1
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Grundmann CO, Guzman J, Vilcinskas A, Pupo MT. The insect microbiome is a vast source of bioactive small molecules. Nat Prod Rep 2024; 41:935-967. [PMID: 38411238 DOI: 10.1039/d3np00054k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Covering: September 1964 to June 2023Bacteria and fungi living in symbiosis with insects have been studied over the last sixty years and found to be important sources of bioactive natural products. Not only classic producers of secondary metabolites such as Streptomyces and other members of the phylum Actinobacteria but also numerous bacteria from the phyla Proteobacteria and Firmicutes and an impressive array of fungi (usually pathogenic) serve as the source of a structurally diverse number of small molecules with important biological activities including antimicrobial, cytotoxic, antiparasitic and specific enzyme inhibitors. The insect niche is often the exclusive provider of microbes producing unique types of biologically active compounds such as gerumycins, pederin, dinactin, and formicamycins. However, numerous insects still have not been described taxonomically, and in most cases, the study of their microbiota is completely unexplored. In this review, we present a comprehensive survey of 553 natural products produced by microorganisms isolated from insects by collating and classifying all the data according to the type of compound (rather than the insect or microbial source). The analysis of the correlations among the metadata related to insects, microbial partners, and their produced compounds provides valuable insights into the intricate dynamics between insects and their symbionts as well as the impact of their metabolites on these relationships. Herein, we focus on the chemical structure, biosynthesis, and biological activities of the most relevant compounds.
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Affiliation(s)
| | - Juan Guzman
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - Andreas Vilcinskas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University, Giessen, Germany
| | - Mônica Tallarico Pupo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
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2
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Timmons CM, Shazib SUA, Katz LA. Epigenetic influences of mobile genetic elements on ciliate genome architecture and evolution. J Eukaryot Microbiol 2022; 69:e12891. [PMID: 35100457 DOI: 10.1111/jeu.12891] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/20/2022] [Accepted: 01/22/2022] [Indexed: 11/27/2022]
Abstract
Mobile genetic elements (MGEs) are transient genetic material that can move either within a single organism's genome or between individuals or species. While historically considered 'junk' DNA (i.e. deleterious or at best neutral), more recent studies reveal the adaptive advantages MGEs provide in lineages across the tree of life. Ciliates, a group of single-celled microbial eukaryotes characterized by nuclear dimorphism, exemplify how epigenetic influences from MGEs shape genome architecture and patterns of molecular evolution. Ciliate nuclear dimorphism may have evolved as a response to transposon invasion and ciliates have since co-opted transposons to carry out programmed DNA deletion. Another example of the effect of MGEs is in providing mechanisms for lateral gene transfer from bacteria, which introduces genetic diversity and, in several cases, drives ecological specialization in ciliates. As a third example, the integration of viral DNA, likely through transduction, provides new genetic material and can change the way host cells defend themselves against other viral pathogens. We argue that the acquisition of MGEs through non-Mendelian patterns of inheritance, coupled with their effects on ciliate genome architecture and expression and persistence throughout evolutionary history, exemplify how the transmission of mobile elements should be considered a mechanism of transgenerational epigenetic inheritance.
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Affiliation(s)
- Caitlin M Timmons
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA
| | - Shahed U A Shazib
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA
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3
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Eichenberger M, Hüppi S, Patsch D, Aeberli N, Berweger R, Dossenbach S, Eichhorn E, Flachsmann F, Hortencio L, Voirol F, Vollenweider S, Bornscheuer UT, Buller R. Asymmetric Cation-Olefin Monocyclization by Engineered Squalene-Hopene Cyclases. Angew Chem Int Ed Engl 2021; 60:26080-26086. [PMID: 34346556 PMCID: PMC9290348 DOI: 10.1002/anie.202108037] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/09/2021] [Indexed: 12/31/2022]
Abstract
Squalene-hopene cyclases (SHCs) have great potential for the industrial synthesis of enantiopure cyclic terpenoids. A limitation of SHC catalysis has been the enzymes' strict (S)-enantioselectivity at the stereocenter formed after the first cyclization step. To gain enantio-complementary access to valuable monocyclic terpenoids, an SHC-wild-type library including 18 novel homologs was set up. A previously not described SHC (AciSHC) was found to synthesize small amounts of monocyclic (R)-γ-dihydroionone from (E/Z)-geranylacetone. Using enzyme and process optimization, the conversion to the desired product was increased to 79 %. Notably, analyzed AciSHC variants could finely differentiate between the geometric geranylacetone isomers: While the (Z)-isomer yielded the desired monocyclic (R)-γ-dihydroionone (>99 % ee), the (E)-isomer was converted to the (S,S)-bicyclic ether (>95 % ee). Applying the knowledge gained from the observed stereodivergent and enantioselective transformations to an additional SHC-substrate pair, access to the complementary (S)-γ-dihydroionone (>99.9 % ee) could be obtained.
