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Li Z, Xue AZ, Maeda GP, Li Y, Nabity PD, Moran NA. Phylloxera and aphids show distinct features of genome evolution despite similar reproductive modes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.555181. [PMID: 37693541 PMCID: PMC10491136 DOI: 10.1101/2023.08.28.555181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Genomes of aphids (family Aphididae) show several unusual evolutionary patterns. In particular, within the XO sex determination system of aphids, the X chromosome exhibits a lower rate of interchromosomal rearrangements, fewer highly expressed genes, and faster evolution at nonsynonymous sites compared to the autosomes. In contrast, other hemipteran lineages have similar rates of interchromosomal rearrangement for autosomes and X chromosomes. One possible explanation for these differences is the aphid's life cycle of cyclical parthenogenesis, where multiple asexual generations alternate with one sexual generation. If true, we should see similar features in the genomes of Phylloxeridae, an outgroup of aphids which also undergoes cyclical parthenogenesis. To investigate this, we generated a chromosome-level assembly for the grape phylloxera, an agriculturally important species of Phylloxeridae, and identified its single X chromosome. We then performed synteny analysis using the phylloxerid genome and 30 high-quality genomes of aphids and other hemipteran species. Unexpectedly, we found that the phylloxera does not share aphids' patterns of chromosome evolution. By estimating interchromosomal rearrangement rates on an absolute time scale, we found that rates are elevated for aphid autosomes compared to their X chromosomes, but this pattern does not extend to the phylloxera branch. Potentially, the conservation of X chromosome gene content is due to selection on XO males that appear in the sexual generation. We also examined gene duplication patterns across Hemiptera and uncovered horizontal gene transfer events contributing to phylloxera evolution.
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Seng S, Ponce GE, Andreas P, Kisiala A, De Clerck-Floate R, Miller DG, Chen MS, Price PW, Tooker JF, Emery RJN, Connor EF. Abscisic Acid: A Potential Secreted Effector Synthesized by Phytophagous Insects for Host-Plant Manipulation. INSECTS 2023; 14:489. [PMID: 37367305 PMCID: PMC10299484 DOI: 10.3390/insects14060489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/18/2023] [Accepted: 05/18/2023] [Indexed: 06/28/2023]
Abstract
Abscisic acid (ABA) is an isoprenoid-derived plant signaling molecule involved in a wide variety of plant processes, including facets of growth and development as well as responses to abiotic and biotic stress. ABA had previously been reported in a wide variety of animals, including insects and humans. We used high-performance liquid chromatography-electrospray ionization tandem mass spectrometry (HPLC-(ESI)-MS/MS) to examine concentrations of ABA in 17 species of phytophagous insects, including gall- and non-gall-inducing species from all insect orders with species known to induce plant galls: Thysanoptera, Hemiptera, Lepidoptera, Coleoptera, Diptera, and Hymenoptera. We found ABA in insect species in all six orders, in both gall-inducing and non-gall-inducing species, with no tendency for gall-inducing insects to have higher concentrations. The concentrations of ABA in insects often markedly exceeded those typically found in plants, suggesting it is highly improbable that insects obtain all their ABA from their host plant via consumption and sequestration. As a follow-up, we used immunohistochemistry to determine that ABA localizes to the salivary glands in the larvae of the gall-inducing Eurosta solidaginis (Diptera: Tephritidae). The high concentrations of ABA, combined with its localization to salivary glands, suggest that insects are synthesizing and secreting ABA to manipulate their host plants. The pervasiveness of ABA among both gall- and non-gall-inducing insects and our current knowledge of the role of ABA in plant processes suggest that insects are using ABA to manipulate source-sink mechanisms of nutrient allocation or to suppress host-plant defenses. ABA joins the triumvirate of phytohormones, along with cytokinins (CKs) and indole-3-acetic acid (IAA), that are abundant, widespread, and localized to glandular organs in insects and used to manipulate host plants.
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Affiliation(s)
- Stephannie Seng
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA;
| | - Gabriela E. Ponce
- Department of Entomology, The Pennsylvania State University, University Park, PA 16802, USA; (G.E.P.); (J.F.T.)
| | - Peter Andreas
- Department of Biology, Trent University, Peterborough, ON K9J 7B8, Canada; (P.A.); (A.K.); (R.J.N.E.)
| | - Anna Kisiala
- Department of Biology, Trent University, Peterborough, ON K9J 7B8, Canada; (P.A.); (A.K.); (R.J.N.E.)
| | | | - Donald G. Miller
- Department of Biological Sciences, California State University, Chico, CA 95929, USA;
| | - Ming-Shun Chen
- USDA-ARS and Department of Entomology, Kansas State University, Manhattan, KS 66506, USA;
| | - Peter W. Price
- Department of Ecology and Evolutionary Biology, Northern Arizona University, Flagstaff, AZ 86001, USA;
| | - John F. Tooker
- Department of Entomology, The Pennsylvania State University, University Park, PA 16802, USA; (G.E.P.); (J.F.T.)
| | - R. J. Neil Emery
- Department of Biology, Trent University, Peterborough, ON K9J 7B8, Canada; (P.A.); (A.K.); (R.J.N.E.)
