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Scanlan JL, Robin C. Phylogenomics of the Ecdysteroid Kinase-like (EcKL) Gene Family in Insects Highlights Roles in Both Steroid Hormone Metabolism and Detoxification. Genome Biol Evol 2024; 16:evae019. [PMID: 38291829 PMCID: PMC10859841 DOI: 10.1093/gbe/evae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/21/2023] [Accepted: 01/23/2024] [Indexed: 02/01/2024] Open
Abstract
The evolutionary dynamics of large gene families can offer important insights into the functions of their individual members. While the ecdysteroid kinase-like (EcKL) gene family has previously been linked to the metabolism of both steroid molting hormones and xenobiotic toxins, the functions of nearly all EcKL genes are unknown, and there is little information on their evolution across all insects. Here, we perform comprehensive phylogenetic analyses on a manually annotated set of EcKL genes from 140 insect genomes, revealing the gene family is comprised of at least 13 subfamilies that differ in retention and stability. Our results show the only two genes known to encode ecdysteroid kinases belong to different subfamilies and therefore ecdysteroid metabolism functions must be spread throughout the EcKL family. We provide comparative phylogenomic evidence that EcKLs are involved in detoxification across insects, with positive associations between family size and dietary chemical complexity, and we also find similar evidence for the cytochrome P450 and glutathione S-transferase gene families. Unexpectedly, we find that the size of the clade containing a known ecdysteroid kinase is positively associated with host plant taxonomic diversity in Lepidoptera, possibly suggesting multiple functional shifts between hormone and xenobiotic metabolism. Our evolutionary analyses provide hypotheses of function and a robust framework for future experimental studies of the EcKL gene family. They also open promising new avenues for exploring the genomic basis of dietary adaptation in insects, including the classically studied coevolution of butterflies with their host plants.
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Affiliation(s)
- Jack L Scanlan
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Charles Robin
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
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Sanchez Granel ML, Siburu NG, Fricska A, Maldonado LL, Gargiulo LB, Nudel CB, Uttaro AD, Nusblat AD. A novel Tetrahymena thermophila sterol C-22 desaturase belongs to the Fatty Acid Hydroxylase/Desaturase superfamily. J Biol Chem 2022; 298:102397. [PMID: 35988640 PMCID: PMC9485055 DOI: 10.1016/j.jbc.2022.102397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/09/2022] [Accepted: 08/15/2022] [Indexed: 11/27/2022] Open
Abstract
Sterols in eukaryotic cells play important roles in modulating membrane fluidity and in cell signaling and trafficking. During evolution, a combination of gene losses and acquisitions gave rise to an extraordinary diversity of sterols in different organisms. The sterol C-22 desaturase identified in plants and fungi as a cytochrome P-450 monooxygenase evolved from the first eukaryotic cytochrome P450 and was lost in many lineages. Although the ciliate Tetrahymena thermophila desaturates sterols at the C-22 position, no cytochrome P-450 orthologs are present in the genome. Here, we aim to identify the genes responsible for the desaturation as well as their probable origin. We used gene knockout and yeast heterologous expression approaches to identify two putative genes, retrieved from a previous transcriptomic analysis, as sterol C-22 desaturases. Furthermore, we demonstrate using bioinformatics and evolutionary analyses that both genes encode a novel type of sterol C-22 desaturase that belongs to the large fatty acid hydroxylase/desaturase superfamily and the genes originated by genetic duplication prior to functional diversification. These results stress the widespread existence of nonhomologous isofunctional enzymes among different lineages of the tree of life as well as the suitability for the use of T. thermophila as a valuable model to investigate the evolutionary process of large enzyme families.
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Affiliation(s)
- María L Sanchez Granel
- Instituto de Nanobiotecnología (NANOBIOTEC), CONICET, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina
| | - Nicolás G Siburu
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda s/n, S2000FHQ, Rosario, Argentina
| | - Annamária Fricska
- Instituto de Nanobiotecnología (NANOBIOTEC), CONICET, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina
| | - Lucas L Maldonado
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), CONICET, Facultad de Medicina, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina
| | - Laura B Gargiulo
- Instituto de Nanobiotecnología (NANOBIOTEC), CONICET, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina
| | - Clara B Nudel
- Instituto de Nanobiotecnología (NANOBIOTEC), CONICET, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina
| | - Antonio D Uttaro
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda s/n, S2000FHQ, Rosario, Argentina.
| | - Alejandro D Nusblat
- Instituto de Nanobiotecnología (NANOBIOTEC), CONICET, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina.