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Affiliation(s)
- Michael Eichenberger
- Zurich University of Applied SciencesLife Sciences and Facility ManagementEinsiedlerstrasse 318820WädenswilSwitzerland
| | - Sean Hüppi
- Zurich University of Applied SciencesLife Sciences and Facility ManagementEinsiedlerstrasse 318820WädenswilSwitzerland
- Department of BiotechnologyDelft University of TechnologyVan der Maasweg 92629HZDelftThe Netherlands
| | - David Patsch
- Zurich University of Applied SciencesLife Sciences and Facility ManagementEinsiedlerstrasse 318820WädenswilSwitzerland
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme CatalysisGreifswald UniversityFelix-Hausdorff-Strasse 417487GreifswaldGermany
| | - Natalie Aeberli
- Fragrances S&TIngredients ResearchGivaudan Schweiz AGKemptpark 508310KemptthalSwitzerland
| | - Raphael Berweger
- Fragrances S&TIngredients ResearchGivaudan Schweiz AGKemptpark 508310KemptthalSwitzerland
| | - Sandro Dossenbach
- Fragrances S&TIngredients ResearchGivaudan Schweiz AGKemptpark 508310KemptthalSwitzerland
| | - Eric Eichhorn
- Fragrances S&TIngredients ResearchGivaudan Schweiz AGKemptpark 508310KemptthalSwitzerland
| | - Felix Flachsmann
- Fragrances S&TIngredients ResearchGivaudan Schweiz AGKemptpark 508310KemptthalSwitzerland
| | - Lucas Hortencio
- Fragrances S&TIngredients ResearchGivaudan Schweiz AGKemptpark 508310KemptthalSwitzerland
| | - Francis Voirol
- Fragrances S&TIngredients ResearchGivaudan Schweiz AGKemptpark 508310KemptthalSwitzerland
| | - Sabine Vollenweider
- Science & TechnologyGivaudan International SAKemptpark 508310KemptthalSwitzerland
| | - Uwe T. Bornscheuer
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme CatalysisGreifswald UniversityFelix-Hausdorff-Strasse 417487GreifswaldGermany
| | - Rebecca Buller
- Zurich University of Applied SciencesLife Sciences and Facility ManagementEinsiedlerstrasse 318820WädenswilSwitzerland
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4
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Eichenberger M, Hüppi S, Patsch D, Aeberli N, Berweger R, Dossenbach S, Eichhorn E, Flachsmann F, Hortencio L, Voirol F, Vollenweider S, Bornscheuer UT, Buller R. Asymmetric Cation‐Olefin Monocyclization by Engineered Squalene–Hopene Cyclases. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Michael Eichenberger
- Zurich University of Applied Sciences Life Sciences and Facility Management Einsiedlerstrasse 31 8820 Wädenswil Switzerland
| | - Sean Hüppi
- Zurich University of Applied Sciences Life Sciences and Facility Management Einsiedlerstrasse 31 8820 Wädenswil Switzerland
- Department of Biotechnology Delft University of Technology Van der Maasweg 9 2629 HZ Delft The Netherlands
| | - David Patsch
- Zurich University of Applied Sciences Life Sciences and Facility Management Einsiedlerstrasse 31 8820 Wädenswil Switzerland
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme Catalysis Greifswald University Felix-Hausdorff-Strasse 4 17487 Greifswald Germany
| | - Natalie Aeberli
- Fragrances S&T Ingredients Research Givaudan Schweiz AG Kemptpark 50 8310 Kemptthal Switzerland
| | - Raphael Berweger
- Fragrances S&T Ingredients Research Givaudan Schweiz AG Kemptpark 50 8310 Kemptthal Switzerland
| | - Sandro Dossenbach
- Fragrances S&T Ingredients Research Givaudan Schweiz AG Kemptpark 50 8310 Kemptthal Switzerland
| | - Eric Eichhorn
- Fragrances S&T Ingredients Research Givaudan Schweiz AG Kemptpark 50 8310 Kemptthal Switzerland
| | - Felix Flachsmann
- Fragrances S&T Ingredients Research Givaudan Schweiz AG Kemptpark 50 8310 Kemptthal Switzerland
| | - Lucas Hortencio
- Fragrances S&T Ingredients Research Givaudan Schweiz AG Kemptpark 50 8310 Kemptthal Switzerland
| | - Francis Voirol
- Fragrances S&T Ingredients Research Givaudan Schweiz AG Kemptpark 50 8310 Kemptthal Switzerland
| | - Sabine Vollenweider
- Science & Technology Givaudan International SA Kemptpark 50 8310 Kemptthal Switzerland
| | - Uwe T. Bornscheuer
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme Catalysis Greifswald University Felix-Hausdorff-Strasse 4 17487 Greifswald Germany
| | - Rebecca Buller
- Zurich University of Applied Sciences Life Sciences and Facility Management Einsiedlerstrasse 31 8820 Wädenswil Switzerland
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5
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Bouwknegt J, Wiersma SJ, Ortiz-Merino RA, Doornenbal ESR, Buitenhuis P, Giera M, Müller C, Pronk JT. A squalene-hopene cyclase in Schizosaccharomyces japonicus represents a eukaryotic adaptation to sterol-limited anaerobic environments. Proc Natl Acad Sci U S A 2021; 118:e2105225118. [PMID: 34353908 PMCID: PMC8364164 DOI: 10.1073/pnas.2105225118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Biosynthesis of sterols, which are key constituents of canonical eukaryotic membranes, requires molecular oxygen. Anaerobic protists and deep-branching anaerobic fungi are the only eukaryotes in which a mechanism for sterol-independent growth has been elucidated. In these organisms, tetrahymanol, formed through oxygen-independent cyclization of squalene by a squalene-tetrahymanol cyclase, acts as a sterol surrogate. This study confirms an early report [C. J. E. A. Bulder, Antonie Van Leeuwenhoek, 37, 353-358 (1971)] that Schizosaccharomyces japonicus is exceptional among yeasts in growing anaerobically on synthetic media lacking sterols and unsaturated fatty acids. Mass spectrometry of lipid fractions of anaerobically grown Sch. japonicus showed the presence of hopanoids, a class of cyclic triterpenoids not previously detected in yeasts, including hop-22(29)-ene, hop-17(21)-ene, hop-21(22)-ene, and hopan-22-ol. A putative gene in Sch. japonicus showed high similarity to bacterial squalene-hopene cyclase (SHC) genes and in particular to those of Acetobacter species. No orthologs of the putative Sch. japonicus SHC were found in other yeast species. Expression of the Sch. japonicus SHC gene (Sjshc1) in Saccharomyces cerevisiae enabled hopanoid synthesis and stimulated anaerobic growth in sterol-free media, thus indicating that one or more of the hopanoids produced by SjShc1 could at least partially replace sterols. Use of hopanoids as sterol surrogates represents a previously unknown adaptation of eukaryotic cells to anaerobic growth. The fast anaerobic growth of Sch. japonicus in sterol-free media is an interesting trait for developing robust fungal cell factories for application in anaerobic industrial processes.