| | - Edward F. Connor
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA;
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Trissi N, Troczka BJ, Ozsanlav-Harris L, Singh KS, Mallott M, Aishwarya V, O'Reilly A, Bass C, Wilding CS. Differential regulation of the Tor gene homolog drives the red/green pigmentation phenotype in the aphid Myzuspersicae. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 153:103896. [PMID: 36587809 DOI: 10.1016/j.ibmb.2022.103896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/22/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
In some aphid species, intraspecific variation in body colour is caused by differential carotenoid content: whilst green aphids contain only yellow carotenoids (β-, γ-, and β,γ-carotenes), red aphids additionally possess red carotenoids (torulene and 3,4-didehydrolycopene). Unusually, within animals who typically obtain carotenoids from their diet, ancestral horizontal gene transfer of carotenoid biosynthetic genes from fungi (followed by gene duplication), have imbued aphids with the intrinsic gene repertoire necessary to biosynthesise carotenoids. In the pea aphid, Acyrthosiphon pisum a lycopene (phytoene) desaturase gene (Tor) underpins the red/green phenotype, with this locus present in heterozygous form in red individuals but absent in green aphids, resulting in them being unable to convert lycopene into the red compounds 3,4-didehydrolycopene and torulene. The green peach aphid, Myzus persicae, separated from the pea aphid for ≈45MY also exists as distinct colour variable morphs, with both red and green individuals present. Here, we examined genomic data for both red and green morphs of M. persicae and identified an enlarged (compared to A. pisum) repertoire of 16 carotenoid biosynthetic genes (11 carotenoid desaturases and five carotenoid cyclase/synthase genes). From these, we identify the homolog of A. pisum Tor (here called carotene desaturase 2 or CDE-2) and show through 3D modelling that this homolog can accommodate the torulene precursor lycopene and, through RNA knockdown feeding experiments, demonstrate that disabling CDE-2 expression in red M. persicae clones results in green-coloured offspring. Unlike in A. pisum, we show that functional CDE-2 is present in the genomes of both red and green aphids. However, expression differences between the two colour morphs (350-700 fold CDE-2 overexpression in red clones), potentially driven by variants identified in upstream putative regulatory elements, underpin this phenotype. Thus, whilst aphids have a common origin of their carotenoid biosynthetic pathway, two aphid species separated for over 40MY have evolved very different drivers of intraspecific colour variation.
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Affiliation(s)
- Nasser Trissi
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Bartlomiej J Troczka
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Luke Ozsanlav-Harris
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Kumar Saurabh Singh
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Mark Mallott
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | | | - Andrias O'Reilly
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Chris Bass
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK.
| | - Craig S Wilding
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK.
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Tan K, Zhang H, Zheng H. Carotenoid content and composition: A special focus on commercially important fish and shellfish. Crit Rev Food Sci Nutr 2022; 64:544-561. [PMID: 35930379 DOI: 10.1080/10408398.2022.2106937] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Carotenoids are natural pigments that provide many health benefits to living organisms. Although terrestrial plants are the major dietary source of carotenoids for humans, aquatic animals (especially fish and shellfish) are equally important because they are rich in certain important carotenoids lacking in fruits and vegetables. Although extensive research has focused on exploring the carotenoid content and composition in fish and shellfish, this information is poorly organized. This paper reviews the scientific evidence for the carotenoid content and composition in fish and shellfish. It makes serious attempts to summarize the relevant data published on specific research questions in order to improve the understanding of various evidence to clarify the research status of carotenoids in fish and shellfish and defining topics for future studies. From the analysis of published data, it is obvious that most fish and shellfish are rich in complex carotenoids (e.g. astaxanthin, fucoxanthin, fucoxanthinol, lutein). These carotenoids have stronger antioxidant effect, higher efficiency in removing the singlet oxygen and the peroxyl radicals, and have a variety of health benefits. Carotenoid levels in fish and shellfish depend on genotype, climatic conditions of the production area, storage and cooking methods. However, the information of the bioavailability of fish/shellfish carotenoids to human is very limited, which hinders the actual contributions to health. The findings of this study can be used as a guide to select appropriate fish and shellfish as dietary sources of carotenoids, and provide information about potential fish and shellfish species for aquaculture to produce carotenoids to meet part of the growing demand for natural carotenoids.
