad Nacional de Río Cuarto; Río Cuarto Argentina
| | - Jonathan Gershenzon
- Biochemistry Department; Max Planck Institute for Chemical Ecology; Jena Germany
| | - Martin Kaltenpoth
- Department for Evolutionary Ecology; Johannes Gutenberg University Mainz; Mainz Germany
| | - Axel Schmidt
- Biochemistry Department; Max Planck Institute for Chemical Ecology; Jena Germany
| |
Collapse
|
7
|
Martín-Moldes Z, Zamarro MT, del Cerro C, Valencia A, Gómez MJ, Arcas A, Udaondo Z, García JL, Nogales J, Carmona M, Díaz E. Whole-genome analysis of Azoarcus sp. strain CIB provides genetic insights to its different lifestyles and predicts novel metabolic features. Syst Appl Microbiol 2015; 38:462-71. [DOI: 10.1016/j.syapm.2015.07.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 06/29/2015] [Accepted: 07/06/2015] [Indexed: 11/25/2022]
|
8
|
Janocha S, Schmitz D, Bernhardt R. Terpene hydroxylation with microbial cytochrome P450 monooxygenases. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 148:215-50. [PMID: 25682070 DOI: 10.1007/10_2014_296] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Terpenoids comprise a highly diverse group of natural products. In addition to their basic carbon skeleton, they differ from one another in their functional groups. Functional groups attached to the carbon skeleton are the basis of the terpenoids' diverse properties. Further modifications of terpene olefins include the introduction of acyl-, aryl-, or sugar moieties and usually start with oxidations catalyzed by cytochrome P450 monooxygenases (P450s, CYPs). P450s are ubiquitously distributed throughout nature, involved in essential biological pathways such as terpenoid biosynthesis as well as the tailoring of terpenoids and other natural products. Their ability to introduce oxygen into nonactivated C-H bonds is unique and makes P450s very attractive for applications in biotechnology. Especially in the field of terpene oxidation, biotransformation methods emerge as an attractive alternative to classical chemical synthesis. For this reason, microbial P450s depict a highly interesting target for protein engineering approaches in order to increase selectivity and activity, respectively. Microbial P450s have been described to convert industrial and pharmaceutically interesting terpenoids such as ionones, limone, valencene, resin acids, and triterpenes (including steroids) as well as vitamin D3. Highly selective and active mutants have been evolved by applying classical site-directed mutagenesis as well as directed evolution of proteins. As P450s usually depend on electron transfer proteins, mutagenesis has also been applied to improve the interactions between P450s and their respective redox partners. This chapter provides an overview of terpenoid hydroxylation reactions catalyzed by bacterial P450s and highlights the achievements made by protein engineering to establish productive hydroxylation processes.
Collapse
Affiliation(s)
- Simon Janocha
- Department of Biochemistry, Saarland University, Campus B2 2, 66123, Saarbruecken, Germany
| | | | | |
Collapse
|
9
|
Grishko VV, Nogovitsina YM, Ivshina IB. Bacterial transformation of terpenoids. RUSSIAN CHEMICAL REVIEWS 2014. [DOI: 10.1070/rc2014v083n04abeh004396] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
10
|
Design and characterization of an efficient CYP105A1-based whole-cell biocatalyst for the conversion of resin acid diterpenoids in permeabilized Escherichia coli. Appl Microbiol Biotechnol 2013; 97:7639-49. [PMID: 23793341 DOI: 10.1007/s00253-013-5008-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 05/02/2013] [Accepted: 05/19/2013] [Indexed: 10/26/2022]
Abstract
Cytochrome P450 enzymes exhibit a tremendous potential for biotechnological applications due to their ability to introduce oxygen into non-activated carbon atoms. Their catalytic diversity is complemented by a broad substrate range covering many natural compounds. Especially the functionalization of terpenoids by P450s becomes increasingly interesting due to the diverse biological effects of these compounds. The bacterial CYP105A1 from Streptomyces griseolus was recently identified to carry out a one-step hydroxylation of several abietane-type resin acids. In this work, a whole-cell system for CYP105A1 with its heterologous electron transfer proteins Arh1 and Etp1(fd) from Schizosaccharomyces pombe was designed in Escherichia coli JM109 cells. Additionally, an enzyme-coupled cofactor regeneration system was integrated by co-expression of alcohol dehydrogenase from Lactobacillus brevis. In order to overcome mass transfer limitations of substrate into the cell, different agents were tested towards their permeabilizing activity on the E. coli membrane. The peptide antibiotic polymyxin B proved to be the most effective permeabilizer. After optimising the expression and conversion conditions, the cells were able to completely convert 200 μM of abietic acid into 15-hydroxyabietic acid within 2 h, exhibiting an initial conversion rate of 125 μM/h. These results demonstrate the high potential of this whole-cell system for the synthesis of functionalized resin acid diterpenoids.
Collapse
|
11
|
Suárez-Moreno ZR, Caballero-Mellado J, Coutinho BG, Mendonça-Previato L, James EK, Venturi V. Common features of environmental and potentially beneficial plant-associated Burkholderia. MICROBIAL ECOLOGY 2012; 63:249-266. [PMID: 21850446 DOI: 10.1007/s00248-011-9929-1] [Citation(s) in RCA: 212] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 08/01/2011] [Indexed: 05/31/2023]
Abstract
The genus Burkholderia comprises more than 60 species isolated from a wide range of niches. Although they have been shown to be diverse and ubiquitously distributed, most studies have thus far focused on the pathogenic species due to their clinical importance. However, the increasing number of recently described Burkholderia species associated with plants or with the environment has highlighted the division of the genus into two main clusters, as suggested by phylogenetical analyses. The first cluster includes human, animal, and plant pathogens, such as Burkholderia glumae, Burkholderia pseudomallei, and Burkholderia mallei, as well as the 17 defined species of the Burkholderia cepacia complex, while the other, more recently established cluster comprises more than 30 non-pathogenic species, which in most cases have been found to be associated with plants, and thus might be considered to be potentially beneficial. Several species from the latter group share characteristics that are of use when associating with plants, such as a quorum sensing system, the presence of nitrogen fixation and/or nodulation genes, and the ability to degrade aromatic compounds. This review examines the commonalities in this growing subgroup of Burkholderia species and discusses their prospective biotechnological applications.
Collapse
Affiliation(s)
- Zulma Rocío Suárez-Moreno
- Bacteriology Group, International Centre for Genetic Engineering & Biotechnology, Padriciano 99, 34149 Trieste, Italy
| | | | | | | | | | | |
Collapse
|