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Affiliation(s)
- Jonna Bouwknegt
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Sanne J Wiersma
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Raúl A Ortiz-Merino
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Eline S R Doornenbal
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Petrik Buitenhuis
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Christoph Müller
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximillians University Munich, 81377 Munich, Germany
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands;
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6
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Geng Y, Cai C, McAdam SAM, Banks JA, Wisecaver JH, Zhou Y. A De Novo Transcriptome Assembly of Ceratopteris richardii Provides Insights into the Evolutionary Dynamics of Complex Gene Families in Land Plants. Genome Biol Evol 2021; 13:6157829. [PMID: 33681974 PMCID: PMC7975763 DOI: 10.1093/gbe/evab042] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2021] [Indexed: 01/26/2023] Open
Abstract
As the closest extant sister group to seed plants, ferns are an important reference point to study the origin and evolution of plant genes and traits. One bottleneck to the use of ferns in phylogenetic and genetic studies is the fact that genome-level sequence information of this group is limited, due to the extreme genome sizes of most ferns. Ceratopteris richardii (hereafter Ceratopteris) has been widely used as a model system for ferns. In this study, we generated a transcriptome of Ceratopteris, through the de novo assembly of the RNA-seq data from 17 sequencing libraries that are derived from two sexual types of gametophytes and five different sporophyte tissues. The Ceratopteris transcriptome, together with 38 genomes and transcriptomes from other species across the Viridiplantae, were used to uncover the evolutionary dynamics of orthogroups (predicted gene families using OrthoFinder) within the euphyllophytes and identify proteins associated with the major shifts in plant morphology and physiology that occurred in the last common ancestors of euphyllophytes, ferns, and seed plants. Furthermore, this resource was used to identify and classify the GRAS domain transcriptional regulators of many developmental processes in plants. Through the phylogenetic analysis within each of the 15 GRAS orthogroups, we uncovered which GRAS family members are conserved or have diversified in ferns and seed plants. Taken together, the transcriptome database and analyses reported here provide an important platform for exploring the evolution of gene families in land plants and for studying gene function in seed-free vascular plants.
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Affiliation(s)
- Yuan Geng
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | - Chao Cai
- Purdue University Libraries and School of Information Studies, Purdue University, West Lafayette, Indiana, USA
| | - Scott A M McAdam
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | - Jo Ann Banks
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | - Jennifer H Wisecaver
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA.,Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Yun Zhou
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
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7
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Santana-Molina C, Rivas-Marin E, Rojas AM, Devos DP. Origin and Evolution of Polycyclic Triterpene Synthesis. Mol Biol Evol 2020; 37:1925-1941. [PMID: 32125435 PMCID: PMC7306690 DOI: 10.1093/molbev/msaa054] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Polycyclic triterpenes are members of the terpene family produced by the cyclization of squalene. The most representative polycyclic triterpenes are hopanoids and sterols, the former are mostly found in bacteria, whereas the latter are largely limited to eukaryotes, albeit with a growing number of bacterial exceptions. Given their important role and omnipresence in most eukaryotes, contrasting with their scant representation in bacteria, sterol biosynthesis was long thought to be a eukaryotic innovation. Thus, their presence in some bacteria was deemed to be the result of lateral gene transfer from eukaryotes. Elucidating the origin and evolution of the polycyclic triterpene synthetic pathways is important to understand the role of these compounds in eukaryogenesis and their geobiological value as biomarkers in fossil records. Here, we have revisited the phylogenies of the main enzymes involved in triterpene synthesis, performing gene neighborhood analysis and phylogenetic profiling. Squalene can be biosynthesized by two different pathways containing the HpnCDE or Sqs proteins. Our results suggest that the HpnCDE enzymes are derived from carotenoid biosynthesis ones and that they assembled in an ancestral squalene pathway in bacteria, while remaining metabolically versatile. Conversely, the Sqs enzyme is prone to be involved in lateral gene transfer, and its emergence is possibly related to the specialization of squalene biosynthesis. The biosynthesis of hopanoids seems to be ancestral in the Bacteria domain. Moreover, no triterpene cyclases are found in Archaea, invoking a potential scenario in which eukaryotic genes for sterol biosynthesis assembled from ancestral bacterial contributions in early eukaryotic lineages.
