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Almhjell PJ, Johnston KE, Porter NJ, Kennemur JL, Bhethanabotla VC, Ducharme J, Arnold FH. The β-subunit of tryptophan synthase is a latent tyrosine synthase. Nat Chem Biol 2024:10.1038/s41589-024-01619-z. [PMID: 38744987 DOI: 10.1038/s41589-024-01619-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 04/04/2024] [Indexed: 05/16/2024]
Abstract
Aromatic amino acids and their derivatives are diverse primary and secondary metabolites with critical roles in protein synthesis, cell structure and integrity, defense and signaling. All de novo aromatic amino acid production relies on a set of ancient and highly conserved chemistries. Here we introduce a new enzymatic transformation for L-tyrosine synthesis by demonstrating that the β-subunit of tryptophan synthase-which natively couples indole and L-serine to form L-tryptophan-can act as a latent 'tyrosine synthase'. A single substitution of a near-universally conserved catalytic residue unlocks activity toward simple phenol analogs and yields exclusive para carbon-carbon bond formation to furnish L-tyrosines. Structural and mechanistic studies show how a new active-site water molecule orients phenols for a nonnative mechanism of alkylation, with additional directed evolution resulting in a net >30,000-fold rate enhancement. This new biocatalyst can be used to efficiently prepare valuable L-tyrosine analogs at gram scales and provides the missing chemistry for a conceptually different pathway to L-tyrosine.
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Affiliation(s)
- Patrick J Almhjell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Kadina E Johnston
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Merck & Co., Inc, South San Francisco, CA, USA
| | - Nicholas J Porter
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Codexis, Inc., Redwood City, CA, USA
| | - Jennifer L Kennemur
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Vignesh C Bhethanabotla
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Julie Ducharme
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Quebec Government Office, Los Angeles, CA, USA
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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2
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Iummato MM, Sabatini SE, Rocchetta I, Yusseppone MS, Del Carmen Ríos de Molina M, Juárez ÁB. Oxidative stress in the bivalve Diplodon chilensis under direct and dietary glyphosate-based formulation exposure. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:23610-23622. [PMID: 38418793 DOI: 10.1007/s11356-024-32639-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
The aim of this study was to evaluate and compare the effects on biochemical parameters and organosomatic indices in the freshwater bivalve Diplodon chilensis exposed to a glyphosate-based formulation under direct and dietary exposures (4 mg a.p./L). After 1, 7, and 14 days of exposure, reduced glutathione (GSH) and thiobarbituric acid reactive substances (TBARS) levels and the activities of glutathione-S- transferase (GST), superoxide dismutase (SOD), and catalase (CAT) were evaluated in the gills and digestive gland. The hepatosomatic (HSI) and branchiosomatic (BSI) indices were also analyzed. Direct and dietary glyphosate-based formulation exposure altered the redox homeostasis in the gills and digestive gland throughout the experimental time, inducing the detoxification response (GST), the antioxidant defenses (SOD, CAT, GSH), and causing lipid peroxidation. After 14 days of exposure, the HSI and BSI increased significantly (43% and 157%, respectively) only in the bivalves under direct exposure. Greater changes in the biochemical parameters were induced by the dietary exposure than by the direct exposure. Furthermore, the gills presented an earlier response compared to the digestive gland. These results suggested that direct and dietary exposure to a glyphosate-based formulation induced oxidative stress in the gills and digestive glands of D. chilensis. Thus, the presence of glyphosate-based formulations in aquatic ecosystems could represent a risk for filter-feeding organisms like bivalves.
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Affiliation(s)
- María Mercedes Iummato
- Faculty of Exact and Natural Sciences, Department of Biological Chemistry, University of Buenos Aires, Buenos Aires, Argentina
- Aquatic Ecotoxicology Laboratory, Research Institute in the Environment and Biodiversity (INIBIOMA), CONICET-National University of Comahue, Neuquén, Argentina
| | - Sebastián Eduardo Sabatini
- Institute of Biological Chemistry of the Faculty of Exact and Natural Sciences (IQUIBICEN), CONICET, University of Buenos Aires, Buenos Aires, Argentina
- Faculty of Exact and Natural Sciences, Department of Biodiversity and Experimental Biology, University of Buenos Aires, Buenos Aires, Argentina
| | - Iara Rocchetta
- Faculty of Exact and Natural Sciences, Department of Biological Chemistry, University of Buenos Aires, Buenos Aires, Argentina
- Aquatic Ecotoxicology Laboratory, Research Institute in the Environment and Biodiversity (INIBIOMA), CONICET-National University of Comahue, Neuquén, Argentina
| | - María Soledad Yusseppone
- Faculty of Exact and Natural Sciences, Department of Biological Chemistry, University of Buenos Aires, Buenos Aires, Argentina
- Ecology Laboratory, Institute of Marine and Coastal Research (IIMYC), CONICET-National University of Mar del Plata, Mar del Plata, Argentina
| | - María Del Carmen Ríos de Molina
- Faculty of Exact and Natural Sciences, Department of Biological Chemistry, University of Buenos Aires, Buenos Aires, Argentina
- Institute of Biological Chemistry of the Faculty of Exact and Natural Sciences (IQUIBICEN), CONICET, University of Buenos Aires, Buenos Aires, Argentina
| | - Ángela Beatriz Juárez
- Faculty of Exact and Natural Sciences, Department of Biological Chemistry, University of Buenos Aires, Buenos Aires, Argentina.
- Faculty of Exact and Natural Sciences, Department of Biodiversity and Experimental Biology, University of Buenos Aires, Buenos Aires, Argentina.
- Institute of Biodiversity and Applied and Experimental Biology (IBBEA UBA), CONICET, University of Buenos Aires, Intendente Güiraldes 2160, C1428EGA, Buenos Aires, Argentina.
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3
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Rassbach J, Hilsberg N, Haensch VG, Dörner S, Gressler J, Sonnabend R, Semm C, Voigt K, Hertweck C, Gressler M. Non-canonical two-step biosynthesis of anti-oomycete indole alkaloids in Kickxellales. Fungal Biol Biotechnol 2023; 10:19. [PMID: 37670394 PMCID: PMC10478498 DOI: 10.1186/s40694-023-00166-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/06/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND Fungi are prolific producers of bioactive small molecules of pharmaceutical or agricultural interest. The secondary metabolism of higher fungi (Dikarya) has been well-investigated which led to > 39,000 described compounds. However, natural product researchers scarcely drew attention to early-diverging fungi (Mucoro- and Zoopagomycota) as they are considered to rarely produce secondary metabolites. Indeed, only 15 compounds have as yet been isolated from the entire phylum of the Zoopagomycota. RESULTS Here, we showcase eight species of the order Kickxellales (phylum Zoopagomycota) as potent producers of the indole-3-acetic acid (IAA)-derived compounds lindolins A and B. The compounds are produced both under laboratory conditions and in the natural soil habitat suggesting a specialized ecological function. Indeed, lindolin A is a selective agent against plant-pathogenic oomycetes such as Phytophthora sp. Lindolin biosynthesis was reconstituted in vitro and relies on the activity of two enzymes of dissimilar evolutionary origin: Whilst the IAA-CoA ligase LinA has evolved from fungal 4-coumaryl-CoA synthetases, the subsequently acting IAA-CoA:anthranilate N-indole-3-acetyltransferase LinB is a unique enzyme across all kingdoms of life. CONCLUSIONS This is the first report on bioactive secondary metabolites in the subphylum Kickxellomycotina and the first evidence for a non-clustered, two-step biosynthetic route of secondary metabolites in early-diverging fungi. Thus, the generally accepted "gene cluster hypothesis" for natural products needs to be reconsidered for early diverging fungi.
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Affiliation(s)
- Johannes Rassbach
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Nathalie Hilsberg
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Veit G Haensch
- Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Adolf-Reichwein-Strasse 23, 07745, Jena, Germany
| | - Sebastian Dörner
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Julia Gressler
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Robin Sonnabend
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Caroline Semm
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
- Jena Microbial Resource Collection (JMRC), Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Adolf-Reichwein-Strasse 23, 07745, Jena, Germany
| | - Kerstin Voigt
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
- Jena Microbial Resource Collection (JMRC), Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Adolf-Reichwein-Strasse 23, 07745, Jena, Germany
| | - Christian Hertweck
- Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Adolf-Reichwein-Strasse 23, 07745, Jena, Germany
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
| | - Markus Gressler
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany.
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany.
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4
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Smith-Roe SL, Swartz CD, Rashid A, Christy NC, Sly JE, Chang X, Sipes NS, Shockley KR, Harris SF, McBride SJ, Larson GJ, Collins BJ, Mutlu E, Witt KL. Evaluation of the herbicide glyphosate, (aminomethyl)phosphonic acid, and glyphosate-based formulations for genotoxic activity using in vitro assays. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2023; 64:202-233. [PMID: 36880770 PMCID: PMC10266336 DOI: 10.1002/em.22534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/03/2023] [Accepted: 02/14/2023] [Indexed: 05/03/2023]
Abstract
Glyphosate, the most heavily used herbicide world-wide, is applied to plants in complex formulations that promote absorption. The National Toxicology Program reported in 1992 that glyphosate, administered to rats and mice at doses up to 50,000 ppm in feed for 13 weeks, showed little evidence of toxicity, and no induction of micronuclei was observed in the mice in this study. Subsequently, mechanistic studies of glyphosate and glyphosate-based formulations (GBFs) that have focused on DNA damage and oxidative stress suggest that glyphosate may have genotoxic potential. However, few of these studies directly compared glyphosate to GBFs, or effects among GBFs. To address these data gaps, we tested glyphosate, glyphosate isopropylamine (IPA), and (aminomethyl)phosphonic acid (AMPA, a microbial metabolite of glyphosate), 9 high-use agricultural GBFs, 4 residential-use GBFs, and additional herbicides (metolachlor, mesotrione, and diquat dibromide) present in some of the GBFs in bacterial mutagenicity tests, and in human TK6 cells using a micronucleus assay and a multiplexed DNA damage assay. Our results showed no genotoxicity or notable cytotoxicity for glyphosate or AMPA at concentrations up to 10 mM, while all GBFs and herbicides other than glyphosate were cytotoxic, and some showed genotoxic activity. An in vitro to in vivo extrapolation of results for glyphosate suggests that it is of low toxicological concern for humans. In conclusion, these results demonstrate a lack of genotoxicity for glyphosate, consistent with observations in the NTP in vivo study, and suggest that toxicity associated with GBFs may be related to other components of these formulations.