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Rau EM, Aasen IM, Ertesvåg H. A non-canonical Δ9-desaturase synthesizing palmitoleic acid identified in the thraustochytrid Aurantiochytrium sp. T66. Appl Microbiol Biotechnol 2021; 105:5931-5941. [PMID: 34292356 PMCID: PMC8390409 DOI: 10.1007/s00253-021-11425-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/14/2021] [Accepted: 06/22/2021] [Indexed: 11/28/2022]
Abstract
Abstract Thraustochytrids are oleaginous marine eukaryotic microbes currently used to produce the essential omega-3 fatty acid docosahexaenoic acid (DHA, C22:6 n-3). To improve the production of this essential fatty acid by strain engineering, it is important to deeply understand how thraustochytrids synthesize fatty acids. While DHA is synthesized by a dedicated enzyme complex, other fatty acids are probably synthesized by the fatty acid synthase, followed by desaturases and elongases. Which unsaturated fatty acids are produced differs between different thraustochytrid genera and species; for example, Aurantiochytrium sp. T66, but not Aurantiochytrium limacinum SR21, synthesizes palmitoleic acid (C16:1 n-7) and vaccenic acid (C18:1 n-7). How strain T66 can produce these fatty acids has not been known, because BLAST analyses suggest that strain T66 does not encode any Δ9-desaturase-like enzyme. However, it does encode one Δ12-desaturase-like enzyme. In this study, the latter enzyme was expressed in A. limacinum SR21, and both C16:1 n-7 and C18:1 n-7 could be detected in the transgenic cells. Our results show that this desaturase, annotated T66Des9, is a Δ9-desaturase accepting C16:0 as a substrate. Phylogenetic studies indicate that the corresponding gene probably has evolved from a Δ12-desaturase-encoding gene. This possibility has not been reported earlier and is important to consider when one tries to deduce the potential a given organism has for producing unsaturated fatty acids based on its genome sequence alone. Key points • In thraustochytrids, automatic gene annotation does not always explain the fatty acids produced. • T66Des9 is shown to synthesize palmitoleic acid (C16:1 n-7). • T66des9 has probably evolved from Δ12-desaturase-encoding genes. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11425-5.
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Affiliation(s)
- E-Ming Rau
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Inga Marie Aasen
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Helga Ertesvåg
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway.
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Nachtschatt M, Okada S, Speight R. Integral Membrane Fatty Acid Desaturases: A Review of Biochemical, Structural, and Biotechnological Advances. EUR J LIPID SCI TECH 2020. [DOI: 10.1002/ejlt.202000181] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Matthias Nachtschatt
- Commonwealth Scientific and Industrial Research Organisation Clunies Ross St. Canberra ACT 2601 Australia
- Queensland University of Technology 2 George St. Brisbane QLD 4000 Australia
| | - Shoko Okada
- Commonwealth Scientific and Industrial Research Organisation Clunies Ross St. Canberra ACT 2601 Australia
| | - Robert Speight
- Queensland University of Technology 2 George St. Brisbane QLD 4000 Australia
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Jermiin LS, Catullo RA, Holland BR. A new phylogenetic protocol: dealing with model misspecification and confirmation bias in molecular phylogenetics. NAR Genom Bioinform 2020; 2:lqaa041. [PMID: 33575594 PMCID: PMC7671319 DOI: 10.1093/nargab/lqaa041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/18/2020] [Accepted: 06/04/2020] [Indexed: 12/15/2022] Open
Abstract
Molecular phylogenetics plays a key role in comparative genomics and has increasingly significant impacts on science, industry, government, public health and society. In this paper, we posit that the current phylogenetic protocol is missing two critical steps, and that their absence allows model misspecification and confirmation bias to unduly influence phylogenetic estimates. Based on the potential offered by well-established but under-used procedures, such as assessment of phylogenetic assumptions and tests of goodness of fit, we introduce a new phylogenetic protocol that will reduce confirmation bias and increase the accuracy of phylogenetic estimates.