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Affiliation(s)
- Carlos Santana-Molina
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, Junta de Andalucía, Universidad Pablo de Olavide, Seville, Spain
| | - Elena Rivas-Marin
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, Junta de Andalucía, Universidad Pablo de Olavide, Seville, Spain
| | - Ana M Rojas
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, Junta de Andalucía, Universidad Pablo de Olavide, Seville, Spain
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, Junta de Andalucía, Universidad Pablo de Olavide, Seville, Spain
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8
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Liu Z, Zhang Y, Sun J, Huang WC, Xue C, Mao X. A Novel Soluble Squalene-Hopene Cyclase and Its Application in Efficient Synthesis of Hopene. Front Bioeng Biotechnol 2020; 8:426. [PMID: 32478051 PMCID: PMC7232578 DOI: 10.3389/fbioe.2020.00426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/14/2020] [Indexed: 11/13/2022] Open
Abstract
Hopene is an important precursor for synthesizing bioactive hopanoids with great commercial value. However, the chemical methods for synthesizing hopene are not efficient to date. Hopene is commonly obtained by extracting from plants or bacteria like other terpenoids, but the complicated extraction process is inefficient and unfriendly to the environment. Hopene can be biological synthesized by squalene-hopene cyclase (SHC) from squalene. However, hopene production by SHC remained at a low level until now. In this work, we found a novel SHC named OUC-SaSHC from Streptomyces albolongus ATCC 27414. An easy procedure for expression and purification of OUC-SaSHC was established. The conditions for OUC-SaSHC to convert squalene into hopene are optimized as in 100 mM sodium phosphate buffer (pH 7.0) containing 0.5% Tween 80, 20 mM squalene and 0.14 mg/mL OUC-SaSHC at 30°C. In the scale-up reaction with the final volume of 100 mL, the yield of squalene could be up to 99% at 36 h, and 8.07 mg/mL hopene was produced. Our work showed a great potential of OUC-SaSHC as biocatalyst on scale-up production of hopene, hence improves the SHC-catalyzing enzyme synthesis of hopene from laboratory level to application level.
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Affiliation(s)
- Zhen Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Yinan Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Jianan Sun
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Wen-Can Huang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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9
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Welander PV. Deciphering the evolutionary history of microbial cyclic triterpenoids. Free Radic Biol Med 2019; 140:270-278. [PMID: 31071437 DOI: 10.1016/j.freeradbiomed.2019.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 05/02/2019] [Accepted: 05/02/2019] [Indexed: 11/26/2022]
Abstract
Cyclic triterpenoids are a class of lipids that have fascinated chemists, biologist, and geologist alike for many years. These molecules have diverse physiological roles in a variety of bacterial and eukaryotic organisms and a shared evolutionary ancestry that is reflected in the elegant biochemistry required for their synthesis. Cyclic triterpenoids are also quite recalcitrant and are preserved in sedimentary rocks where they are utilized as "molecular fossils" or biomarkers that can physically link microbial taxa and their metabolisms to a specific time or event in Earth's history. However, a proper interpretation of cyclic triterpenoid biosignatures requires a robust understanding of their function in extant organisms and in the evolutionary history of their biosynthetic pathways. Here, I review two potential cyclic triterpenoid evolutionary scenarios and the recent genetic and biochemical studies that are providing experimental evidence to distinguish between these hypotheses. The study of cyclic triterpenoids will continue to provide a wealth of information that can significantly impact the interpretation of lipid biosignatures in the rock record and provides a compelling model of how two natural repositories of evolutionary history available on Earth, the geologic record in sedimentary rocks and the molecular record in living organisms, can be linked.
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Affiliation(s)
- Paula V Welander
- Department of Earth System Science, Stanford University, 473 Via Ortega, Rm 140, Stanford, CA, 94305, USA.
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10
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Ma K, Zhang P, Tao Q, Keller NP, Yang Y, Yin WB, Liu H. Characterization and Biosynthesis of a Rare Fungal Hopane-Type Triterpenoid Glycoside Involved in the Antistress Property of Aspergillus fumigatus. Org Lett 2019; 21:3252-3256. [DOI: 10.1021/acs.orglett.9b00984] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ke Ma
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Peng Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Qiaoqiao Tao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Yanlong Yang
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People’s Republic of China
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Hongwei Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
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11
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Kuhnert E, Li Y, Lan N, Yue Q, Chen L, Cox RJ, An Z, Yokoyama K, Bills GF. Enfumafungin synthase represents a novel lineage of fungal triterpene cyclases. Environ Microbiol 2018; 20:3325-3342. [PMID: 30051576 DOI: 10.1111/1462-2920.14333] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/18/2018] [Accepted: 06/19/2018] [Indexed: 01/12/2023]
Abstract
Enfumafungin is a glycosylated fernene-type triterpenoid produced by the fungus Hormonema carpetanum. Its potent antifungal activity, mediated by its interaction with β-1,3-glucan synthase and the fungal cell wall, has led to its development into the semi-synthetic clinical candidate, ibrexafungerp (=SCY-078). We report on the preliminary identification of the enfumafungin biosynthetic gene cluster (BGC) based on genome sequencing, phylogenetic reconstruction, gene disruption, and cDNA sequencing studies. Enfumafungin synthase (efuA) consists of a terpene cyclase domain (TC) fused to a glycosyltransferase (GT) domain and thus represents a novel multifunctional enzyme. Moreover, the TC domain bears a phylogenetic relationship to bacterial squalene-hopene cyclases (SHC) and includes a typical DXDD motif within the active centre suggesting that efuA evolved from SHCs. Phylogenetic reconstruction of the GT domain indicated that this portion of the fusion gene originated from fungal sterol GTs. Eleven genes flanking efuA are putatively involved in the biosynthesis, regulation, transport and self-resistance of enfumafungin and include an acetyltransferase, three P450 monooxygenases, a dehydrogenase, a desaturase and a reductase. A hypothetical scheme for enfumafungin assembly is proposed in which the E-ring is oxidatively cleaved to yield the four-ring system of enfumafungin. EfuA represents the first member of a widespread lineage of fungal SHCs.