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Affiliation(s)
- Stephanie L. Smith-Roe
- Division of Translational Toxicology, NIEHS, Research
Triangle Park, North Carolina, USA
| | - Carol D. Swartz
- Integrated Laboratory Systems, LLC†, Research Triangle Park, North Carolina,
USA
| | - Asma Rashid
- Integrated Laboratory Systems, LLC†, Research Triangle Park, North Carolina,
USA
| | - Nicholas C. Christy
- Integrated Laboratory Systems, LLC†, Research Triangle Park, North Carolina,
USA
| | - Jamie E. Sly
- Integrated Laboratory Systems, LLC†, Research Triangle Park, North Carolina,
USA
| | - Xiaoqing Chang
- Integrated Laboratory Systems, LLC†, Research Triangle Park, North Carolina,
USA
| | - Nisha S. Sipes
- Division of Translational Toxicology, NIEHS, Research
Triangle Park, North Carolina, USA
| | - Keith R. Shockley
- Biostatistics and Computational Biology Branch, NIEHS,
Research Triangle Park, North Carolina, USA
| | - Shawn F. Harris
- Social & Scientific Systems, Inc., Durham, North
Carolina, USA
| | | | - Gary J. Larson
- Social & Scientific Systems, Inc., Durham, North
Carolina, USA
| | - Bradley J. Collins
- Division of Translational Toxicology, NIEHS, Research
Triangle Park, North Carolina, USA
| | - Esra Mutlu
- Division of Translational Toxicology, NIEHS, Research
Triangle Park, North Carolina, USA
| | - Kristine L. Witt
- Division of Translational Toxicology, NIEHS, Research
Triangle Park, North Carolina, USA
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V. K P, Sinha S. A systems level approach to study metabolic networks in prokaryotes with the aromatic amino acid biosynthesis pathway. Front Genet 2023; 13:1084727. [PMID: 36726720 PMCID: PMC9885046 DOI: 10.3389/fgene.2022.1084727] [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: 10/30/2022] [Accepted: 12/30/2022] [Indexed: 01/18/2023] Open
Abstract
Metabolism of an organism underlies its phenotype, which depends on many factors, such as the genetic makeup, habitat, and stresses to which it is exposed. This is particularly important for the prokaryotes, which undergo significant vertical and horizontal gene transfers. In this study we have used the energy-intensive Aromatic Amino Acid (Tryptophan, Tyrosine and Phenylalanine, TTP) biosynthesis pathway, in a large number of prokaryotes, as a model system to query the different levels of organization of metabolism in the whole intracellular biochemical network, and to understand how perturbations, such as mutations, affects the metabolic flux through the pathway - in isolation and in the context of other pathways connected to it. Using an agglomerative approach involving complex network analysis and Flux Balance Analyses (FBA), of the Tryptophan, Tyrosine and Phenylalanine and other pathways connected to it, we identify several novel results. Using the reaction network analysis and Flux Balance Analyses of the Tryptophan, Tyrosine and Phenylalanine and the genome-scale reconstructed metabolic pathways, many common hubs between the connected networks and the whole genome network are identified. The results show that the connected pathway network can act as a proxy for the whole genome network in Prokaryotes. This systems level analysis also points towards designing functional smaller synthetic pathways based on the reaction network and Flux Balance Analyses analysis.
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Affiliation(s)
- Priya V. K
- National Institute of Technology Calicut, Kattangal, Kerala, India,*Correspondence: Priya V. K, ; Somdatta Sinha,
| | - Somdatta Sinha
- Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India,*Correspondence: Priya V. K, ; Somdatta Sinha,
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6
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Metabolic Engineering of Shikimic Acid Biosynthesis Pathway for the Production of Shikimic Acid and Its Branched Products in Microorganisms: Advances and Prospects. Molecules 2022; 27:molecules27154779. [PMID: 35897952 PMCID: PMC9332510 DOI: 10.3390/molecules27154779] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/10/2022] [Accepted: 07/12/2022] [Indexed: 02/06/2023] Open
Abstract
The shikimate pathway is a necessary pathway for the synthesis of aromatic compounds. The intermediate products of the shikimate pathway and its branching pathway have promising properties in many fields, especially in the pharmaceutical industry. Many important compounds, such as shikimic acid, quinic acid, chlorogenic acid, gallic acid, pyrogallol, catechol and so on, can be synthesized by the shikimate pathway. Among them, shikimic acid is the key raw material for the synthesis of GS4104 (Tamiflu®), an inhibitor of neuraminidase against avian influenza virus. Quininic acid is an important intermediate for synthesis of a variety of raw chemical materials and drugs. Gallic acid and catechol receive widespread attention as pharmaceutical intermediates. It is one of the hotspots to accumulate many kinds of target products by rationally modifying the shikimate pathway and its branches in recombinant strains by means of metabolic engineering. This review considers the effects of classical metabolic engineering methods, such as central carbon metabolism (CCM) pathway modification, key enzyme gene modification, blocking the downstream pathway on the shikimate pathway, as well as several expansion pathways and metabolic engineering strategies of the shikimate pathway, and expounds the synthetic biology in recent years in the application of the shikimate pathway and the future development direction.
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7
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Rethinking the Intrinsic Sensitivity of Fungi to Glyphosate. BIOTECH 2022; 11:biotech11030028. [PMID: 35892933 PMCID: PMC9394408 DOI: 10.3390/biotech11030028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/13/2022] [Accepted: 07/22/2022] [Indexed: 11/17/2022] Open
Abstract
The 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) is the central enzyme of the shikimate pathway to synthesize the three aromatic amino acids in fungi, plants, and prokaryotes. This enzyme is the target of the herbicide glyphosate. In most plants and prokaryotes, the EPSPS protein is constituted by a single domain family, the EPSP synthase (PF00275) domain, whereas in fungi, the protein is formed by a multi-domain structure from combinations of 22 EPSPS-associated domains. The most common multi-domain EPSPS structure in fungi involves five EPSPS-associated domains of the shikimate pathway. In this article, we analyze 390 EPSPS proteins of fungi to determine the extent of the EPSPS-associated domains. Based on the current classification of the EPSPS protein, most fungal species are intrinsically sensitive to glyphosate. However, complex domain architectures may have multiple responses to the herbicide. Further empirical studies are needed to determine the effect of glyphosate on fungi, taking into account the diversity of multi-domain architectures of the EPSPS. This research opens the door to novel biotechnological applications for microbial degradation of glyphosate.
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8
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Yokoyama R, Kleven B, Gupta A, Wang Y, Maeda HA. 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase as the gatekeeper of plant aromatic natural product biosynthesis. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102219. [PMID: 35550985 DOI: 10.1016/j.pbi.2022.102219] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/23/2022] [Accepted: 03/21/2022] [Indexed: 06/15/2023]
Abstract
The shikimate pathway connects the central carbon metabolism with the biosynthesis of aromatic amino acids-l-tyrosine, l-phenylalanine, and l-tryptophan-which play indispensable roles as precursors of numerous aromatic phytochemicals. Despite the importance of the shikimate pathway-derived products for both plant physiology and human society, the regulatory mechanism of the shikimate pathway remains elusive. This review summarizes the recent progress and current understanding on the plant 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHP synthase or DHS) enzymes that catalyze the committed reaction of the shikimate pathway. We particularly focus on how the DHS activity is regulated in plants in comparison to those of microbes and discuss potential roles of DHS as the critical gatekeeper for the production of plant aromatic compounds.
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Affiliation(s)
- Ryo Yokoyama
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53705, USA.
| | - Bailey Kleven
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Anika Gupta
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Yuer Wang
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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9
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Abstract
Tremendous chemical diversity is the hallmark of plants and is supported by highly complex biochemical machinery. Plant metabolic enzymes originated and were transferred from eukaryotic and prokaryotic ancestors and further diversified by the unprecedented rates of gene duplication and functionalization experienced in land plants. Unlike microbes, which have frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO2 and have experienced very few, if any, gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner and on existing networks under various evolutionary constraints. This review aims to take a broader view of plant metabolic evolution and lay a framework to further explore evolutionary mechanisms of the complex metabolic network. Understanding the underlying metabolic and genetic constraints is also an empirical prerequisite for rational engineering and redesigning of plant metabolic pathways.
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Affiliation(s)
- Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany;
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10
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Rainio MJ, Ruuskanen S, Helander M, Saikkonen K, Saloniemi I, Puigbò P. Adaptation of bacteria to glyphosate: a microevolutionary perspective of the enzyme 5-enolpyruvylshikimate-3-phosphate synthase. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:309-316. [PMID: 33530134 DOI: 10.1111/1758-2229.12931] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/20/2021] [Indexed: 06/12/2023]
Abstract
Glyphosate is the leading herbicide worldwide, but it also affects prokaryotes because it targets the central enzyme (5-enolpyruvylshikimate-3-phosphate, EPSP) of the shikimate pathway in the synthesis of the three essential aromatic amino acids in bacteria, fungi and plants. Our results reveal that bacteria may easily become resistant to glyphosate through changes in the 5-enolpyruvylshikimate-3-phosphate synthase active site. This indicates the importance of examining how glyphosate affects microbe-mediated ecosystem functions and human microbiomes.
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Affiliation(s)
- Miia J Rainio
- Department of Biology, University of Turku, Turku, Finland
| | - Suvi Ruuskanen
- Department of Biology, University of Turku, Turku, Finland
| | - Marjo Helander
- Department of Biology, University of Turku, Turku, Finland
| | | | - Irma Saloniemi
- Department of Biology, University of Turku, Turku, Finland
| | - Pere Puigbò
- Department of Biology, University of Turku, Turku, Finland
- Nutrition and Health Unit, Eurecat Technology Centre of Catalonia, Reus, Catalonia, Spain
- Department of Biochemistry and Biotechnology, Rovira i Virgili University, Tarragona, Catalonia, Spain
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11
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Yokoyama R, de Oliveira MVV, Kleven B, Maeda HA. The entry reaction of the plant shikimate pathway is subjected to highly complex metabolite-mediated regulation. THE PLANT CELL 2021; 33:671-696. [PMID: 33955484 PMCID: PMC8136874 DOI: 10.1093/plcell/koaa042] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 11/19/2020] [Indexed: 05/22/2023]
Abstract
The plant shikimate pathway directs bulk carbon flow toward biosynthesis of aromatic amino acids (AAAs, i.e. tyrosine, phenylalanine, and tryptophan) and numerous aromatic phytochemicals. The microbial shikimate pathway is feedback inhibited by AAAs at the first enzyme, 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DHS). However, AAAs generally do not inhibit DHS activities from plant extracts and how plants regulate the shikimate pathway remains elusive. Here, we characterized recombinant Arabidopsis thaliana DHSs (AthDHSs) and found that tyrosine and tryptophan inhibit AthDHS2, but not AthDHS1 or AthDHS3. Mixing AthDHS2 with AthDHS1 or 3 attenuated its inhibition. The AAA and phenylpropanoid pathway intermediates chorismate and caffeate, respectively, strongly inhibited all AthDHSs, while the arogenate intermediate counteracted the AthDHS1 or 3 inhibition by chorismate. AAAs inhibited DHS activity in young seedlings, where AthDHS2 is highly expressed, but not in mature leaves, where AthDHS1 is predominantly expressed. Arabidopsis dhs1 and dhs3 knockout mutants were hypersensitive to tyrosine and tryptophan, respectively, while dhs2 was resistant to tyrosine-mediated growth inhibition. dhs1 and dhs3 also had reduced anthocyanin accumulation under high light stress. These findings reveal the highly complex regulation of the entry reaction of the plant shikimate pathway and lay the foundation for efforts to control the production of AAAs and diverse aromatic natural products in plants.