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Affiliation(s)
- Karsoon Tan
- Key Laboratory of Marine Biotechnology of Guangdong Province, Marine Sciences Institute, Shantou University, Shantou, China
- Mariculture Research Center for Subtropical Shellfish & Algae of Guangdong Province, Shantou, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Hongkuan Zhang
- Key Laboratory of Marine Biotechnology of Guangdong Province, Marine Sciences Institute, Shantou University, Shantou, China
- Mariculture Research Center for Subtropical Shellfish & Algae of Guangdong Province, Shantou, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Huaiping Zheng
- Key Laboratory of Marine Biotechnology of Guangdong Province, Marine Sciences Institute, Shantou University, Shantou, China
- Mariculture Research Center for Subtropical Shellfish & Algae of Guangdong Province, Shantou, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
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Lyu X, Lyu Y, Yu H, Chen W, Ye L, Yang R. Biotechnological advances for improving natural pigment production: a state-of-the-art review. BIORESOUR BIOPROCESS 2022; 9:8. [PMID: 38647847 PMCID: PMC10992905 DOI: 10.1186/s40643-022-00497-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/17/2022] [Indexed: 12/14/2022] Open
Abstract
In current years, natural pigments are facing a fast-growing global market due to the increase of people's awareness of health and the discovery of novel pharmacological effects of various natural pigments, e.g., carotenoids, flavonoids, and curcuminoids. However, the traditional production approaches are source-dependent and generally subject to the low contents of target pigment compounds. In order to scale-up industrial production, many efforts have been devoted to increasing pigment production from natural producers, via development of both in vitro plant cell/tissue culture systems, as well as optimization of microbial cultivation approaches. Moreover, synthetic biology has opened the door for heterologous biosynthesis of pigments via design and re-construction of novel biological modules as well as biological systems in bio-platforms. In this review, the innovative methods and strategies for optimization and engineering of both native and heterologous producers of natural pigments are comprehensively summarized. Current progress in the production of several representative high-value natural pigments is also presented; and the remaining challenges and future perspectives are discussed.
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Affiliation(s)
- Xiaomei Lyu
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Yan Lyu
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Hongwei Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, People's Republic of China
| | - WeiNing Chen
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, Singapore, 637459, Singapore
| | - Lidan Ye
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, People's Republic of China.
| | - Ruijin Yang
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.
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Abstract
Carotenoids constitute an essential dietary component of animals and other non-carotenogenic species which use these pigments in both their modified and unmodified forms. Animals utilize uncleaved carotenoids to mitigate light damage and oxidative stress and to signal fitness and health. Carotenoids also serve as precursors of apocarotenoids including retinol, and its retinoid metabolites, which carry out essential functions in animals by forming the visual chromophore 11-cis-retinaldehyde. Retinoids, such as all-trans-retinoic acid, can also act as ligands of nuclear hormone receptors. The fact that enzymes and biochemical pathways responsible for the metabolism of carotenoids in animals bear resemblance to the ones in plants and other carotenogenic species suggests an evolutionary relationship. We will explore some of the modes of transmission of carotenoid genes from carotenogenic species to metazoans. This apparent relationship has been successfully exploited in the past to identify and characterize new carotenoid and retinoid modifying enzymes. We will review approaches used to identify putative animal carotenoid enzymes, and we will describe methods used to functionally validate and analyze the biochemistry of carotenoid modifying enzymes encoded by animals.
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Affiliation(s)
- Alexander R Moise
- Northern Ontario School of Medicine, Sudbury, ON, Canada; Department of Chemistry and Biochemistry, Biology and Biomolecular Sciences Program, Laurentian University, Sudbury, ON, Canada.
| | - Sepalika Bandara
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Johannes von Lintig
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
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Takemura M, Maoka T, Koyanagi T, Kawase N, Nishida R, Tsuchida T, Hironaka M, Ueda T, Misawa N. Elucidation of the whole carotenoid biosynthetic pathway of aphids at the gene level and arthropodal food chain involving aphids and the red dragonfly. BMC ZOOL 2021; 6:19. [PMID: 37170139 PMCID: PMC10127341 DOI: 10.1186/s40850-021-00082-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 04/29/2021] [Indexed: 02/01/2023] Open
Abstract
Abstract
Background
Aphids can be positioned as robust pest insects in farming and as ones of the model organisms for arthropods in molecular biology. Carotenoids are pigments that protect organisms from photooxidative damage caused by excessive light. Aphids were shown to possess genes of fungal origin for carotenoid biosynthesis, whereas a little knowledge was available about the functions of the genes and the biosynthetic pathway. Even carotenoid species contained in aphids were not enough understood. Main purpose of this study is to clarify these insufficient findings.
Results
The whole carotenoid biosynthetic pathway of the pea aphid (Acyrthosiphon pisum) was elucidated at the gene level, through comprehensive functional analysis of its carotenogenic genes, using Escherichia coli that synthesized carotenoid substrates, along with structural and quantitative analysis of carotenoids from various aphid species. Four genes were needed to synthesize all carotenoids accumulated in aphids from geranylgeranyl diphosphate. The tor gene mediated desaturation reaction from phytoene to 3,4-didehydrolycopene. It was revealed that a gene designated ApCrtYB3, which was considered to have functionally evolved in aphids, can convert lycopene into uncommon carotenoids with the γ-ring such as (6′S)-β,γ-carotene and γ,γ-carotene. We further demonstrated that the atypical carotenoids work as ecological indicators for estimating the food chain from aphids to predatory arthropods, and showed that aphids contributed with significant levels to the food chain from insect herbivores to several predatory arthropods, i.e., the red dragonfly (Sympetrum frequens; adults), seven-spotted ladybird (Coccinella septempunctata), and two spiders, Oxyopes sertatus and Nephila clavata. Gut microflora of the dragonfly (mature adults) was also found to include endosymbiotic bacteria such as Serratia symbiotica specific to the black bean aphid (Aphis fabae).