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Affiliation(s)
- Eric Kuhnert
- Texas Therapeutics Institute, the Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA.,Leibniz University Hannover, Institute for Organic Chemistry and BMWZ, Hannover, Germany
| | - Yan Li
- Texas Therapeutics Institute, the Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA.,Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nan Lan
- Texas Therapeutics Institute, the Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Qun Yue
- Texas Therapeutics Institute, the Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA.,Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li Chen
- Texas Therapeutics Institute, the Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Russell J Cox
- Leibniz University Hannover, Institute for Organic Chemistry and BMWZ, Hannover, Germany
| | - Zhiqiang An
- Texas Therapeutics Institute, the Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Kenichi Yokoyama
- Duke University School of Medicine, Department of Biochemistry, Durham, NC, USA
| | - Gerald F Bills
- Texas Therapeutics Institute, the Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
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12
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C-4 sterol demethylation enzymes distinguish bacterial and eukaryotic sterol synthesis. Proc Natl Acad Sci U S A 2018; 115:5884-5889. [PMID: 29784781 DOI: 10.1073/pnas.1802930115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sterols are essential eukaryotic lipids that are required for a variety of physiological roles. The diagenetic products of sterol lipids, sterane hydrocarbons, are preserved in ancient sedimentary rocks and are utilized as geological biomarkers, indicating the presence of both eukaryotes and oxic environments throughout Earth's history. However, a few bacterial species are also known to produce sterols, bringing into question the significance of bacterial sterol synthesis for our interpretation of sterane biomarkers. Recent studies suggest that bacterial sterol synthesis may be distinct from what is observed in eukaryotes. In particular, phylogenomic analyses of sterol-producing bacteria have failed to identify homologs of several key eukaryotic sterol synthesis enzymes, most notably those required for demethylation at the C-4 position. In this study, we identified two genes of previously unknown function in the aerobic methanotrophic γ-Proteobacterium Methylococcus capsulatus that encode sterol demethylase proteins (Sdm). We show that a Rieske-type oxygenase (SdmA) and an NAD(P)-dependent reductase (SdmB) are responsible for converting 4,4-dimethylsterols to 4α-methylsterols. Identification of intermediate products synthesized during heterologous expression of SdmA-SdmB along with 13C-labeling studies support a sterol C-4 demethylation mechanism distinct from that of eukaryotes. SdmA-SdmB homologs were identified in several other sterol-producing bacterial genomes but not in any eukaryotic genomes, indicating that these proteins are unrelated to the eukaryotic C-4 sterol demethylase enzymes. These findings reveal a separate pathway for sterol synthesis exclusive to bacteria and show that demethylation of sterols evolved at least twice-once in bacteria and once in eukaryotes.
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13
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Belin BJ, Busset N, Giraud E, Molinaro A, Silipo A, Newman DK. Hopanoid lipids: from membranes to plant-bacteria interactions. Nat Rev Microbiol 2018; 16:304-315. [PMID: 29456243 PMCID: PMC6087623 DOI: 10.1038/nrmicro.2017.173] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Lipid research represents a frontier for microbiology, as showcased by hopanoid lipids. Hopanoids, which resemble sterols and are found in the membranes of diverse bacteria, have left an extensive molecular fossil record. They were first discovered by petroleum geologists. Today, hopanoid-producing bacteria remain abundant in various ecosystems, such as the rhizosphere. Recently, great progress has been made in our understanding of hopanoid biosynthesis, facilitated in part by technical advances in lipid identification and quantification. A variety of genetically tractable, hopanoid-producing bacteria have been cultured, and tools to manipulate hopanoid biosynthesis and detect hopanoids are improving. However, we still have much to learn regarding how hopanoid production is regulated, how hopanoids act biophysically and biochemically, and how their production affects bacterial interactions with other organisms, such as plants. The study of hopanoids thus offers rich opportunities for discovery.
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Affiliation(s)
- Brittany J. Belin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Nicolas Busset
- Institut de Recherche pour le Développement, LSTM, UMR IRD, SupAgro, INRA, University of Montpellier, CIRAD, France
| | - Eric Giraud
- Institut de Recherche pour le Développement, LSTM, UMR IRD, SupAgro, INRA, University of Montpellier, CIRAD, France
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy
| | - Dianne K. Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
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14
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Staley JT, Fuerst JA. Ancient, highly conserved proteins from a LUCA with complex cell biology provide evidence in support of the nuclear compartment commonality (NuCom) hypothesis. Res Microbiol 2017; 168:395-412. [PMID: 28111289 DOI: 10.1016/j.resmic.2017.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 01/08/2017] [Accepted: 01/09/2017] [Indexed: 12/23/2022]
Abstract
The nuclear compartment commonality (NuCom) hypothesis posits a complex last common ancestor (LUCA) with membranous compartments including a nuclear membrane. Such a LUCA then evolved to produce two nucleated lineages of the tree of life: the Planctomycetes-Verrucomicrobia-Chlamydia superphylum (PVC) within the Bacteria, and the Eukarya. We propose that a group of ancient essential protokaryotic signature proteins (PSPs) originating in LUCA were incorporated into ancestors of PVC Bacteria and Eukarya. Tubulins, ubiquitin system enzymes and sterol-synthesizing enzymes are consistent with early origins of these features shared between the PVC superphylum and Eukarya.
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Affiliation(s)
- James T Staley
- Department of Microbiology and Astrobiology Program, University of Washington, Seattle 98195, USA
| | - John A Fuerst
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, Queensland 4072, Australia.