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Affiliation(s)
- Ryo Yokoyama
- Department of Botany, University of Wisconsin–Madison, 430 Lincoln Dr. Madison, WI 53706, USA
| | - Marcos V V de Oliveira
- Department of Botany, University of Wisconsin–Madison, 430 Lincoln Dr. Madison, WI 53706, USA
| | - Bailey Kleven
- Department of Botany, University of Wisconsin–Madison, 430 Lincoln Dr. Madison, WI 53706, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin–Madison, 430 Lincoln Dr. Madison, WI 53706, USA
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12
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Leino L, Tall T, Helander M, Saloniemi I, Saikkonen K, Ruuskanen S, Puigbò P. Classification of the glyphosate target enzyme (5-enolpyruvylshikimate-3-phosphate synthase) for assessing sensitivity of organisms to the herbicide. JOURNAL OF HAZARDOUS MATERIALS 2021; 408:124556. [PMID: 33243645 DOI: 10.1016/j.jhazmat.2020.124556] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/01/2020] [Accepted: 11/10/2020] [Indexed: 06/11/2023]
Abstract
Glyphosate is the most common broad-spectrum herbicide. It targets the key enzyme of the shikimate pathway, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), which synthesizes three essential aromatic amino acids (phenylalanine, tyrosine and tryptophan) in plants. Because the shikimate pathway is also found in many prokaryotes and fungi, the widespread use of glyphosate may have unsuspected impacts on the diversity and composition of microbial communities, including the human gut microbiome. Here, we introduce the first bioinformatics method to assess the potential sensitivity of organisms to glyphosate based on the type of EPSPS enzyme. We have precomputed a dataset of EPSPS sequences from thousands of species that will be an invaluable resource to advancing the research field. This novel methodology can classify sequences from nearly 90% of eukaryotes and >80% of prokaryotes. A conservative estimate from our results shows that 54% of species in the core human gut microbiome are sensitive to glyphosate.
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Affiliation(s)
- Lyydia Leino
- Department of Biology, University of Turku, Turku, Finland
| | - Tuomas Tall
- Department of Biology, University of Turku, Turku, Finland
| | - Marjo Helander
- Department of Biology, University of Turku, Turku, Finland
| | - Irma Saloniemi
- Department of Biology, University of Turku, Turku, Finland
| | | | - Suvi Ruuskanen
- Department of Biology, University of Turku, Turku, Finland
| | - Pere Puigbò
- Department of Biology, University of Turku, Turku, Finland; Nutrition and Health Unit, Eurecat Technology Centre of Catalonia, Reus, Catalonia, Spain; Department of Biochemistry and Biotechnology, Rovira i Virgili University, Tarragona, Catalonia, Spain.
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13
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Microbiome reduction and endosymbiont gain from a switch in sea urchin life history. Proc Natl Acad Sci U S A 2021; 118:2022023118. [PMID: 33853946 DOI: 10.1073/pnas.2022023118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Animal gastrointestinal tracts harbor a microbiome that is integral to host function, yet species from diverse phyla have evolved a reduced digestive system or lost it completely. Whether such changes are associated with alterations in the diversity and/or abundance of the microbiome remains an untested hypothesis in evolutionary symbiosis. Here, using the life history transition from planktotrophy (feeding) to lecithotrophy (nonfeeding) in the sea urchin Heliocidaris, we demonstrate that the lack of a functional gut corresponds with a reduction in microbial community diversity and abundance as well as the association with a diet-specific microbiome. We also determine that the lecithotroph vertically transmits a Rickettsiales that may complement host nutrition through amino acid biosynthesis and influence host reproduction. Our results indicate that the evolutionary loss of a functional gut correlates with a reduction in the microbiome and the association with an endosymbiont. Symbiotic transitions can therefore accompany life history transitions in the evolution of developmental strategies.
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14
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Derelle R, Philippe H, Colbourne JK. Broccoli: Combining Phylogenetic and Network Analyses for Orthology Assignment. Mol Biol Evol 2021; 37:3389-3396. [PMID: 32602888 DOI: 10.1093/molbev/msaa159] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Orthology assignment is a key step of comparative genomic studies, for which many bioinformatic tools have been developed. However, all gene clustering pipelines are based on the analysis of protein distances, which are subject to many artifacts. In this article, we introduce Broccoli, a user-friendly pipeline designed to infer, with high precision, orthologous groups, and pairs of proteins using a phylogeny-based approach. Briefly, Broccoli performs ultrafast phylogenetic analyses on most proteins and builds a network of orthologous relationships. Orthologous groups are then identified from the network using a parameter-free machine learning algorithm. Broccoli is also able to detect chimeric proteins resulting from gene-fusion events and to assign these proteins to the corresponding orthologous groups. Tested on two benchmark data sets, Broccoli outperforms current orthology pipelines. In addition, Broccoli is scalable, with runtimes similar to those of recent distance-based pipelines. Given its high level of performance and efficiency, this new pipeline represents a suitable choice for comparative genomic studies. Broccoli is freely available at https://github.com/rderelle/Broccoli.
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Affiliation(s)
- Romain Derelle
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Hervé Philippe
- Station d'Ecologie Théorique et Expérimentale, UMR CNRS 5321, Moulis, France.,Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Montréal, QC, Canada
| | - John K Colbourne
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
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15
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Karki S, Moniruzzaman M, Aylward FO. Comparative Genomics and Environmental Distribution of Large dsDNA Viruses in the Family Asfarviridae. Front Microbiol 2021; 12:657471. [PMID: 33790885 PMCID: PMC8005611 DOI: 10.3389/fmicb.2021.657471] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 02/22/2021] [Indexed: 12/14/2022] Open
Abstract
The family Asfarviridae is a group of nucleo-cytoplasmic large DNA viruses (NCLDVs) of which African swine fever virus (ASFV) is well-characterized. Recently the discovery of several Asfarviridae members other than ASFV has suggested that this family represents a diverse and cosmopolitan group of viruses, but the genomics and distribution of this family have not been studied in detail. To this end we analyzed five complete genomes and 35 metagenome-assembled genomes (MAGs) of viruses from this family to shed light on their evolutionary relationships and environmental distribution. The Asfarvirus MAGs derive from diverse marine, freshwater, and terrestrial habitats, underscoring the broad environmental distribution of this family. We present phylogenetic analyses using conserved marker genes and whole-genome comparison of pairwise average amino acid identity (AAI) values, revealing a high level of genomic divergence across disparate Asfarviruses. Further, we found that Asfarviridae genomes encode genes with diverse predicted metabolic roles and detectable sequence homology to proteins in bacteria, archaea, and eukaryotes, highlighting the genomic chimerism that is a salient feature of NCLDV. Our read mapping from Tara oceans metagenomic data also revealed that three Asfarviridae MAGs were present in multiple marine samples, indicating that they are widespread in the ocean. In one of these MAGs we identified four marker genes with > 95% AAI to genes sequenced from a virus that infects the dinoflagellate Heterocapsa circularisquama (HcDNAV). This suggests a potential host for this MAG, which would thereby represent a reference genome of a dinoflagellate-infecting giant virus. Together, these results show that Asfarviridae are ubiquitous, comprise similar sequence divergence as other NCLDV families, and include several members that are widespread in the ocean and potentially infect ecologically important protists.
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Affiliation(s)
- Sangita Karki
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | | | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
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16
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Chaudhary K, Geeta R, Panjabi P. Origin and diversification of ECERIFERUM1 (CER1) and ECERIFERUM3 (CER3) genes in land plants and phylogenetic evidence that the ancestral CER1/3 gene resulted from the fusion of pre-existing domains. Mol Phylogenet Evol 2021; 159:107101. [PMID: 33592235 DOI: 10.1016/j.ympev.2021.107101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 01/24/2021] [Accepted: 02/01/2021] [Indexed: 12/28/2022]
Abstract
ECERIFERUM1 (CER1) and ECERIFERUM3 (CER3) are key genes in synthesis of alkanes, a major component of cuticular waxes in land plants. The genes share extensive similarity, including the N-terminal (ERG3/FAH) and C-terminal (WAX2) domains. This study, traces the origin, evolutionary history, phylogenetic relationships and variation in copy number of the two genes within and beyond the Viridiplantae (green plants). Protein homologs of both CER1 and CER3 were identified across most Embryophyta (land plants), a single homolog (CER1/3) in charophytes and prasinophytes, and none in the other green, red or brown algae. Ancestral state reconstructions in 100 sequenced Archaeplastida using presence/absence of CER1/3 family genes revealed that the CER1/3 gene probably originated in the common ancestor of Viridiplantae. Phylogenetic analysis of CER1 and CER3 protein sequences from 146 plant species strongly suggests that the two genes originated by duplication of CER1/3 in the ancestral embryophyte. The evolution of CER1 and CER3 genes involved differential divergence of the two domains. Outside Embryophyta, CER1/3 similar sequences identified in diatoms and a cryptophyte, were the closest relatives of the CER1/3 family proteins. Proteins harbouring WAX2-wxAR (WAX2 associated region) similar regions were identified in proteins of bacteria, Archaea, cryptophytes, dinoflagellates and Stramenopiles. The independent existence of both ERG3/FAH and WAX2-wxAR domains in diverse lineages strongly points to the origin of CER1/3 gene in green plants by the fusion of pre-existing domains.
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Affiliation(s)
- Komal Chaudhary
- Department of Botany, University of Delhi, Delhi 110007, India
| | - R Geeta
- Department of Botany, University of Delhi, Delhi 110007, India.
| | - Priya Panjabi
- Department of Botany, University of Delhi, Delhi 110007, India.
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17
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Schmitz J, Hüdig M, Meier D, Linka N, Maurino VG. The genome of Ricinus communis encodes a single glycolate oxidase with different functions in photosynthetic and heterotrophic organs. PLANTA 2020; 252:100. [PMID: 33170407 PMCID: PMC7655567 DOI: 10.1007/s00425-020-03504-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 10/23/2020] [Indexed: 06/11/2023]
Abstract
The biochemical characterization of glycolate oxidase in Ricinus communis hints to different physiological functions of the enzyme depending on the organ in which it is active. Enzymatic activities of the photorespiratory pathway are not restricted to green tissues but are present also in heterotrophic organs. High glycolate oxidase (GOX) activity was detected in the endosperm of Ricinus communis. Phylogenetic analysis of the Ricinus L-2-hydroxy acid oxidase (Rc(L)-2-HAOX) family indicated that Rc(L)-2-HAOX1 to Rc(L)-2-HAOX3 cluster with the group containing streptophyte long-chain 2-hydroxy acid oxidases, whereas Rc(L)-2-HAOX4 clusters with the group containing streptophyte GOX. Rc(L)-2-HAOX4 is the closest relative to the photorespiratory GOX genes of Arabidopsis. We obtained Rc(L)-2-HAOX4 as a recombinant protein and analyze its kinetic properties in comparison to the Arabidopsis photorespiratory GOX. We also analyzed the expression of all Rc(L)-2-HAOXs and conducted metabolite profiling of different Ricinus organs. Phylogenetic analysis indicates that Rc(L)-2-HAOX4 is the only GOX encoded in the Ricinus genome (RcGOX). RcGOX has properties resembling those of the photorespiratory GOX of Arabidopsis. We found that glycolate, the substrate of GOX, is highly abundant in non-green tissues, such as roots, embryo of germinating seeds and dry seeds. We propose that RcGOX fulfills different physiological functions depending on the organ in which it is active. In autotrophic organs it oxidizes glycolate into glyoxylate as part of the photorespiratory pathway. In fast growing heterotrophic organs, it is most probably involved in the production of serine to feed the folate pathway for special demands of those tissues.