Conclusions
We revealed the whole carotenoid biosynthetic pathway of aphids, including functional identification of the corresponding genes. Subsequently, we showed that arthropodal food chain can be estimated using the uncommon carotenoids of aphids as ecological indicators. This result indicated that aphids made significant contributions to the food chain of several predatory arthropods including the red-dragonfly adults. Aphids are likely to be positioned as an important “phytochemicals” source for some predatory insects and arachnids, which are often active under bright sunlight.
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Jockusch EL, Fisher CR. Something old, something new, something borrowed, something red: the origin of ecologically relevant novelties in Hemiptera. Curr Opin Genet Dev 2021; 69:154-162. [PMID: 34058515 DOI: 10.1016/j.gde.2021.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/19/2021] [Accepted: 04/15/2021] [Indexed: 10/21/2022]
Abstract
Comparative transcriptomics, applied in an evolutionary context, has transformed the possibilities for studying phenotypic evolution in non-model taxa. We review recent discoveries about the development of novel, ecologically relevant phenotypes in hemipteran insects. These discoveries highlight the diverse genomic substrates of novelty: 'something old', when novelty results from changes in the regulation of existing genes or gene duplication; 'something new', wherein lineage-restricted genes contribute to the evolution of new phenotypes; and 'something borrowed', showcasing contributions of horizontal gene transfer to the evolution of novelty, including carotenoid synthesis (resulting in 'something red'). These findings show the power and flexibility of comparative transcriptomic approaches for expanding beyond the 'toolkit' model for the evolution of development. We conclude by raising questions about the relationship between new genes and new traits and outlining a research framework for answering them in Hemiptera.
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Affiliation(s)
- Elizabeth L Jockusch
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Rd., U-3043, Storrs, CT 06269, USA.
| | - Cera R Fisher
- Cornell University, Department of Entomology, 2126 Comstock Hall, Ithaca, NY 14853, USA
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Misawa N, Takemura M, Maoka T. Carotenoid Biosynthesis in Animals: Case of Arthropods. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1261:217-220. [PMID: 33783744 DOI: 10.1007/978-981-15-7360-6_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
All the organisms that belong to the animal kingdom had been believed not to synthesize carotenoids de novo. However, several groups of arthropods, which contain aphids, spider mites, and flies belonging to the family Cecidomyiidae, have been unexpectedly shown to possess carotenoid biosynthesis genes of fungal origin since 2010. On the other hand, few reports have shown direct evidence corroborating the catalytic functions of the enzymes that the carotenogenic genes encode. In the present review, we want to overview the carotenoid biosynthetic pathway of the pea aphid (Acyrthosiphon pisum), which was elucidated through functional analysis of carotenogenic genes that exist on its genome using Escherichia coli that accumulates carotenoid substrates, in addition to carotenoid biosynthesis in the other carotenogenic arthropods.
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Affiliation(s)
- Norihiko Misawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Ishikawa, Japan.
| | - Miho Takemura
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Ishikawa, Japan
| | - Takashi Maoka
- Research Institute for Production Development, Kyoto, Japan
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10
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Whitefly genomes contain ribotoxin coding genes acquired from plants. Sci Rep 2020; 10:15503. [PMID: 32968092 PMCID: PMC7511414 DOI: 10.1038/s41598-020-72267-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 08/28/2020] [Indexed: 11/21/2022] Open
Abstract
Ribosome inactivating proteins (RIPs) are RNA N-glycosidases that depurinate a specific adenine residue in the conserved sarcin/ricin loop of 28S rRNA. These enzymes are widely distributed among plants and bacteria. Previously, we have described for the first time RIP genes in mosquitoes belonging to the Culicidae family. We showed that these genes are derived from a single event of horizontal gene transfer (HGT) from a prokaryotic donor. Mosquito RIP genes are evolving under purifying selection, strongly suggesting that these toxins have acquired a functional role. In this work, we show the existence of two RIP encoding genes in the genome of the whitefly Bemisia tabaci, a hemiptera species belonging to the Aleyrodidae family distantly related to mosquitoes. Contamination artifacts were ruled out analyzing three independent B. tabaci genome databases. In contrast to mosquito RIPs, whitefly genes harbor introns and according to transcriptomic evidence are transcribed and spliced. Phylogeny and the taxonomic distribution strongly support that whitefly RIP genes are derived from an independent HGT event from a plant source. These results, along with our previous description of RIPs in Diptera, suggest that the acquired genes are functional in these insects and confer some fitness advantage.