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15
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Wei JH, Yin X, Welander PV. Sterol Synthesis in Diverse Bacteria. Front Microbiol 2016; 7:990. [PMID: 27446030 PMCID: PMC4919349 DOI: 10.3389/fmicb.2016.00990] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/09/2016] [Indexed: 11/13/2022] Open
Abstract
Sterols are essential components of eukaryotic cells whose biosynthesis and function has been studied extensively. Sterols are also recognized as the diagenetic precursors of steranes preserved in sedimentary rocks where they can function as geological proxies for eukaryotic organisms and/or aerobic metabolisms and environments. However, production of these lipids is not restricted to the eukaryotic domain as a few bacterial species also synthesize sterols. Phylogenomic studies have identified genes encoding homologs of sterol biosynthesis proteins in the genomes of several additional species, indicating that sterol production may be more widespread in the bacterial domain than previously thought. Although the occurrence of sterol synthesis genes in a genome indicates the potential for sterol production, it provides neither conclusive evidence of sterol synthesis nor information about the composition and abundance of basic and modified sterols that are actually being produced. Here, we coupled bioinformatics with lipid analyses to investigate the scope of bacterial sterol production. We identified oxidosqualene cyclase (Osc), which catalyzes the initial cyclization of oxidosqualene to the basic sterol structure, in 34 bacterial genomes from five phyla (Bacteroidetes, Cyanobacteria, Planctomycetes, Proteobacteria, and Verrucomicrobia) and in 176 metagenomes. Our data indicate that bacterial sterol synthesis likely occurs in diverse organisms and environments and also provides evidence that there are as yet uncultured groups of bacterial sterol producers. Phylogenetic analysis of bacterial and eukaryotic Osc sequences confirmed a complex evolutionary history of sterol synthesis in this domain. Finally, we characterized the lipids produced by Osc-containing bacteria and found that we could generally predict the ability to synthesize sterols. However, predicting the final modified sterol based on our current knowledge of sterol synthesis was difficult. Some bacteria produced demethylated and saturated sterol products even though they lacked homologs of the eukaryotic proteins required for these modifications emphasizing that several aspects of bacterial sterol synthesis are still completely unknown.
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Affiliation(s)
| | | | - Paula V. Welander
- Department of Earth System Science, Stanford UniversityStanford, CA, USA
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16
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Abstract
The functionality of cellular membranes relies on the molecular order imparted by lipids. In eukaryotes, sterols such as cholesterol modulate membrane order, yet they are not typically found in prokaryotes. The structurally similar bacterial hopanoids exhibit similar ordering properties as sterols in vitro, but their exact physiological role in living bacteria is relatively uncharted. We present evidence that hopanoids interact with glycolipids in bacterial outer membranes to form a highly ordered bilayer in a manner analogous to the interaction of sterols with sphingolipids in eukaryotic plasma membranes. Furthermore, multidrug transport is impaired in a hopanoid-deficient mutant of the gram-negative Methylobacterium extorquens, which introduces a link between membrane order and an energy-dependent, membrane-associated function in prokaryotes. Thus, we reveal a convergence in the architecture of bacterial and eukaryotic membranes and implicate the biosynthetic pathways of hopanoids and other order-modulating lipids as potential targets to fight pathogenic multidrug resistance.
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17
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Abstract
Fungi (Ascomycota and Basidiomycota) are prolific producers of structurally diverse terpenoid compounds. Classes of terpenoids identified in fungi include the sesqui-, di- and triterpenoids. Biosynthetic pathways and enzymes to terpenoids from each of these classes have been described. These typically involve the scaffold generating terpene synthases and cyclases, and scaffold tailoring enzymes such as e.g. cytochrome P450 monoxygenases, NAD(P)+ and flavin dependent oxidoreductases, and various group transferases that generate the final bioactive structures. The biosynthesis of several sesquiterpenoid mycotoxins and bioactive diterpenoids has been well-studied in Ascomycota (e.g. filamentous fungi). Little is known about the terpenoid biosynthetic pathways in Basidiomycota (e.g. mushroom forming fungi), although they produce a huge diversity of terpenoid natural products. Specifically, many trans-humulyl cation derived sesquiterpenoid natural products with potent bioactivities have been isolated. Biosynthetic gene clusters responsible for the production of trans-humulyl cation derived protoilludanes, and other sesquiterpenoids, can be rapidly identified by genome sequencing and bioinformatic methods. Genome mining combined with heterologous biosynthetic pathway refactoring has the potential to facilitate discovery and production of pharmaceutically relevant fungal terpenoids.
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Affiliation(s)
- Maureen B Quin
- University of Minnesota, Dept. of Biochemistry, Molecular Biology and Biophysics, 1479 Gortner Avenue, St. Paul, MN 55108, USA
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18
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Tomazic ML, Poklepovich TJ, Nudel CB, Nusblat AD. Incomplete sterols and hopanoids pathways in ciliates: Gene loss and acquisition during evolution as a source of biosynthetic genes. Mol Phylogenet Evol 2014; 74:122-34. [DOI: 10.1016/j.ympev.2014.01.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 12/16/2013] [Accepted: 01/27/2014] [Indexed: 10/25/2022]
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19
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Hammer SC, Syrén PO, Seitz M, Nestl BM, Hauer B. Squalene hopene cyclases: highly promiscuous and evolvable catalysts for stereoselective CC and CX bond formation. Curr Opin Chem Biol 2013; 17:293-300. [PMID: 23485581 DOI: 10.1016/j.cbpa.2013.01.016] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 01/20/2013] [Accepted: 01/23/2013] [Indexed: 11/18/2022]
Abstract
We review here how the inherent promiscuous nature, as well as the evolvability of terpene cyclase enzymes enables new applications in chemistry. We mainly focus on squalene hopene cyclases, class II triterpene synthases that use a proton-initiated cationic polycyclization cascade to form carbopolycyclic products. We highlight recent findings to demonstrate that these enzymes are capable of activating different functionalities other than the traditional terminal isoprene C=C-group as well as being compatible with a wide range of nucleophiles beyond the 'ene-functionality'. Thus, squalene hopene cyclases demonstrate a great potential to be used as a toolbox for general Brønsted acid catalysis.