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Affiliation(s)
- Jessica Schmitz
- Plant Molecular Physiology and Biotechnology Division, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Meike Hüdig
- Plant Molecular Physiology and Biotechnology Division, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
- Molecular Plant Physiology Division, Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Dieter Meier
- Plant Molecular Physiology and Biotechnology Division, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Nicole Linka
- Institute for Plant Biochemistry, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Veronica G Maurino
- Plant Molecular Physiology and Biotechnology Division, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany.
- Molecular Plant Physiology Division, Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Kirschallee 1, 53115, Bonn, Germany.
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18
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Muhammad A, Feng X, Rasool A, Sun W, Li C. Production of plant natural products through engineered Yarrowia lipolytica. Biotechnol Adv 2020; 43:107555. [DOI: 10.1016/j.biotechadv.2020.107555] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/13/2020] [Accepted: 05/12/2020] [Indexed: 12/18/2022]
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19
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20
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Arora Verasztó H, Logotheti M, Albrecht R, Leitner A, Zhu H, Hartmann MD. Architecture and functional dynamics of the pentafunctional AROM complex. Nat Chem Biol 2020; 16:973-978. [PMID: 32632294 DOI: 10.1038/s41589-020-0587-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 06/05/2020] [Indexed: 12/13/2022]
Abstract
The AROM complex is a multifunctional metabolic machine with ten enzymatic domains catalyzing the five central steps of the shikimate pathway in fungi and protists. We determined its crystal structure and catalytic behavior, and elucidated its conformational space using a combination of experimental and computational approaches. We derived this space in an elementary approach, exploiting an abundance of conformational information from its monofunctional homologs in the Protein Data Bank. It demonstrates how AROM is optimized for spatial compactness while allowing for unrestricted conformational transitions and a decoupled functioning of its individual enzymatic entities. With this architecture, AROM poses a tractable test case for the effects of active site proximity on the efficiency of both natural metabolic systems and biotechnological pathway optimization approaches. We show that a mere colocalization of enzymes is not sufficient to yield a detectable improvement of metabolic throughput.
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Affiliation(s)
- Harshul Arora Verasztó
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Maria Logotheti
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Reinhard Albrecht
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Hongbo Zhu
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.
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21
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Exploration of space to achieve scientific breakthroughs. Biotechnol Adv 2020; 43:107572. [PMID: 32540473 DOI: 10.1016/j.biotechadv.2020.107572] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/05/2020] [Accepted: 05/29/2020] [Indexed: 12/13/2022]
Abstract
Living organisms adapt to changing environments using their amazing flexibility to remodel themselves by a process called evolution. Environmental stress causes selective pressure and is associated with genetic and phenotypic shifts for better modifications, maintenance, and functioning of organismal systems. The natural evolution process can be used in complement to rational strain engineering for the development of desired traits or phenotypes as well as for the production of novel biomaterials through the imposition of one or more selective pressures. Space provides a unique environment of stressors (e.g., weightlessness and high radiation) that organisms have never experienced on Earth. Cells in the outer space reorganize and develop or activate a range of molecular responses that lead to changes in cellular properties. Exposure of cells to the outer space will lead to the development of novel variants more efficiently than on Earth. For instance, natural crop varieties can be generated with higher nutrition value, yield, and improved features, such as resistance against high and low temperatures, salt stress, and microbial and pest attacks. The review summarizes the literature on the parameters of outer space that affect the growth and behavior of cells and organisms as well as complex colloidal systems. We illustrate an understanding of gravity-related basic biological mechanisms and enlighten the possibility to explore the outer space environment for application-oriented aspects. This will stimulate biological research in the pursuit of innovative approaches for the future of agriculture and health on Earth.
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22
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The Effects of Glyphosate and Its Commercial Formulations to Marine Invertebrates: A Review. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2020. [DOI: 10.3390/jmse8060399] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Glyphosate is the active ingredient of numerous commercial formulations of herbicides applied in different sectors, from agriculture to aquaculture. Due to its widespread use around the world, relatively high concentrations of glyphosate have been detected in soil and aquatic environments. The presence of glyphosate in aquatic ecosystems has aroused the attention of researchers because of its potential negative effects on living organisms, both animals and plants. In this context, this review intends to summarize results of studies aimed at evaluating the effects of glyphosate (both as active ingredient and component of commercial formulations) on marine invertebrates. Generally, data obtained in acute toxicity tests indicate that glyphosate and its commercial formulations are lethal at high concentrations (not environmentally realistic), whereas results of long-lasting experiments indicate that glyphosate can markedly affect biological responses of marine invertebrates. Consequently, more efforts should be addressed at evaluating chronic or sub-chronic effects of such substances to marine invertebrate species.
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23
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Butenko A, Opperdoes FR, Flegontova O, Horák A, Hampl V, Keeling P, Gawryluk RMR, Tikhonenkov D, Flegontov P, Lukeš J. Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids. BMC Biol 2020; 18:23. [PMID: 32122335 PMCID: PMC7052976 DOI: 10.1186/s12915-020-0754-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/17/2020] [Indexed: 12/24/2022] Open
Abstract
Background The Euglenozoa are a protist group with an especially rich history of evolutionary diversity. They include diplonemids, representing arguably the most species-rich clade of marine planktonic eukaryotes; trypanosomatids, which are notorious parasites of medical and veterinary importance; and free-living euglenids. These different lifestyles, and particularly the transition from free-living to parasitic, likely require different metabolic capabilities. We carried out a comparative genomic analysis across euglenozoan diversity to see how changing repertoires of enzymes and structural features correspond to major changes in lifestyles. Results We find a gradual loss of genes encoding enzymes in the evolution of kinetoplastids, rather than a sudden decrease in metabolic capabilities corresponding to the origin of parasitism, while diplonemids and euglenids maintain more metabolic versatility. Distinctive characteristics of molecular machines such as kinetochores and the pre-replication complex that were previously considered specific to parasitic kinetoplastids were also identified in their free-living relatives. Therefore, we argue that they represent an ancestral rather than a derived state, as thought until the present. We also found evidence of ancient redundancy in systems such as NADPH-dependent thiol-redox. Only the genus Euglena possesses the combination of trypanothione-, glutathione-, and thioredoxin-based systems supposedly present in the euglenozoan common ancestor, while other representatives of the phylum have lost one or two of these systems. Lastly, we identified convergent losses of specific metabolic capabilities between free-living kinetoplastids and ciliates. Although this observation requires further examination, it suggests that certain eukaryotic lineages are predisposed to such convergent losses of key enzymes or whole pathways. Conclusions The loss of metabolic capabilities might not be associated with the switch to parasitic lifestyle in kinetoplastids, and the presence of a highly divergent (or unconventional) kinetochore machinery might not be restricted to this protist group. The data derived from the transcriptomes of free-living early branching prokinetoplastids suggests that the pre-replication complex of Trypanosomatidae is a highly divergent version of the conventional machinery. Our findings shed light on trends in the evolution of metabolism in protists in general and open multiple avenues for future research.
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Affiliation(s)
- Anzhelika Butenko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Fred R Opperdoes
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Olga Flegontova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Vladimír Hampl
- Faculty of Science, Charles University, Biocev, Vestec, Czech Republic
| | - Patrick Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada
| | | | - Denis Tikhonenkov
- Department of Botany, University of British Columbia, Vancouver, Canada.,Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia
| | - Pavel Flegontov
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic. .,Faculty of Science, University of Ostrava, Ostrava, Czech Republic. .,Present address: Department of Genetics, Harvard Medical School, Boston, USA.
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic. .,Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic.
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Krishnan A, Kloehn J, Lunghi M, Soldati-Favre D. Vitamin and cofactor acquisition in apicomplexans: Synthesis versus salvage. J Biol Chem 2020; 295:701-714. [PMID: 31767680 PMCID: PMC6970920 DOI: 10.1074/jbc.aw119.008150] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Apicomplexa phylum comprises diverse parasitic organisms that have evolved from a free-living ancestor. These obligate intracellular parasites exhibit versatile metabolic capabilities reflecting their capacity to survive and grow in different hosts and varying niches. Determined by nutrient availability, they either use their biosynthesis machineries or largely depend on their host for metabolite acquisition. Because vitamins cannot be synthesized by the mammalian host, the enzymes required for their synthesis in apicomplexan parasites represent a large repertoire of potential therapeutic targets. Here, we review recent advances in metabolic reconstruction and functional studies coupled to metabolomics that unravel the interplay between biosynthesis and salvage of vitamins and cofactors in apicomplexans. A particular emphasis is placed on Toxoplasma gondii, during both its acute and latent stages of infection.
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Affiliation(s)
- Aarti Krishnan
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva CMU, 1 Rue Michel-Servet, 1211 Geneva 4 Switzerland
| | - Joachim Kloehn
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva CMU, 1 Rue Michel-Servet, 1211 Geneva 4 Switzerland
| | - Matteo Lunghi
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva CMU, 1 Rue Michel-Servet, 1211 Geneva 4 Switzerland
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva CMU, 1 Rue Michel-Servet, 1211 Geneva 4 Switzerland
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25
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Krishnan A, Kloehn J, Lunghi M, Soldati-Favre D. Vitamin and cofactor acquisition in apicomplexans: Synthesis versus salvage. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49928-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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26
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Matveeva TV, Otten L. Widespread occurrence of natural genetic transformation of plants by Agrobacterium. PLANT MOLECULAR BIOLOGY 2019; 101:415-437. [PMID: 31542868 DOI: 10.1007/s11103-019-00913-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/21/2019] [Indexed: 05/03/2023]
Abstract
Naturally transgenic plant species occur on an unexpectedly large scale. Agrobacterium-mediated gene transfer leads to the formation of crown galls or hairy roots, due to expression of transferred T-DNA genes. Spontaneous regeneration of transformed cells can produce natural transformants carrying cellular T-DNA (cT-DNA) sequences of bacterial origin. This particular type of horizontal gene transfer (HGT) could play a role in plant evolution. However, the material available today is not enough for generalizations concerning the role of Agrobacterium in HGT from bacteria to plants. In this study, we searched for T-DNA-like genes in the sequenced genomes of dicots and monocots. We demonstrate the presence of cT-DNAs in 23 out of 275 dicot species, within genera Eutrema, Arachis, Nissolia, Quillaja, Euphorbia, Parasponia, Trema, Humulus, Psidium, Eugenia, Juglans, Azadirachta, Silene, Dianthus, Vaccinium, Camellia, and Cuscuta. Analysis of transcriptome data of 356 dicot species yielded 16 additional naturally transgenic species. Thus, HGT from Agrobacterium to dicots is remarkably widespread. Opine synthesis genes are most frequent, followed by plast genes. Species in the genera Parasponia, Trema, Camellia, Azadirachta, Quillaja, and Diospyros contain a combination of plast and opine genes. Some are intact and expressed, but the majority have internal stop codons. Among the sequenced monocot species, Dioscorea alata (greater yam) and Musa acuminata (banana) also contain T-DNA-like sequences. The identified examples are valuable material for future research on the role of Agrobacterium-derived genes in plant evolution, for investigations on Agrobacterium strain diversity, and for studies on the function and evolution of cT-DNA genes in natural transformants.