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Rispe C, Legeai F, Nabity PD, Fernández R, Arora AK, Baa-Puyoulet P, Banfill CR, Bao L, Barberà M, Bouallègue M, Bretaudeau A, Brisson JA, Calevro F, Capy P, Catrice O, Chertemps T, Couture C, Delière L, Douglas AE, Dufault-Thompson K, Escuer P, Feng H, Forneck A, Gabaldón T, Guigó R, Hilliou F, Hinojosa-Alvarez S, Hsiao YM, Hudaverdian S, Jacquin-Joly E, James EB, Johnston S, Joubard B, Le Goff G, Le Trionnaire G, Librado P, Liu S, Lombaert E, Lu HL, Maïbèche M, Makni M, Marcet-Houben M, Martínez-Torres D, Meslin C, Montagné N, Moran NA, Papura D, Parisot N, Rahbé Y, Lopes MR, Ripoll-Cladellas A, Robin S, Roques C, Roux P, Rozas J, Sánchez-Gracia A, Sánchez-Herrero JF, Santesmasses D, Scatoni I, Serre RF, Tang M, Tian W, Umina PA, van Munster M, Vincent-Monégat C, Wemmer J, Wilson ACC, Zhang Y, Zhao C, Zhao J, Zhao S, Zhou X, Delmotte F, Tagu D. The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest. BMC Biol 2020; 18:90. [PMID: 32698880 PMCID: PMC7376646 DOI: 10.1186/s12915-020-00820-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 06/22/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Although native to North America, the invasion of the aphid-like grape phylloxera Daktulosphaira vitifoliae across the globe altered the course of grape cultivation. For the past 150 years, viticulture relied on grafting-resistant North American Vitis species as rootstocks, thereby limiting genetic stocks tolerant to other stressors such as pathogens and climate change. Limited understanding of the insect genetics resulted in successive outbreaks across the globe when rootstocks failed. Here we report the 294-Mb genome of D. vitifoliae as a basic tool to understand host plant manipulation, nutritional endosymbiosis, and enhance global viticulture. RESULTS Using a combination of genome, RNA, and population resequencing, we found grape phylloxera showed high duplication rates since its common ancestor with aphids, but similarity in most metabolic genes, despite lacking obligate nutritional symbioses and feeding from parenchyma. Similarly, no enrichment occurred in development genes in relation to viviparity. However, phylloxera evolved > 2700 unique genes that resemble putative effectors and are active during feeding. Population sequencing revealed the global invasion began from the upper Mississippi River in North America, spread to Europe and from there to the rest of the world. CONCLUSIONS The grape phylloxera genome reveals genetic architecture relative to the evolution of nutritional endosymbiosis, viviparity, and herbivory. The extraordinary expansion in effector genes also suggests novel adaptations to plant feeding and how insects induce complex plant phenotypes, for instance galls. Finally, our understanding of the origin of this invasive species and its genome provide genetics resources to alleviate rootstock bottlenecks restricting the advancement of viticulture.
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Affiliation(s)
| | - Fabrice Legeai
- BIPAA, IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
| | - Paul D. Nabity
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Rosa Fernández
- Bioinformatics and Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003 Barcelona, Spain
- Present address: Institute of Evolutionary Biology (CSIC-UPF), Passeig marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - Arinder K. Arora
- Department of Entomology, Cornell University, Ithaca, NY 14853 USA
| | | | | | | | - Miquel Barberà
- Institut de Biologia Integrativa de Sistemes, Parc Cientific Universitat de Valencia, C/ Catedrático José Beltrán n° 2, 46980 Paterna, València Spain
| | - Maryem Bouallègue
- Université de Tunis El Manar, Faculté des Sciences de Tunis, LR01ES05 Biochimie et Biotechnologie, 2092 Tunis, Tunisia
| | - Anthony Bretaudeau
- BIPAA, IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
| | | | - Federica Calevro
- Univ Lyon, INSA-Lyon, INRAE, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Pierre Capy
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Univ. Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Olivier Catrice
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Thomas Chertemps
- Sorbonne Université, UPEC, Université Paris 7, INRAE, CNRS, IRD, Institute of Ecology and Environmental Sciences, Paris, France
| | - Carole Couture
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d’Ornon, France
| | - Laurent Delière
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d’Ornon, France
| | - Angela E. Douglas
- Department of Entomology, Cornell University, Ithaca, NY 14853 USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853 USA
| | - Keith Dufault-Thompson
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI USA
| | - Paula Escuer
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Honglin Feng
- Department of Biology, University of Miami, Coral Gables, USA
- Current affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, USA
| | | | - Toni Gabaldón
- Bioinformatics and Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Frédérique Hilliou
- Université Côte d’Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Silvia Hinojosa-Alvarez
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Yi-min Hsiao
- Institute of Biotechnology and Department of Entomology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Present affiliation: Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Sylvie Hudaverdian
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
| | | | - Edward B. James
- Department of Biology, University of Miami, Coral Gables, FL 33146 USA
| | - Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843 USA
| | | | - Gaëlle Le Goff
- Université Côte d’Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Gaël Le Trionnaire