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Affiliation(s)
- Stephan C Hammer
- Institute of Technical Biochemistry, Universitaet Stuttgart, Allmandring 31, D-70569 Stuttgart, Germany
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20
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Budd A, Devos DP. Evaluating the Evolutionary Origins of Unexpected Character Distributions within the Bacterial Planctomycetes-Verrucomicrobia-Chlamydiae Superphylum. Front Microbiol 2012; 3:401. [PMID: 23189077 PMCID: PMC3505017 DOI: 10.3389/fmicb.2012.00401] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 10/31/2012] [Indexed: 12/26/2022] Open
Abstract
Recently, several characters that are absent from most bacteria, but which are found in many eukaryotes or archaea, have been identified within the bacterial Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum. Hypotheses of the evolutionary history of such characters are commonly based on the inference of phylogenies of gene or protein families associated with the traits, estimated from multiple sequence alignments (MSAs). So far, studies of this kind have focused on the distribution of (i) two genes involved in the synthesis of sterol, (ii) tubulin genes, and (iii) c1 transfer genes. In many cases, these analyses have concluded that horizontal gene transfer (HGT) is likely to have played a role in shaping the taxonomic distribution of these gene families. In this article, we describe several issues with the inference of HGT from such analyses, in particular concerning the considerable uncertainty associated with our estimation of both gene family phylogenies (especially those containing ancient lineage divergences) and the Tree of Life (ToL), and the need for wider use and further development of explicit probabilistic models to compare hypotheses of vertical and horizontal genetic transmission. We suggest that data which is often taken as evidence for the occurrence of ancient HGT events may not be as convincing as is commonly described, and consideration of alternative theories is recommended. While focusing on analyses including PVCs, this discussion is also relevant for inferences of HGT involving other groups of organisms.
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Affiliation(s)
- A. Budd
- European Molecular Biology LaboratoryHeidelberg, Germany
| | - D. P. Devos
- European Molecular Biology LaboratoryHeidelberg, Germany
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21
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Racolta S, Juhl PB, Sirim D, Pleiss J. The triterpene cyclase protein family: a systematic analysis. Proteins 2012; 80:2009-19. [PMID: 22488823 DOI: 10.1002/prot.24089] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/16/2012] [Accepted: 03/20/2012] [Indexed: 01/12/2023]
Abstract
Triterpene cyclases catalyze a broad range of cyclization reactions to form polycyclic triterpenes. Triterpene cyclases that convert squalene to hopene are named squalene-hopene cyclases (SHC) and triterpene cyclases that convert oxidosqualene are named oxidosqualene cyclases (OSC). Many sequences have been published, but there is only one structure available for each of SHCs and OSCs. Although they catalyze a similar reaction, the sequence similarity between SHCs and OSCs is low. A family classification based on phylogenetic analysis revealed 20 homologous families which are grouped into two superfamilies, SHCs and OSCs. Based on this family assignment, the Triterpene Cyclase Engineering Database (TTCED) was established. It integrates available information on sequence and structure of 639 triterpene cyclases as well as on structurally and functionally relevant amino acids. Family specific multiple sequence alignments were generated to identify the functionally relevant residues. Based on sequence alignments, conserved residues in SHCs and OSCs were analyzed and compared to experimentally confirmed mutational data. Functional schematic models of the central cavities of OSCs and SHCs were derived from structure comparison and sequence conservation analysis. These models demonstrate the high similarity of the substrate binding cavity of SHCs and OSCs and the equivalences of the respective residues. The TTCED is a novel source for comprehensive information on the triterpene cyclase family, including a compilation of previously described mutational data. The schematic models present the conservation analysis in a readily available fashion and facilitate the correlation of residues to a specific function or substrate interaction.
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Affiliation(s)
- Silvia Racolta
- Institute of Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
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22
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Fuerst JA, Sagulenko E. Keys to eukaryality: planctomycetes and ancestral evolution of cellular complexity. Front Microbiol 2012; 3:167. [PMID: 22586422 PMCID: PMC3343278 DOI: 10.3389/fmicb.2012.00167] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 04/13/2012] [Indexed: 12/26/2022] Open
Abstract
Planctomycetes are known to display compartmentalization via internal membranes, thus resembling eukaryotes. Significantly, the planctomycete Gemmata obscuriglobus has not only a nuclear region surrounded by a double-membrane, but is also capable of protein uptake via endocytosis. In order to clearly analyze implications for homology of their characters with eukaryotes, a correct understanding of planctomycete structure is an essential starting point. Here we outline the major features of such structure necessary for assessing the case for or against homology with eukaryote cell complexity. We consider an evolutionary model for cell organization involving reductive evolution of Planctomycetes from a complex proto-eukaryote-like last universal common ancestor, and evaluate alternative models for origins of the unique planctomycete cell plan. Overall, the structural and molecular evidence is not consistent with convergent evolution of eukaryote-like features in a bacterium and favors a homologous relationship of Planctomycetes and eukaryotes.