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Affiliation(s)
- Tatiana V Matveeva
- St. Petersburg State University, University Emb., 7/9, Saint Petersburg, Russia
| | - Léon Otten
- Institut de Biologie Moléculaire des Plantes, 12 Rue du Général Zimmer, 67084, Strasbourg, France.
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Lepore R, Kryshtafovych A, Alahuhta M, Veraszto HA, Bomble YJ, Bufton JC, Bullock AN, Caba C, Cao H, Davies OR, Desfosses A, Dunne M, Fidelis K, Goulding CW, Gurusaran M, Gutsche I, Harding CJ, Hartmann MD, Hayes CS, Joachimiak A, Leiman PG, Loppnau P, Lovering AL, Lunin VV, Michalska K, Mir-Sanchis I, Mitra AK, Moult J, Phillips GN, Pinkas DM, Rice PA, Tong Y, Topf M, Walton JD, Schwede T. Target highlights in CASP13: Experimental target structures through the eyes of their authors. Proteins 2019; 87:1037-1057. [PMID: 31442339 PMCID: PMC6851490 DOI: 10.1002/prot.25805] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/09/2019] [Accepted: 08/19/2019] [Indexed: 01/10/2023]
Abstract
The functional and biological significance of selected CASP13 targets are described by the authors of the structures. The structural biologists discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP13 experiment.
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Affiliation(s)
- Rosalba Lepore
- BSC-CNS Barcelona Supercomputing Center, Barcelona, Spain
| | | | - Markus Alahuhta
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado
| | - Harshul A Veraszto
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Yannick J Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado
| | - Joshua C Bufton
- Nuffield Department of Medicine; Structural Genomics Consortium, University of Oxford, Oxford, UK.,School of Biochemistry, University of Bristol, Bristol, UK
| | - Alex N Bullock
- Nuffield Department of Medicine; Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Cody Caba
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Hongnan Cao
- Department of BioSciences, Rice University, Houston, Texas.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin
| | - Owen R Davies
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Ambroise Desfosses
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Matthew Dunne
- Institute of Food, Nutrition and Health, Zurich, Switzerland
| | | | - Celia W Goulding
- Department of Molecular Biology and Biochemistry; Pharmaceutical Sciences, University of California Irvine, Irvine, California
| | - Manickam Gurusaran
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Irina Gutsche
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | | | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, Biomolecular Science and Engineering Program, University of California, Santa Barbara, California
| | - Andrzej Joachimiak
- Structural Biology Center, Biosciences Division, Midwest Center for Structural Genomics, Argonne.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois
| | - Petr G Leiman
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | - Vladimir V Lunin
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado
| | - Karolina Michalska
- Structural Biology Center, Biosciences Division, Midwest Center for Structural Genomics, Argonne
| | - Ignacio Mir-Sanchis
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - A K Mitra
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - John Moult
- Institute for Bioscience and Biotechnology Research, Department of Cell Biology and Molecular genetics, University of Maryland, Rockville, Maryland, USA
| | - George N Phillips
- Department of BioSciences, Rice University, Houston, Texas.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin
| | - Daniel M Pinkas
- Nuffield Department of Medicine; Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Phoebe A Rice
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Yufeng Tong
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada.,Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Maya Topf
- Institute of Structural and Molecular Biology, Birkbeck, University College London, London, UK
| | - Jonathan D Walton
- Great Lakes Bioenergy Research Center and Department of Plant Biology, Michigan State University, East Lansing, Michigan
| | - Torsten Schwede
- Biozentrum University of Basel, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Biozentrum University of Basel, Basel, Switzerland
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28
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Khera HK, Singh SK, Singh S. Chorismate synthase from malaria parasites is bifunctional enzyme. Mol Biochem Parasitol 2019; 233:111202. [PMID: 31381947 DOI: 10.1016/j.molbiopara.2019.111202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 07/13/2019] [Accepted: 07/31/2019] [Indexed: 11/16/2022]
Abstract
Chorismate synthase (Cs) is the last enzyme of the main trunk of shikimate pathway and catalyzes formation of chorismate, a major aromatic metabolite precursor. We have previously reported that Cs is highly conserved across different Plasmodium sp. Here we report that Cs from malaria parasites are bifunctional enzymes through expression and functional studies of two recombinant proteins rPfCs (Cs from P. falciparum) and rPvCs (Cs from P. vivax). We confirm bifunctional activity of both rPfCs and rPvCs based on their ability to catalyze formation of chorismate under aerobic conditions as well as their ability to catalyze generation of reduced flavin mononucleotide (FMN) as assessed through diaphorase assay.
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Affiliation(s)
- Harvinder Kour Khera
- Pharmacology Division, Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu, Jammu and Kashmir, 180001, India; Academy of Scientific & Innovative Research (AcSIR), New Delhi, India
| | - Susheel Kumar Singh
- Pharmacology Division, Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu, Jammu and Kashmir, 180001, India
| | - Subhash Singh
- Pharmacology Division, Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu, Jammu and Kashmir, 180001, India; Academy of Scientific & Innovative Research (AcSIR), New Delhi, India.
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29
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Koontz JM, Dancy BCR, Horton CL, Stallings JD, DiVito VT, Lewis JA. The Role of the Human Microbiome in Chemical Toxicity. Int J Toxicol 2019; 38:251-264. [PMID: 31220972 DOI: 10.1177/1091581819849833] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
There is overwhelming evidence that the microbiome must be considered when evaluating the toxicity of chemicals. Disruption of the normal microbial flora is a known effect of toxic exposure, and these disruptions may lead to human health effects. In addition, the biotransformation of numerous compounds has been shown to be dependent on microbial enzymes, with the potential for different host health outcomes resulting from variations in the microbiome. Evidence suggests that such metabolism of environmental chemicals by enzymes from the host's microbiota can affect the toxicity of that chemical to the host. Chemical-microbial interactions can be categorized into two classes: Microbiome Modulation of Toxicity (MMT) and Toxicant Modulation of the Microbiome (TMM). MMT refers to transformation of a chemical by microbial enzymes or metabolites to modify the chemical in a way that makes it more or less toxic. TMM is a change in the microbiota that results from a chemical exposure. These changes span a large magnitude of effects and may vary from microbial gene regulation, to inhibition of a specific enzyme, to the death of the microbes. Certain microbiomes or microbiota may become associated with different health outcomes, such as resistance or susceptibility to exposure to certain toxic chemicals, the ability to recover following a chemical-induced injury, the presence of disease-associated phenotypes, and the effectiveness of immune responses. Future work in toxicology will require an understanding of how the microbiome interacts with toxicants to fully elucidate how a compound will affect a diverse, real-world population.
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Affiliation(s)
- Jason M Koontz
- 1 US Army Center for Environmental Health Research, Fort Detrick, MD, USA
| | - Blair C R Dancy
- 1 US Army Center for Environmental Health Research, Fort Detrick, MD, USA
| | | | | | - Valerie T DiVito
- 1 US Army Center for Environmental Health Research, Fort Detrick, MD, USA
| | - John A Lewis
- 1 US Army Center for Environmental Health Research, Fort Detrick, MD, USA
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30
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Inwongwan S, Kruger NJ, Ratcliffe RG, O'Neill EC. Euglena Central Metabolic Pathways and Their Subcellular Locations. Metabolites 2019; 9:E115. [PMID: 31207935 PMCID: PMC6630311 DOI: 10.3390/metabo9060115] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/03/2019] [Accepted: 06/11/2019] [Indexed: 01/16/2023] Open
Abstract
Euglenids are a group of algae of great interest for biotechnology, with a large and complex metabolic capability. To study the metabolic network, it is necessary to know where the component enzymes are in the cell, but despite a long history of research into Euglena, the subcellular locations of many major pathways are only poorly defined. Euglena is phylogenetically distant from other commonly studied algae, they have secondary plastids bounded by three membranes, and they can survive after destruction of their plastids. These unusual features make it difficult to assume that the subcellular organization of the metabolic network will be equivalent to that of other photosynthetic organisms. We analysed bioinformatic, biochemical, and proteomic information from a variety of sources to assess the subcellular location of the enzymes of the central metabolic pathways, and we use these assignments to propose a model of the metabolic network of Euglena. Other than photosynthesis, all major pathways present in the chloroplast are also present elsewhere in the cell. Our model demonstrates how Euglena can synthesise all the metabolites required for growth from simple carbon inputs, and can survive in the absence of chloroplasts.
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Affiliation(s)
- Sahutchai Inwongwan
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
| | - Nicholas J Kruger
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
| | - R George Ratcliffe
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
| | - Ellis C O'Neill
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
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31
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John U, Lu Y, Wohlrab S, Groth M, Janouškovec J, Kohli GS, Mark FC, Bickmeyer U, Farhat S, Felder M, Frickenhaus S, Guillou L, Keeling PJ, Moustafa A, Porcel BM, Valentin K, Glöckner G. An aerobic eukaryotic parasite with functional mitochondria that likely lacks a mitochondrial genome. SCIENCE ADVANCES 2019; 5:eaav1110. [PMID: 31032404 PMCID: PMC6482013 DOI: 10.1126/sciadv.aav1110] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 03/07/2019] [Indexed: 05/30/2023]
Abstract
Dinoflagellates are microbial eukaryotes that have exceptionally large nuclear genomes; however, their organelle genomes are small and fragmented and contain fewer genes than those of other eukaryotes. The genus Amoebophrya (Syndiniales) comprises endoparasites with high genetic diversity that can infect other dinoflagellates, such as those forming harmful algal blooms (e.g., Alexandrium). We sequenced the genome (~100 Mb) of Amoebophrya ceratii to investigate the early evolution of genomic characters in dinoflagellates. The A. ceratii genome encodes almost all essential biosynthetic pathways for self-sustaining cellular metabolism, suggesting a limited dependency on its host. Although dinoflagellates are thought to have descended from a photosynthetic ancestor, A. ceratii appears to have completely lost its plastid and nearly all genes of plastid origin. Functional mitochondria persist in all life stages of A. ceratii, but we found no evidence for the presence of a mitochondrial genome. Instead, all mitochondrial proteins appear to be lost or encoded in the A. ceratii nucleus.