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
| | - Pablo Librado
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Shanlin Liu
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083 Guangdong Province People’s Republic of China
- BGI-Shenzhen, Shenzhen, 518083 Guangdong Province People’s Republic of China
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Eric Lombaert
- Université Côte d’Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Hsiao-ling Lu
- Department of Post-Modern Agriculture, MingDao University, Changhua, Taiwan
| | - Martine Maïbèche
- Sorbonne Université, UPEC, Université Paris 7, INRAE, CNRS, IRD, Institute of Ecology and Environmental Sciences, Paris, France
| | - Mohamed Makni
- Université de Tunis El Manar, Faculté des Sciences de Tunis, LR01ES05 Biochimie et Biotechnologie, 2092 Tunis, Tunisia
| | - Marina Marcet-Houben
- Bioinformatics and Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003 Barcelona, Spain
| | - David Martínez-Torres
- Institut de Biologia Integrativa de Sistemes, Parc Cientific Universitat de Valencia, C/ Catedrático José Beltrán n° 2, 46980 Paterna, València Spain
| | - Camille Meslin
- INRAE, Institute of Ecology and Environmental Sciences, Versailles, France
| | - Nicolas Montagné
- Sorbonne Université, Institute of Ecology and Environmental Sciences, Paris, France
| | - Nancy A. Moran
- Department of Integrative Biology, University of Texas at Austin, Austin, USA
| | - Daciana Papura
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d’Ornon, France
| | - Nicolas Parisot
- Univ Lyon, INSA-Lyon, INRAE, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Yvan Rahbé
- Univ Lyon, INRAE, INSA-Lyon, CNRS, UCBL, UMR5240 MAP, F-69622 Villeurbanne, France
| | | | - Aida Ripoll-Cladellas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Stéphanie Robin
- BIPAA IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
| | - Céline Roques
- Plateforme Génomique GeT-PlaGe, Centre INRAE de Toulouse Midi-Pyrénées, 24 Chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Pascale Roux
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d’Ornon, France
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Alejandro Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Jose F. Sánchez-Herrero
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Didac Santesmasses
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | | | - Rémy-Félix Serre
- Plateforme Génomique GeT-PlaGe, Centre INRAE de Toulouse Midi-Pyrénées, 24 Chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Ming Tang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Wenhua Tian
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Paul A. Umina
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Manuella van Munster
- BGPI, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | | | - Joshua Wemmer
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Alex C. C. Wilson
- Department of Biology, University of Miami, Coral Gables, FL 33146 USA
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI USA
| | - Chaoyang Zhao
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Jing Zhao
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083 Guangdong Province People’s Republic of China
- BGI-Shenzhen, Shenzhen, 518083 Guangdong Province People’s Republic of China
| | - Serena Zhao
- Department of Integrative Biology, University of Texas at Austin, Austin, USA
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193 People’s Republic of China
| | | | - Denis Tagu
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
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12
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Streckaite S, Macernis M, Li F, Kuthanová Trsková E, Litvin R, Yang C, Pascal AA, Valkunas L, Robert B, Llansola-Portoles MJ. Modeling Dynamic Conformations of Organic Molecules: Alkyne Carotenoids in Solution. J Phys Chem A 2020; 124:2792-2801. [PMID: 32163283 PMCID: PMC7313542 DOI: 10.1021/acs.jpca.9b11536] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
Calculating
the spectroscopic properties of complex conjugated
organic molecules in their relaxed state is far from simple. An additional complexity arises for
flexible molecules in solution, where the rotational energy barriers
are low enough so that nonminimum conformations may become dynamically
populated. These metastable conformations quickly relax during the
minimization procedures preliminary to density functional theory calculations,
and so accounting for their contribution to the experimentally observed
properties is problematic. We describe a strategy for stabilizing
these nonminimum conformations in silico, allowing
their properties to be calculated. Diadinoxanthin and alloxanthin
present atypical vibrational properties in solution, indicating the
presence of several conformations. Performing energy calculations in vacuo and polarizable continuum model calculations in
different solvents, we found three different conformations with values
for the δ dihedral angle of the end ring ca. 0, 180, and 90°
with respect to the plane of the conjugated chain. The latter conformation,
a nonglobal minimum, is not stable during the minimization necessary
for modeling its spectroscopic properties. To circumvent this classical
problem, we used a Car–Parinello MD supermolecular approach,
in which diadinoxanthin was solvated by water molecules so that metastable
conformations were stabilized by hydrogen-bonding interactions. We
progressively removed the number of solvating waters to find the minimum
required for this stabilization. This strategy represents the first
modeling of a carotenoid in a distorted conformation and provides
an accurate interpretation of the experimental data.