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Affiliation(s)
- John A Fuerst
- School of Chemistry and Molecular Biosciences, The University of Queensland St Lucia, QLD, Australia
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23
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Xue Z, Duan L, Liu D, Guo J, Ge S, Dicks J, ÓMáille P, Osbourn A, Qi X. Divergent evolution of oxidosqualene cyclases in plants. THE NEW PHYTOLOGIST 2012; 193:1022-1038. [PMID: 22150097 DOI: 10.1111/j.1469-8137.2011.03997.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Triterpenes are one of the largest classes of plant metabolites and have important functions. A diverse array of triterpenoid skeletons are synthesized via the isoprenoid pathway by enzymatic cyclization of 2,3-oxidosqualene. The genomes of the lower plants Chlamydomonas reinhardtii and moss (Physcomitrella patens) contain just one oxidosqualene cyclase (OSC) gene (for sterol biosynthesis), whereas the genomes of higher plants contain nine to 16 OSC genes. Here we carry out functional analysis of rice OSCs and rigorous phylogenetic analysis of 96 OSCs from higher plants, including Arabidopsis thaliana, Oryza sativa, Sorghum bicolor and Brachypodium distachyon. The functional analysis identified an amino acid sequence for isoarborinol synthase (OsIAS) (encoded by Os11g35710/OsOSC11) in rice. Our phylogenetic analysis suggests that expansion of OSC members in higher plants has occurred mainly through tandem duplication followed by positive selection and diversifying evolution, and consolidated the previous suggestion that dicot triterpene synthases have been derived from an ancestral lanosterol synthase instead of directly from their cycloartenol synthases. The phylogenetic trees are consistent with the reaction mechanisms of the protosteryl and dammarenyl cations which parent a wide variety of triterpene skeletal types, allowing us to predict the functions of the uncharacterized OSCs.
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Affiliation(s)
- Zheyong Xue
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing 100093, China
| | - Lixin Duan
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing 100093, China
| | - Dan Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing 100093, China
| | - Jie Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing 100093, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing 100093, China
| | - Jo Dicks
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Paul ÓMáille
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Xiaoquan Qi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing 100093, China
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24
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Takishita K, Chikaraishi Y, Leger MM, Kim E, Yabuki A, Ohkouchi N, Roger AJ. Lateral transfer of tetrahymanol-synthesizing genes has allowed multiple diverse eukaryote lineages to independently adapt to environments without oxygen. Biol Direct 2012; 7:5. [PMID: 22296756 PMCID: PMC3317845 DOI: 10.1186/1745-6150-7-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 02/01/2012] [Indexed: 11/10/2022] Open
Abstract
Sterols are key components of eukaryotic cellular membranes that are synthesized by multi-enzyme pathways that require molecular oxygen. Because prokaryotes fundamentally lack sterols, it is unclear how the vast diversity of bacterivorous eukaryotes that inhabit hypoxic environments obtain, or synthesize, sterols. Here we show that tetrahymanol, a triterpenoid that does not require molecular oxygen for its biosynthesis, likely functions as a surrogate of sterol in eukaryotes inhabiting oxygen-poor environments. Genes encoding the tetrahymanol synthesizing enzyme squalene-tetrahymanol cyclase were found from several phylogenetically diverged eukaryotes that live in oxygen-poor environments and appear to have been laterally transferred among such eukaryotes.
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Affiliation(s)
- Kiyotaka Takishita
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa, 237-0061, Japan.
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25
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Abstract
Hopanoids and sterols are members of a large group of cyclic triterpenoic compounds that have important functions in many prokaryotic and eukaryotic organisms. They are biochemically synthesized from linear precursors (squalene, 2,3-oxidosqualene) in only one enzymatic step that is catalyzed by squalene-hopene cyclase (SHC) or oxidosqualene cyclase (OSC). SHCs and OSCs are related in amino acid sequences and probably are derived from a common ancestor. The SHC reaction requires the formation of five ring structures, 13 covalent bonds, and nine stereo centers and therefore is one of the most complex one-step enzymatic reactions. We summarize the knowledge of the properties of triterpene cyclases and details of the reaction mechanism of Alicyclobacillus acidocaldarius SHC. Properties of other SHCs are included.
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Affiliation(s)
| | - Dieter Jendrossek
- Institute for Microbiology, University of Stuttgart, Stuttgart, Germany
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26
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Mizutani M, Ohta D. Diversification of P450 genes during land plant evolution. ANNUAL REVIEW OF PLANT BIOLOGY 2010; 61:291-315. [PMID: 20192745 DOI: 10.1146/annurev-arplant-042809-112305] [Citation(s) in RCA: 231] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plant cytochromes P450 (P450s) catalyze a wide variety of monooxygenation/hydroxylation reactions in primary and secondary metabolism. The number of P450 genes in plant genomes is estimated to be up to 1% of total gene annotations of each plant species. This implies that diversification within P450 gene superfamilies has led to the emergence of new metabolic pathways throughout land plant evolution. The conserved P450 families contribute to chemical defense mechanisms under terrestrial conditions and several are involved in hormone biosynthesis and catabolism. Species-specific P450 families are essential for the biosynthetic pathways of species-specialized metabolites. Future genome-wide analyses of P450 gene clusters and coexpression networks should help both in identifying the functions of many orphan P450s and in understanding the evolution of this versatile group of enzymes.
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Affiliation(s)
- Masaharu Mizutani
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan.
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