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Affiliation(s)
- Uwe John
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany
| | - Yameng Lu
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Sylke Wohlrab
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany
| | - Marco Groth
- Leibniz Institute on Aging, Fritz Lipmann Institute, Beutenbergstr. 11, Jena, Germany
| | - Jan Janouškovec
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Gurjeet S. Kohli
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Felix C. Mark
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Ulf Bickmeyer
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Sarah Farhat
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Marius Felder
- Leibniz Institute on Aging, Fritz Lipmann Institute, Beutenbergstr. 11, Jena, Germany
| | - Stephan Frickenhaus
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Hochschule Bremerhaven, Bremerhaven, Germany
| | - Laure Guillou
- CNRS, UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Place Georges Teissier, CS90074, 29688 Roscoff cedex, France
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 6, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, CS90074, 29688 Roscoff cedex, France
| | - Patrick J. Keeling
- Botany Department, University of British Columbia, Vancouver, BC, Canada
| | - Ahmed Moustafa
- Department of Biology and Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
| | - Betina M. Porcel
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Klaus Valentin
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Gernot Glöckner
- Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
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32
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Santos SAD, Tuffi-Santos LD, Tanaka FAO, Sant'Anna-Santos BF, Rodrigues FDÁ, Alfenas AC. Carfentrazone-ethyl and glyphosate drift inhibits uredinial formation of Austropuccinia psidii on Eucalyptus grandis leaves. PEST MANAGEMENT SCIENCE 2019; 75:53-62. [PMID: 30073761 DOI: 10.1002/ps.5163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/31/2018] [Accepted: 07/31/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND The response to infection of Austropuccinia psidii in resistant (CLR-383) and susceptible (CLR-384) Eucalyptus grandis clones, exposed to herbicide drift of carfentrazone-ethyl, glyphosate and a mixture of these two herbicides, was evaluated at microscopic and physiological levels. RESULTS Plants of the two clones showed symptoms of phytotoxicity caused by herbicide drift. However, net CO2 assimilation rate, height and shoot dry matter were lower in CLR-384 than in CLR-383. At the ultrastructure level, the leaves of both clones exposed to the herbicides showed thylakoid disorganization and accumulation of starch grains in the chloroplasts. Only plants of CLR-384 were infected by A. psidii, but when exposed to herbicide drift, rust severity was lower than in control plants. Six days after inoculation (dai), plants of this clone exposed to the herbicides had smaller uredinia than control plants. At 12 dai, non-herbicide treated plants showed normal uredinia, containing abundant urediniospores. By contrast, plants exposed to the herbicides were less colonized by the fungus, and the uredinia were smaller with reduced production of urediniospores, which were sometimes not even detected. CONCLUSION Glyphosate and carfentrazone-ethyl herbicide drift reduce infection and uredinial formation of A. psidii and to some extent induce basal resistance in a susceptible clone of E. grandis. © 2018 Society of Chemical Industry.
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Affiliation(s)
| | | | - Francisco André Ossamu Tanaka
- Department of Plant Pathology, Escola Superior de Agricultura 'Luiz de Queiroz' - Universidade de São Paulo, Piracicaba, Brazil
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33
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Liu C, Liu B, Zhang Y, Jiang F, Ren Y, Li S, Wang H, Fan W. Ancient horizontally transferred genes in the genome of California two-spot octopus, Octopus bimaculoides. Gene 2018; 667:34-44. [PMID: 29738840 DOI: 10.1016/j.gene.2018.05.013] [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: 11/25/2017] [Revised: 04/10/2018] [Accepted: 05/02/2018] [Indexed: 11/28/2022]
Abstract
Horizontal gene transfer (HGT), a mechanism that shares genetic material between the host and donor from separated offspring branches, has been described as a means of producing novel and beneficial phenotypes for the host organisms. However, in molluscs, the second most diverse group, the existence of HGT is still controversial. In the present study, 12 HGT genes were identified from California two-spot octopus Octopus bimaculoides based on a similarity search, phylogenetic construction, gene composition analysis and PCR (Polymerase Chain Reaction) validation. Based on the phylogenetic topologies, ten HGT genes were identified to have been transferred into the possible molluscan ancestor, possibly before its radiation. Furthermore, most of the donor organisms were predicted to be familiar bacteria in marine environments. These horizontally transferred genes were under a strong negative selection and could be transcribed in octopus functionally. The predicted biochemical functions of these genes include metabolism, neurotransmission, immune defense and tissue integrity. Seven Zn-metalloproteinases were validated as the main type of HGT genes in octopus with divergent motif composition, intron presence and phylogenetic relationship to the endogenous ones. Furthermore, the functions of Zn-metalloproteinase were predicted to be responsible for immune defense and tissue remolding. Three HGT genes were distributed mainly in the nervous system and were predicted to regulate the neurotransmission through glia-neuronal interactions. The results collectively indicated the existence of HGT in molluscs and its potential contribution to the evolution of octopus with regards to functional innovation and adaptability.
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Affiliation(s)
- Conghui Liu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
| | - Bo Liu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yan Zhang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Fan Jiang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yuwei Ren
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Shuqu Li
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Hengchao Wang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Wei Fan
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
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34
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Catharina L, Carels N. Specific enzyme functionalities of Fusarium oxysporum compared to host plants. Gene 2018; 676:219-226. [PMID: 29981422 DOI: 10.1016/j.gene.2018.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 05/14/2018] [Accepted: 07/01/2018] [Indexed: 11/29/2022]
Abstract
The genus Fusarium contains some of the most studied and important species of plant pathogens that economically affect world agriculture and horticulture. Fusarium spp. are ubiquitous fungi widely distributed in soil, plants as well as in different organic substrates and are also considered as opportunistic human pathogens. The identification of specific enzymes essential to the metabolism of these fungi is expected to provide molecular targets to control the diseases they induce to their hosts. Through applications of traditional techniques of sequence homology comparison by similarity search and Markov modeling, this report describes the characterization of enzymatic functionalities associated to protein targets that could be considered for the control of root rots induced by Fusarium oxysporum. From the analysis of 318 F. graminearum enzymes, we retrieved 30 enzymes that are specific of F. oxysporum compared to 15 species of host plants. By comparing these 30 specific enzymes of F. oxysporum with the genome of Arabidopsis thaliana, Brassica rapa, Glycine max, Jatropha curcas and Ricinus communis, we found 7 key specific enzymes whose inhibition is expected to affect significantly the development of the fungus and 5 specific enzymes that were considered here to be secondary because they are inserted in pathways with alternative routes.
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Affiliation(s)
- Larissa Catharina
- Laboratório de Modelagem de Sistemas Biológicos, Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas (INCT-IDPN), Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz (Fiocruz), Av. Brasil, 4036, Prédio da Expansão, 8° andar, sala 814, CEP: 21040-361 Rio de Janeiro, Brazil.
| | - Nicolas Carels
- Laboratório de Modelagem de Sistemas Biológicos, Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas (INCT-IDPN), Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz (Fiocruz), Av. Brasil, 4036, Prédio da Expansão, 8° andar, sala 814, CEP: 21040-361 Rio de Janeiro, Brazil.
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35
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Hernandez AM, Ryan JF. Horizontally transferred genes in the ctenophore Mnemiopsis leidyi. PeerJ 2018; 6:e5067. [PMID: 29922518 PMCID: PMC6005172 DOI: 10.7717/peerj.5067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/04/2018] [Indexed: 12/16/2022] Open
Abstract
Horizontal gene transfer (HGT) has had major impacts on the biology of a wide range of organisms from antibiotic resistance in bacteria to adaptations to herbivory in arthropods. A growing body of literature shows that HGT between non-animals and animals is more commonplace than previously thought. In this study, we present a thorough investigation of HGT in the ctenophore Mnemiopsis leidyi. We applied tests of phylogenetic incongruence to identify nine genes that were likely transferred horizontally early in ctenophore evolution from bacteria and non-metazoan eukaryotes. All but one of these HGTs (an uncharacterized protein) are homologous to characterized enzymes, supporting previous observations that genes encoding enzymes are more likely to be retained after HGT events. We found that the majority of these nine horizontally transferred genes were expressed during development, suggesting that they are active and play a role in the biology of M. leidyi. This is the first report of HGT in ctenophores, and contributes to an ever-growing literature on the prevalence of genetic information flowing between non-animals and animals.
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Affiliation(s)
- Alexandra M Hernandez
- Whitney Laboratory for Marine Bioscience, St. Augustine, FL, USA.,Department of Biology, University of Florida, Gainesville, FL, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, St. Augustine, FL, USA.,Department of Biology, University of Florida, Gainesville, FL, USA
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36
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Carrington Y, Guo J, Le CH, Fillo A, Kwon J, Tran LT, Ehlting J. Evolution of a secondary metabolic pathway from primary metabolism: shikimate and quinate biosynthesis in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:823-833. [PMID: 29894016 DOI: 10.1111/tpj.13990] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/23/2018] [Accepted: 05/29/2018] [Indexed: 05/18/2023]
Abstract
The shikimate pathway synthesizes aromatic amino acids essential for protein biosynthesis. Shikimate dehydrogenase (SDH) is a central enzyme of this primary metabolic pathway, producing shikimate. The structurally similar quinate is a secondary metabolite synthesized by quinate dehydrogenase (QDH). SDH and QDH belong to the same gene family, which diverged into two phylogenetic clades after a defining gene duplication just prior to the angiosperm/gymnosperm split. Non-seed plants that diverged before this duplication harbour only a single gene of this family. Extant representatives from the chlorophytes (Chlamydomonas reinhardtii), bryophytes (Physcomitrella patens) and lycophytes (Selaginella moellendorfii) encoded almost exclusively SDH activity in vitro. A reconstructed ancestral sequence representing the node just prior to the gene duplication also encoded SDH activity. Quinate dehydrogenase activity was gained only in seed plants following gene duplication. Quinate dehydrogenases of gymnosperms, represented here by Pinus taeda, may be reminiscent of an evolutionary intermediate since they encode equal SDH and QDH activities. The second copy in P. taeda maintained specificity for shikimate similar to the activity found in the angiosperm SDH sister clade. The codon for a tyrosine residue within the active site displayed a signature of positive selection at the node defining the QDH clade, where it changed to a glycine. Replacing the tyrosine with a glycine in a highly shikimate-specific angiosperm SDH was sufficient to gain some QDH function. Thus, very few mutations were necessary to facilitate the evolution of QDH genes.
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Affiliation(s)
- Yuriko Carrington
- Department of Biology and Centre for Forest Biology, University of Victoria, PO Box 1700, Station CSC, Victoria, BC, V8W 2Y2, Canada
| | - Jia Guo
- Department of Biology and Centre for Forest Biology, University of Victoria, PO Box 1700, Station CSC, Victoria, BC, V8W 2Y2, Canada
| | - Cuong H Le
- Department of Biochemistry and Microbiology and Centre for Forest Biology, University of Victoria, PO Box 1700, Station CSC, Victoria, BC, V8W 2Y2, Canada
| | - Alexander Fillo
- Department of Biology and Centre for Forest Biology, University of Victoria, PO Box 1700, Station CSC, Victoria, BC, V8W 2Y2, Canada
| | - Junsu Kwon
- Department of Biology and Centre for Forest Biology, University of Victoria, PO Box 1700, Station CSC, Victoria, BC, V8W 2Y2, Canada
| | - Lan T Tran
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Jürgen Ehlting
- Department of Biology and Centre for Forest Biology, University of Victoria, PO Box 1700, Station CSC, Victoria, BC, V8W 2Y2, Canada
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Godde JS, Baichoo S, Mungloo-Dilmohamud Z, Jaufeerally-Fakim Y. Comparison of genomic islands in cyanobacteria: Evidence of bacteriophage-mediated horizontal gene transfer from eukaryotes. Microbiol Res 2018; 211:31-46. [DOI: 10.1016/j.micres.2018.03.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/11/2018] [Accepted: 03/17/2018] [Indexed: 12/21/2022]
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Marchand J, Heydarizadeh P, Schoefs B, Spetea C. Ion and metabolite transport in the chloroplast of algae: lessons from land plants. Cell Mol Life Sci 2018; 75:2153-2176. [PMID: 29541792 PMCID: PMC5948301 DOI: 10.1007/s00018-018-2793-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 03/01/2018] [Accepted: 03/07/2018] [Indexed: 12/28/2022]
Abstract
Chloroplasts are endosymbiotic organelles and play crucial roles in energy supply and metabolism of eukaryotic photosynthetic organisms (algae and land plants). They harbor channels and transporters in the envelope and thylakoid membranes, mediating the exchange of ions and metabolites with the cytosol and the chloroplast stroma and between the different chloroplast subcompartments. In secondarily evolved algae, three or four envelope membranes surround the chloroplast, making more complex the exchange of ions and metabolites. Despite the importance of transport proteins for the optimal functioning of the chloroplast in algae, and that many land plant homologues have been predicted, experimental evidence and molecular characterization are missing in most cases. Here, we provide an overview of the current knowledge about ion and metabolite transport in the chloroplast from algae. The main aspects reviewed are localization and activity of the transport proteins from algae and/or of homologues from other organisms including land plants. Most chloroplast transporters were identified in the green alga Chlamydomonas reinhardtii, reside in the envelope and participate in carbon acquisition and metabolism. Only a few identified algal transporters are located in the thylakoid membrane and play role in ion transport. The presence of genes for putative transporters in green algae, red algae, diatoms, glaucophytes and cryptophytes is discussed, and roles in the chloroplast are suggested. A deep knowledge in this field is required because algae represent a potential source of biomass and valuable metabolites for industry, medicine and agriculture.