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Affiliation(s)
- Lars S Jermiin
- CSIRO Land & Water, Canberra, ACT 2601, Australia
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
- School of Biology & Environment Science, University College Dublin, Belfield, Dublin 4, Ireland
- Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Renee A Catullo
- CSIRO Land & Water, Canberra, ACT 2601, Australia
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
- School of Science and Health & Hawkesbury Institute of the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Barbara R Holland
- School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia
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Li D, Damry AM, Petrie JR, Vanhercke T, Singh SP, Jackson CJ. Consensus Mutagenesis and Ancestral Reconstruction Provide Insight into the Substrate Specificity and Evolution of the Front-End Δ6-Desaturase Family. Biochemistry 2020; 59:1398-1409. [DOI: 10.1021/acs.biochem.0c00110] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dongdi Li
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Adam M. Damry
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - James R. Petrie
- CSIRO Agriculture Flagship, Black Mountain Laboratories, Canberra, ACT 2601, Australia
| | - Thomas Vanhercke
- CSIRO Agriculture Flagship, Black Mountain Laboratories, Canberra, ACT 2601, Australia
| | - Surinder P. Singh
- CSIRO Agriculture Flagship, Black Mountain Laboratories, Canberra, ACT 2601, Australia
| | - Colin J. Jackson
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, 19 Eastern Road, North Ryde, Sydney, NSW 2109, Australia
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Sanchez Granel ML, Cánepa C, Cid NG, Navarro JC, Monroig Ó, Verstraeten SV, Nudel CB, Nusblat AD. Gene identification and functional characterization of a Δ12 fatty acid desaturase in Tetrahymena thermophila and its influence in homeoviscous adaptation to low temperature. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:1644-1655. [PMID: 31421180 DOI: 10.1016/j.bbalip.2019.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 08/07/2019] [Accepted: 08/10/2019] [Indexed: 01/26/2023]
Abstract
Homeoviscous adaptation in poikilotherms is based in the regulation of the level of desaturation of fatty acids, variation in phospholipids head groups and sterol content in the membrane lipids, in order to maintain the membrane fluidity in response to changes in environmental temperature. Increased proportion of unsaturated fatty acids is thought to be the main response to low-temperature acclimation, which is mostly achieved by fatty acid desaturases. Genome analysis of the ciliate Tetrahymena thermophila and a gene knockout approach has allowed us to identify one Δ12 FAD and to study its activity in the original host and in a yeast heterologous expression system. The "PUFA index" -relative content of polyunsaturated fatty acids compared to the sum of saturated and monounsaturated fatty acid content- was ~57% lower at 15 °C and 35 °C in the Δ12 FAD gene knockout strain (KOΔ12) compared to WT strain. We characterized the role of T. thermophila Δ12 FAD on homeoviscous adaptation and analyzed its involvement in cellular growth, cold stress response, and membrane fluidity, as well as its expression pattern during temperature shifts. Although these alterations allowed normal growth in the KOΔ12 strain at 30 °C or higher temperatures, growth was impaired at temperatures of 20 °C or lower, where homeoviscous adaptation is impaired. These results stress the importance of Δ12 FAD in the regulation of cold adaptation processes, as well as the suitability of T. thermophila as a valuable model to investigate the regulation of membrane lipids and evolutionary conservation and divergence of the underlying mechanisms.
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Affiliation(s)
- Maria L Sanchez Granel
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Nanobiotecnología (NANOBIOTEC), Facultad de Farmacia y Bioquímica, Junín, 956, C1113AAD Ciudad Autónoma de Buenos Aires, Argentina
| | - Camila Cánepa
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones Biomédicas en Retrovirus y SIDA, Facultad de Medicina, Paraguay 2155, C1121ABG Ciudad Autónoma de Buenos Aires, Argentina
| | - Nicolas G Cid
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Nanobiotecnología (NANOBIOTEC), Facultad de Farmacia y Bioquímica, Junín, 956, C1113AAD Ciudad Autónoma de Buenos Aires, Argentina
| | - Juan C Navarro
- Instituto de Acuicultura Torre de la Sal, CSIC (IATS-CSIC), Ribera de Cabanes, 12595, Castellón, Spain
| | - Óscar Monroig
- Instituto de Acuicultura Torre de la Sal, CSIC (IATS-CSIC), Ribera de Cabanes, 12595, Castellón, Spain
| | - Sandra V Verstraeten
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Facultad de Farmacia y Bioquímica, Paraguay 2155, C1121ABG Ciudad Autónoma de Buenos Aires, Argentina
| | - Clara B Nudel
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Nanobiotecnología (NANOBIOTEC), Facultad de Farmacia y Bioquímica, Junín, 956, C1113AAD Ciudad Autónoma de Buenos Aires, Argentina
| | - Alejandro D Nusblat
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Nanobiotecnología (NANOBIOTEC), Facultad de Farmacia y Bioquímica, Junín, 956, C1113AAD Ciudad Autónoma de Buenos Aires, Argentina.
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