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Affiliation(s)
- Simona Streckaite
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Mindaugas Macernis
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Saulėtekio Ave. 3, LT-10222 Vilnius, Lithuania
| | - Fei Li
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.,Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, People's Republic of China
| | - Eliška Kuthanová Trsková
- Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic.,Institute of Microbiology, Academy of Sciences of the Czech Republic, 379 81 Třeboň, Czech Republic
| | - Radek Litvin
- Biology Centre, Czech Academy of Sciences, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic.,Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic
| | - Chunhong Yang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, People's Republic of China
| | - Andrew A Pascal
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Leonas Valkunas
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Saulėtekio Ave. 3, LT-10222 Vilnius, Lithuania.,Molecular Compounds Physics Department, Center for Physical Sciences and Technology, Sauletekio Ave. 3, LT-10257 Vilnius, Lithuania
| | - Bruno Robert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Manuel J Llansola-Portoles
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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13
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Zolfaghari Emameh R, Masoori L, Taheri RA, Falak R. Identification and characterization of parvalbumin-like protein in Trichophyton violaceum. Fungal Biol 2020; 124:592-600. [PMID: 32448450 DOI: 10.1016/j.funbio.2020.02.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 01/15/2020] [Accepted: 02/23/2020] [Indexed: 01/08/2023]
Abstract
Parvalbumins play crucial physiological roles in neuromuscular systems of vertebrates, such as cell-cycle, development of neurons, contraction of muscles, and regulation of intracellular calcium. To perform these neuromuscular functions, parvalbumin may be in associated with other proteins including calbindin, carbonic anhydrase, and cytochrome oxidase. Humans may show an IgE-specific hypersensitivity to parvalbumins after consumption of some distinct fish species. While this protein is abundant in fish muscles, literature review of publications related to fish parvalbumins, do not point to the presence of parvalbumins in eukaryotic microbes. In this study, we propose that distantly related parvalbumins may be found in some non-fish species. Bioinformatics studies such as multiple sequence alignment (MSA), phylogenetic analysis as well as molecular-based experiments indicate that, at least two parvalbumins sequences (UniProt IDs: A0A178F775 and A0A178F7E4) with EF-hand domains and Ca2+-binding sites could be identified in Trichophyton violaceum, a pathogenic fungal species. It was determined that both genes consisted of a single exon and encoded for parvalbumin proteins possessing conserved amino acid motifs. Antigenicity prediction revealed antigenic sites located in both sides of the Ca2+-binding site of the first EF-hand domain. Our phylogenetic analysis revealed that one of parvalbumins (UniProt ID: 0A178F775) can be evolved to other parvalbumins in T. violaceum (UniProt ID: A0A178F7E4) and fish species through evolutionary phenomenon. To confirm our in-silico findings, we designed three primer pairs to detect one of the T. violaceum parvalbumins (UniProt ID: A0A178F7E4) by polymerase chain reaction (PCR); one primer pair showed a strong and specific band in agarose gel electrophoresis. To evaluate the specificity of the method, the primers were tested on extracted DNA from Trichophyton rubrum and T. mentagrophytes. The results demonstrated that the evaluated parvalbumin gene (UniProt ID: A0A178F7E4) was T. violaceum-specific and this pathogenic fungus can be differentiated from T. rubrum and T. mentagrophytes through identification of parvalbumin genes. Further studies are necessary to unravel the biochemical and physiological functions of parvalbumins in T. violaceum.
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Affiliation(s)
- Reza Zolfaghari Emameh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), 14965/161, Tehran, Iran.
| | - Leila Masoori
- Department of Laboratory Sciences, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Ramezan Ali Taheri
- Nanobiotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Reza Falak
- Immunology Research Center, Iran University of Medical Sciences, Tehran, Iran
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14
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Courtier-Orgogozo V, Martin A. The coding loci of evolution and domestication: current knowledge and implications for bio-inspired genome editing. J Exp Biol 2020; 223:223/Suppl_1/jeb208934. [DOI: 10.1242/jeb.208934] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
ABSTRACT
One promising application of CRISPR/Cas9 is to create targeted mutations to introduce traits of interest into domesticated organisms. However, a major current limitation for crop and livestock improvement is to identify the precise genes and genetic changes that must be engineered to obtain traits of interest. Here, we discuss the advantages of bio-inspired genome editing, i.e. the engineered introduction of natural mutations that have already been associated with traits of interest in other lineages (breeds, populations or species). To obtain a landscape view of potential targets for genome editing, we used Gephebase (www.gephebase.org), a manually curated database compiling published data about the genes responsible for evolutionary and domesticated changes across eukaryotes, and examined the >1200 mutations that have been identified in the coding regions of more than 700 genes in animals, plants and yeasts. We observe that our genetic knowledge is relatively important for certain traits, such as xenobiotic resistance, and poor for others. We also note that protein-null alleles, often owing to nonsense and frameshift mutations, represent a large fraction of the known loci of domestication (42% of identified coding mutations), compared with intraspecific (27%) and interspecific evolution (11%). Although this trend may be subject to detection, publication and curation biases, it is consistent with the idea that breeders have selected large-effect mutations underlying adaptive traits in specific settings, but that these mutations and associated phenotypes would not survive the vagaries of changing external and internal environments. Our compilation of the loci of evolution and domestication uncovers interesting options for bio-inspired and transgene-free genome editing.
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Affiliation(s)
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
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15
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Wang CF, Sun W, Zhang Z. Functional characterization of the horizontally transferred 4,5-DOPA extradiol dioxygenase gene in the domestic silkworm, Bombyx mori. INSECT MOLECULAR BIOLOGY 2019; 28:409-419. [PMID: 30537278 DOI: 10.1111/imb.12558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
4,5-DOPA dioxygenase (DODA) is a crucial enzyme in the biosynthetic pathway of betalain. Previous studies have shown that DODA is present in plants, fungi and bacteria. Using updated data, here we show that DODA genes (BmDODA) in the domestic silkworm (Bombyx mori) and other lepidopteran insects are most likely to be horizontally transferred from fungi. A synteny analysis indicated that BmDODA1 is orthologous to other lepidopteran DODAs and that BmDODA2 is a paralogous gene. To explore the function of DODA in Lepidoptera, we first examined the expression patterns of BmDODA1. BmDODA1 showed high transcriptional and translational levels in the midgut and head. Then, we exogenously expressed the BmDODA1 gene, detected 4,5-DOPA ring-cleaving activity and calculated the kinetic parameters of the recombinant BmDODA1. We found that the transcription levels of BmDODA1 were significantly induced by the pathogens Bacillus bombyseptieus and Escherichia coli. Thus, the horizontal transfer of the BmDODA gene in the silkworm may be involved in dopa metabolism and contribute to antimicrobial activity in this species. Our results provide a documented example of functional horizontal gene transfer (HGT) between fungi and animals and expand our knowledge of HGT amongst eukaryotes.