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Affiliation(s)
- Justine Marchand
- Metabolism, Bioengineering of Microalgal Molecules and Applications (MIMMA), Mer Molécules Santé, IUML, FR 3473 CNRS, Le Mans University, 72000, Le Mans, France
| | - Parisa Heydarizadeh
- Metabolism, Bioengineering of Microalgal Molecules and Applications (MIMMA), Mer Molécules Santé, IUML, FR 3473 CNRS, Le Mans University, 72000, Le Mans, France
| | - Benoît Schoefs
- Metabolism, Bioengineering of Microalgal Molecules and Applications (MIMMA), Mer Molécules Santé, IUML, FR 3473 CNRS, Le Mans University, 72000, Le Mans, France.
| | - Cornelia Spetea
- Department of Biological and Environmental Sciences, University of Gothenburg, 40530, Göteborg, Sweden.
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Milić M, Žunec S, Micek V, Kašuba V, Mikolić A, Lovaković BT, Semren TŽ, Pavičić I, Čermak AMM, Pizent A, Vrdoljak AL, Valencia-Quintana R, Sánchez-Alarcón J, Želježić D. Oxidative stress, cholinesterase activity, and DNA damage in the liver, whole blood, and plasma of Wistar rats following a 28-day exposure to glyphosate. Arh Hig Rada Toksikol 2018; 69:154-168. [PMID: 29990293 DOI: 10.2478/aiht-2018-69-3114] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/01/2018] [Indexed: 11/21/2022] Open
Abstract
In this 28 day-study, we evaluated the effects of herbicide glyphosate administered by gavage to Wistar rats at daily doses equivalent to 0.1 of the acceptable operator exposure level (AOEL), 0.5 of the consumer acceptable daily intake (ADI), 1.75 (corresponding to the chronic population-adjusted dose, cPAD), and 10 mg kg-1 body weight (bw) (corresponding to 100 times the AOEL). At the end of each treatment, the body and liver weights were measured and compared with their baseline values. DNA damage in leukocytes and liver tissue was estimated with the alkaline comet assay. Oxidative stress was evaluated using a battery of endpoints to establish lipid peroxidation via thiobarbituric reactive substances (TBARS) level, level of reactive oxygen species (ROS), glutathione (GSH) level, and the activity of glutathione peroxidase (GSH-Px). Total cholinesterase activity and the activities of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) were also measured. The exposed animals gained less weight than control. Treatment resulted in significantly higher primary DNA damage in the liver cells and leukocytes. Glyphosate exposure significantly lowered TBARS in the liver of the AOEL, ADI, and cPAD groups, and in plasma in the AOEL and cPAD group. AChE was inhibited with all treatments, but the AOEL and ADI groups significantly differed from control. Total ChE and plasma/liver ROS/GSH levels did not significantly differ from control, except for the 35 % decrease in ChE in the AOEL and ADI groups and a significant drop in liver GSH in the cPAD and 100xAOEL groups. AOEL and ADI blood GSH-Px activity dropped significantly, but in the liver it significantly increased in the ADI, cPAD, and 100xAOEL groups vs. control. All these findings show that even exposure to low glyphosate levels can have serious adverse effects and points to a need to change the approach to risk assessment of low-level chronic/sub-chronic glyphosate exposure, where oxidative stress is not necessarily related to the genetic damage and AChE inhibition.
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Affiliation(s)
- Mirta Milić
- Institute for Medical Research and Occupational Health, Zagreb, Croatia
| | - Suzana Žunec
- Institute for Medical Research and Occupational Health, Zagreb, Croatia
| | - Vedran Micek
- Institute for Medical Research and Occupational Health, Zagreb, Croatia
| | - Vilena Kašuba
- Institute for Medical Research and Occupational Health, Zagreb, Croatia
| | - Anja Mikolić
- Institute for Medical Research and Occupational Health, Zagreb, Croatia
| | | | | | - Ivan Pavičić
- Institute for Medical Research and Occupational Health, Zagreb, Croatia
| | | | - Alica Pizent
- Institute for Medical Research and Occupational Health, Zagreb, Croatia
| | | | - Rafael Valencia-Quintana
- Laboratorio "Rafael Villalobos-Pietrini" de Toxicología Genómica y Química Ambiental, Facultad de Agrobiología, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Juana Sánchez-Alarcón
- Laboratorio "Rafael Villalobos-Pietrini" de Toxicología Genómica y Química Ambiental, Facultad de Agrobiología, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Davor Želježić
- Institute for Medical Research and Occupational Health, Zagreb, Croatia
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Schenck CA, Maeda HA. Tyrosine biosynthesis, metabolism, and catabolism in plants. PHYTOCHEMISTRY 2018; 149:82-102. [PMID: 29477627 DOI: 10.1016/j.phytochem.2018.02.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 01/26/2018] [Accepted: 02/02/2018] [Indexed: 05/22/2023]
Abstract
L-Tyrosine (Tyr) is an aromatic amino acid (AAA) required for protein synthesis in all organisms, but synthesized de novo only in plants and microorganisms. In plants, Tyr also serves as a precursor of numerous specialized metabolites that have diverse physiological roles as electron carriers, antioxidants, attractants, and defense compounds. Some of these Tyr-derived plant natural products are also used in human medicine and nutrition (e.g. morphine and vitamin E). While the Tyr biosynthesis and catabolic pathways have been extensively studied in microbes and animals, respectively, those of plants have received much less attention until recently. Accumulating evidence suggest that the Tyr biosynthetic pathways differ between microbes and plants and even within the plant kingdom, likely to support the production of lineage-specific plant specialized metabolites derived from Tyr. The interspecies variations of plant Tyr pathway enzymes can now be used to enhance the production of Tyr and Tyr-derived compounds in plants and other synthetic biology platforms.
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Affiliation(s)
- Craig A Schenck
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Zuo S, Xiao J, Zhang Y, Zhang X, Nomura CT, Chen S, Wang Q. Rational design and medium optimization for shikimate production in recombinant Bacillus licheniformis strains. Process Biochem 2018. [DOI: 10.1016/j.procbio.2017.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Agrobacterium-Mediated Transformation in the Evolution of Plants. Curr Top Microbiol Immunol 2018; 418:421-441. [PMID: 29500560 DOI: 10.1007/82_2018_80] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
In most cases, the genetic engineering of plants uses Agrobacterium-mediated transformation to introduce novel genes. In nature, insertion of T-DNA into the plant genome and its subsequent transfer via sexual reproduction have been shown for several species in the genera Nicotiana, Ipomoea , and Linaria . A sequence homologous to T-DNA of the Ri plasmid of Agrobacterium rhizogenes was found in the genome of wild-type Nicotiana glauca (section Noctiflorae) more than 30 years ago and was named "cellular T-DNA" (cT-DNA). It comprises an imperfect inverted repeat and contains homologs of several T-DNA oncogenes (NgrolB, NgrolC, Ngorf13, Ngorf14) and an opine synthesis gene (Ngmis). Multiple cT-DNAs have also been found in species of the sections Tomentosae and Nicotiana of the genus Nicotiana. These ancient cT-DNA genes are still expressed, indicating that they may play a role in the evolution of these plants. In 2012-2013, cT-DNA was detected and characterized in Linaria vulgaris and L. genistifolia ssp. dalmatica. Their cT-DNA is present in two copies and organized as an imperfect direct tandem repeat, containing LvORF2, LvORF3, LvORF8, LvrolA, LvrolB, LvrolC, LvORF13, LvORF14, and the Lvmis genes. In 2015, cT-DNA was found in Ipomoea. Two types of T-DNA-like sequences were described within this genera, and their distribution varied among cultured hexaploid, tetraploid, and wild diploid forms. Thus, several independent T-DNA integration events occurred in the genomes of these three plant genera. We propose that the events of T-DNA insertion in the plant genome might have affected their evolution, resulting in the creation of new plant species. In this chapter, we focus on the structure and functions of cT-DNA in Linaria, Nicotiana, and Ipomoea and discuss their possible evolutionary role.
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Affiliation(s)
- Qingwei Zhang
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Germany
| | - Dorothea Bartels
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Germany
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Abrahamian M, Kagda M, Ah-Fong AMV, Judelson HS. Rethinking the evolution of eukaryotic metabolism: novel cellular partitioning of enzymes in stramenopiles links serine biosynthesis to glycolysis in mitochondria. BMC Evol Biol 2017; 17:241. [PMID: 29202688 PMCID: PMC5715807 DOI: 10.1186/s12862-017-1087-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/21/2017] [Indexed: 12/17/2022] Open
Abstract
Background An important feature of eukaryotic evolution is metabolic compartmentalization, in which certain pathways are restricted to the cytosol or specific organelles. Glycolysis in eukaryotes is described as a cytosolic process. The universality of this canon has been challenged by recent genome data that suggest that some glycolytic enzymes made by stramenopiles bear mitochondrial targeting peptides. Results Mining of oomycete, diatom, and brown algal genomes indicates that stramenopiles encode two forms of enzymes for the second half of glycolysis, one with and the other without mitochondrial targeting peptides. The predicted mitochondrial targeting was confirmed by using fluorescent tags to localize phosphoglycerate kinase, phosphoglycerate mutase, and pyruvate kinase in Phytophthora infestans, the oomycete that causes potato blight. A genome-wide search for other enzymes with atypical mitochondrial locations identified phosphoglycerate dehydrogenase, phosphoserine aminotransferase, and phosphoserine phosphatase, which form a pathway for generating serine from the glycolytic intermediate 3-phosphoglycerate. Fluorescent tags confirmed the delivery of these serine biosynthetic enzymes to P. infestans mitochondria. A cytosolic form of this serine biosynthetic pathway, which occurs in most eukaryotes, is missing from oomycetes and most other stramenopiles. The glycolysis and serine metabolism pathways of oomycetes appear to be mosaics of enzymes with different ancestries. While some of the noncanonical oomycete mitochondrial enzymes have the closest affinity in phylogenetic analyses with proteins from other stramenopiles, others cluster with bacterial, plant, or animal proteins. The genes encoding the mitochondrial phosphoglycerate kinase and serine-forming enzymes are physically linked on oomycete chromosomes, which suggests a shared origin. Conclusions Stramenopile metabolism appears to have been shaped through the acquisition of genes by descent and lateral or endosymbiotic gene transfer, along with the targeting of the proteins to locations that are novel compared to other eukaryotes. Colocalization of the glycolytic and serine biosynthesis enzymes in mitochondria is apparently necessary since they share a common intermediate. The results indicate that descriptions of metabolism in textbooks do not cover the full diversity of eukaryotic biology. Electronic supplementary material The online version of this article (10.1186/s12862-017-1087-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Melania Abrahamian
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Meenakshi Kagda
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Audrey M V Ah-Fong
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Howard S Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA.
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45
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Schenck CA, Men Y, Maeda HA. Conserved Molecular Mechanism of TyrA Dehydrogenase Substrate Specificity Underlying Alternative Tyrosine Biosynthetic Pathways in Plants and Microbes. Front Mol Biosci 2017; 4:73. [PMID: 29164132 PMCID: PMC5681985 DOI: 10.3389/fmolb.2017.00073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/24/2017] [Indexed: 12/03/2022] Open
Abstract
L-Tyrosine (Tyr) is an aromatic amino acid synthesized de novo in plants and microbes. In animals, Tyr must be obtained through their diet or synthesized from L-phenylalanine. In addition to protein synthesis, Tyr serves as the precursor of neurotransmitters (e.g., dopamine and epinephrine) in animals and of numerous plant natural products, which serve essential functions in both plants and humans (e.g., vitamin E and morphine). Tyr is synthesized via two alternative routes mediated by a TyrA family enzyme, prephenate, or arogenate dehydrogenase (PDH/TyrAp or ADH/TyrAa), typically found in microbes and plants, respectively. Although ADH activity is also found in some bacteria, the origin of arogenate-specific TyrAa enzymes is unknown. We recently identified an acidic Asp222 residue that confers ADH activity in plant TyrAs. In this study, structure-guided phylogenetic analyses identified bacterial homologs, closely-related to plant TyrAs, that also have an acidic 222 residue and ADH activity. A more distant archaeon TyrA that preferred PDH activity had a non-acidic Gln, whose substitution to Glu introduced ADH activity. These results indicate that the conserved molecular mechanism operated during the evolution of arogenate-specific TyrAa in both plants and microbes.
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Affiliation(s)
- Craig A Schenck
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
| | - Yusen Men
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
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46
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Hagel JM, Facchini PJ. Tying the knot: occurrence and possible significance of gene fusions in plant metabolism and beyond. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4029-4043. [PMID: 28521055 DOI: 10.1093/jxb/erx152] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Gene fusions have recently attracted attention especially in the field of plant specialized metabolism. The occurrence of a gene fusion, in which originally separate gene products are combined into a single polypeptide, often corresponds to the functional association of individual components within a single metabolic pathway. Examples include gene fusions implicated in benzylisoquinoline alkaloid (BIA), terpenoid, and amino acid biosynthetic pathways, in which distinct domains within a fusion catalyze consecutive, yet independent reactions. Both genomic and transcriptional mechanisms result in the fusion of gene products, which can include partial or complete domain repeats and extensive domain shuffling as evident in the BIA biosynthetic enzyme norcoclaurine synthase. Artificial gene fusions are commonly deployed in attempts to engineer new or improved pathways in plants or microorganisms, based on the premise that fusions are advantageous. However, a survey of functionally characterized fusions in microbial systems shows that the functional impact of fused gene products is not straightforward. For example, whereas enzyme fusions might facilitate the metabolic channeling of unstable intermediates, this channeling can also occur between tightly associated independent enzymes. The frequent occurrence of both fused and unfused enzymes in plant and microbial metabolism adds additional complexity, in terms of both pathway functionality and evolution.
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Affiliation(s)
- Jillian M Hagel
- Department of Biological Sciences, University of Calgary, 2500 University Dr N.W., Alberta T2N 1N4, Canada
| | - Peter J Facchini
- Department of Biological Sciences, University of Calgary, 2500 University Dr N.W., Alberta T2N 1N4, Canada
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47
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Kamikawa R, Moog D, Zauner S, Tanifuji G, Ishida KI, Miyashita H, Mayama S, Hashimoto T, Maier UG, Archibald JM, Inagaki Y. A Non-photosynthetic Diatom Reveals Early Steps of Reductive Evolution in Plastids. Mol Biol Evol 2017; 34:2355-2366. [DOI: 10.1093/molbev/msx172] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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48
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Dupont PY, Cox MP. Genomic Data Quality Impacts Automated Detection of Lateral Gene Transfer in Fungi. G3 (BETHESDA, MD.) 2017; 7:1301-1314. [PMID: 28235827 PMCID: PMC5386878 DOI: 10.1534/g3.116.038448] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/17/2017] [Indexed: 12/26/2022]
Abstract
Lateral gene transfer (LGT, also known as horizontal gene transfer), an atypical mechanism of transferring genes between species, has almost become the default explanation for genes that display an unexpected composition or phylogeny. Numerous methods of detecting LGT events all rely on two fundamental strategies: primary structure composition or gene tree/species tree comparisons. Discouragingly, the results of these different approaches rarely coincide. With the wealth of genome data now available, detection of laterally transferred genes is increasingly being attempted in large uncurated eukaryotic datasets. However, detection methods depend greatly on the quality of the underlying genomic data, which are typically complex for eukaryotes. Furthermore, given the automated nature of genomic data collection, it is typically impractical to manually verify all protein or gene models, orthology predictions, and multiple sequence alignments, requiring researchers to accept a substantial margin of error in their datasets. Using a test case comprising plant-associated genomes across the fungal kingdom, this study reveals that composition- and phylogeny-based methods have little statistical power to detect laterally transferred genes. In particular, phylogenetic methods reveal extreme levels of topological variation in fungal gene trees, the vast majority of which show departures from the canonical species tree. Therefore, it is inherently challenging to detect LGT events in typical eukaryotic genomes. This finding is in striking contrast to the large number of claims for laterally transferred genes in eukaryotic species that routinely appear in the literature, and questions how many of these proposed examples are statistically well supported.
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Affiliation(s)
- Pierre-Yves Dupont
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
- the Bio-Protection Research Centre, Massey University, Palmerston North 4442, New Zealand
| | - Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
- the Bio-Protection Research Centre, Massey University, Palmerston North 4442, New Zealand
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49
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Liu Y, Luo SH, Schmidt A, Wang GD, Sun GL, Grant M, Kuang C, Yang MJ, Jing SX, Li CH, Schneider B, Gershenzon J, Li SH. A Geranylfarnesyl Diphosphate Synthase Provides the Precursor for Sesterterpenoid (C25) Formation in the Glandular Trichomes of the Mint Species Leucosceptrum canum. THE PLANT CELL 2016; 28:804-22. [PMID: 26941091 PMCID: PMC4826006 DOI: 10.1105/tpc.15.00715] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 02/18/2016] [Accepted: 02/27/2016] [Indexed: 05/19/2023]
Abstract
Plant sesterterpenoids, an important class of terpenoids, are widely distributed in various plants, including food crops. However, little is known about their biosynthesis. Here, we cloned and functionally characterized a plant geranylfarnesyl diphosphate synthase (Lc-GFDPS), the enzyme producing the C25 prenyl diphosphate precursor to all sesterterpenoids, from the glandular trichomes of the woody plant Leucosceptrum canum. GFDPS catalyzed the formation of GFDP after expression in Escherichia coli. Overexpressing GFDPS in Arabidopsis thaliana also gave an extract catalyzing GFDP formation. GFDPS was strongly expressed in glandular trichomes, and its transcript profile was completely in accordance with the sesterterpenoid accumulation pattern. GFDPS is localized to the plastids, and inhibitor studies indicated its use of isoprenyl diphosphate substrates supplied by the 2-C-methyl-D-erythritol 4-phosphate pathway. Application of a jasmonate defense hormone induced GFDPS transcript and sesterterpenoid accumulation, while reducing feeding and growth of the generalist insect Spodoptera exigua, suggesting that these C25 terpenoids play a defensive role. Phylogenetic analysis suggested that GFDPS probably evolved from plant geranylgeranyl diphosphate synthase under the influence of positive selection. The isolation of GFDPS provides a model for investigating sesterterpenoid formation in other species and a tool for manipulating the formation of this group in plants and other organisms.
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Affiliation(s)
- Yan Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, P.R. China
| | - Shi-Hong Luo
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, P.R. China
| | - Axel Schmidt
- Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Guo-Dong Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Gui-Ling Sun
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, P.R. China
| | - Marcus Grant
- Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Ce Kuang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, P.R. China
| | - Min-Jie Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, P.R. China
| | - Shu-Xi Jing
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, P.R. China
| | - Chun-Huan Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, P.R. China
| | - Bernd Schneider
- Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | | | - Sheng-Hong Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, P.R. China
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50
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Light SH, Krishna SN, Minasov G, Anderson WF. An Unusual Cation-Binding Site and Distinct Domain-Domain Interactions Distinguish Class II Enolpyruvylshikimate-3-phosphate Synthases. Biochemistry 2016; 55:1239-45. [PMID: 26813771 DOI: 10.1021/acs.biochem.5b00553] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes a critical step in the biosynthesis of a number of aromatic metabolites. An essential prokaryotic enzyme and the molecular target of the herbicide glyphosate, EPSPSs are the subject of both pharmaceutical and commercial interest. Two EPSPS classes that exhibit low sequence homology, differing substrate/glyphosate affinities, and distinct cation activation properties have previously been described. Here, we report structural studies of the monovalent cation-binding class II Coxiella burnetii EPSPS (cbEPSPS). Three cbEPSPS crystal structures reveal that the enzyme undergoes substantial conformational changes that alter the electrostatic potential of the active site. A complex with shikimate-3-phosphate, inorganic phosphate (Pi), and K(+) reveals that ligand induced domain closure produces an unusual cation-binding site bordered on three sides by the N-terminal domain, C-terminal domain, and the product Pi. A crystal structure of the class I Vibrio cholerae EPSPS (vcEPSPS) clarifies the basis of differential class I and class II cation responsiveness, showing that in class I EPSPSs a lysine side chain occupies the would-be cation-binding site. Finally, we identify distinct patterns of sequence conservation at the domain-domain interface and propose that the two EPSPS classes have evolved to differently optimize domain opening-closing dynamics.
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Affiliation(s)
- Samuel H Light
- Center for Structural Genomics of Infectious Diseases and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University , 303 East Chicago Avenue, Chicago, Illinois 60611, United States
| | - Sankar N Krishna
- Center for Structural Genomics of Infectious Diseases and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University , 303 East Chicago Avenue, Chicago, Illinois 60611, United States
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University , 303 East Chicago Avenue, Chicago, Illinois 60611, United States
| | - Wayne F Anderson
- Center for Structural Genomics of Infectious Diseases and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University , 303 East Chicago Avenue, Chicago, Illinois 60611, United States
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