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Affiliation(s)
- C-F Wang
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing, China
| | - W Sun
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing, China
| | - Z Zhang
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing, China
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16
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Wurtzel ET. Changing Form and Function through Carotenoids and Synthetic Biology. PLANT PHYSIOLOGY 2019; 179:830-843. [PMID: 30361256 PMCID: PMC6393808 DOI: 10.1104/pp.18.01122] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/06/2018] [Indexed: 05/06/2023]
Abstract
The diverse structures and multifaceted roles of carotenoids make these colorful pigments attractive targets for synthetic biology.
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Affiliation(s)
- Eleanore T Wurtzel
- Department of Biological Sciences, Lehman College, The City University of New York, Bronx, New York 10468
- The Graduate School and University Center-CUNY, New York, New York 10016-4309
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17
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Rodriguez-Concepcion M, Avalos J, Bonet ML, Boronat A, Gomez-Gomez L, Hornero-Mendez D, Limon MC, Meléndez-Martínez AJ, Olmedilla-Alonso B, Palou A, Ribot J, Rodrigo MJ, Zacarias L, Zhu C. A global perspective on carotenoids: Metabolism, biotechnology, and benefits for nutrition and health. Prog Lipid Res 2018; 70:62-93. [PMID: 29679619 DOI: 10.1016/j.plipres.2018.04.004] [Citation(s) in RCA: 458] [Impact Index Per Article: 76.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/16/2018] [Accepted: 04/18/2018] [Indexed: 12/22/2022]
Abstract
Carotenoids are lipophilic isoprenoid compounds synthesized by all photosynthetic organisms and some non-photosynthetic prokaryotes and fungi. With some notable exceptions, animals (including humans) do not produce carotenoids de novo but take them in their diets. In photosynthetic systems carotenoids are essential for photoprotection against excess light and contribute to light harvesting, but perhaps they are best known for their properties as natural pigments in the yellow to red range. Carotenoids can be associated to fatty acids, sugars, proteins, or other compounds that can change their physical and chemical properties and influence their biological roles. Furthermore, oxidative cleavage of carotenoids produces smaller molecules such as apocarotenoids, some of which are important pigments and volatile (aroma) compounds. Enzymatic breakage of carotenoids can also produce biologically active molecules in both plants (hormones, retrograde signals) and animals (retinoids). Both carotenoids and their enzymatic cleavage products are associated with other processes positively impacting human health. Carotenoids are widely used in the industry as food ingredients, feed additives, and supplements. This review, contributed by scientists of complementary disciplines related to carotenoid research, covers recent advances and provides a perspective on future directions on the subjects of carotenoid metabolism, biotechnology, and nutritional and health benefits.
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Affiliation(s)
| | - Javier Avalos
- Department of Genetics, Universidad de Sevilla, 41012 Seville, Spain
| | - M Luisa Bonet
- Laboratory of Molecular Biology, Nutrition and Biotechnology, Universitat de les Illes Balears, 07120 Palma de Mallorca, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 07120 Palma de Mallorca, Spain; Institut d'Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
| | - Albert Boronat
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain; Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Lourdes Gomez-Gomez
- Instituto Botánico, Universidad de Castilla-La Mancha, 02071 Albacete, Spain
| | - Damaso Hornero-Mendez
- Department of Food Phytochemistry, Instituto de la Grasa (IG-CSIC), 41013 Seville, Spain
| | - M Carmen Limon
- Department of Genetics, Universidad de Sevilla, 41012 Seville, Spain
| | - Antonio J Meléndez-Martínez
- Food Color & Quality Laboratory, Area of Nutrition & Food Science, Universidad de Sevilla, 41012 Seville, Spain
| | | | - Andreu Palou
- Laboratory of Molecular Biology, Nutrition and Biotechnology, Universitat de les Illes Balears, 07120 Palma de Mallorca, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 07120 Palma de Mallorca, Spain; Institut d'Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
| | - Joan Ribot
- Laboratory of Molecular Biology, Nutrition and Biotechnology, Universitat de les Illes Balears, 07120 Palma de Mallorca, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 07120 Palma de Mallorca, Spain; Institut d'Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
| | - Maria J Rodrigo
- Institute of Agrochemistry and Food Technology (IATA-CSIC), 46980 Valencia, Spain
| | - Lorenzo Zacarias
- Institute of Agrochemistry and Food Technology (IATA-CSIC), 46980 Valencia, Spain
| | - Changfu Zhu
- Department of Plant Production and Forestry Science, Universitat de Lleida-Agrotecnio, 25198 Lleida, Spain
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