1
|
Walt HK, Ahn SJ, Hoffmann FG. Horizontally transferred glycoside hydrolase 26 may aid hemipteran insects in plant tissue digestion. Mol Phylogenet Evol 2024; 198:108134. [PMID: 38901473 DOI: 10.1016/j.ympev.2024.108134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/28/2024] [Accepted: 06/15/2024] [Indexed: 06/22/2024]
Abstract
Glycoside hydrolases are enzymes that break down complex carbohydrates into simple sugars by catalyzing the hydrolysis of glycosidic bonds. There have been multiple instances of adaptive horizontal gene transfer of genes belonging to various glycoside hydrolase families from microbes to insects, as glycoside hydrolases can metabolize constituents of the carbohydrate-rich plant cell wall. In this study, we characterize the horizontal transfer of a gene from the glycoside hydrolase family 26 (GH26) from bacteria to insects of the order Hemiptera. Our phylogenies trace the horizontal gene transfer to the common ancestor of the superfamilies Pentatomoidea and Lygaeoidea, which include stink bugs and seed bugs. After horizontal transfer, the gene was assimilated into the insect genome as indicated by the gain of an intron, and a eukaryotic signal peptide. Subsequently, the gene has undergone independent losses and expansions in copy number in multiple lineages, suggesting an adaptive role of GH26s in some insects. Finally, we measured tissue-level gene expression of multiple stink bugs and the large milkweed bug using publicly available RNA-seq datasets. We found that the GH26 genes are highly expressed in tissues associated with plant digestion, especially in the principal salivary glands of the stink bugs. Our results are consistent with the hypothesis that this horizontally transferred GH26 was co-opted by the insect to aid in plant tissue digestion and that this HGT event was likely adaptive.
Collapse
Affiliation(s)
- Hunter K Walt
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Seung-Joon Ahn
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA; Institute for Genomics, Biotechnology and Biocomputing, Mississippi State University, Mississippi State, MS 39762, USA.
| |
Collapse
|
2
|
Takasu R, Izu T, Nakabachi A. A limited concentration range of diaphorin, a polyketide produced by a bacterial symbiont of the Asian citrus psyllid, promotes the in vitro gene expression with bacterial ribosomes. Microbiol Spectr 2024; 12:e0017024. [PMID: 38832800 PMCID: PMC11218438 DOI: 10.1128/spectrum.00170-24] [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: 01/17/2024] [Accepted: 04/25/2024] [Indexed: 06/05/2024] Open
Abstract
Diaphorin is a polyketide produced by "Candidatus Profftella armatura" (Gammaproteobacteria: Burkholderiales), an obligate symbiont of a devastating agricultural pest, the Asian citrus psyllid Diaphorina citri (Hemiptera: Psyllidae). Physiological concentrations of diaphorin, which D. citri contains at levels as high as 2-20 mM, are inhibitory to various eukaryotes and Bacillus subtilis (Firmicutes: Bacilli) but promote the growth and metabolic activity of Escherichia coli (Gammaproteobacteria: Enterobacterales). Our previous study demonstrated that 5-mM diaphorin, which exhibits significant inhibitory and promoting effects on cultured B. subtilis and E. coli, respectively, inhibits in vitro gene expression utilizing purified B. subtilis and E. coli ribosomes. This suggested that the adverse effects of diaphorin on B. subtilis are partly due to its influence on gene expression. However, the result appeared inconsistent with the positive impact on E. coli. Moreover, the diaphorin concentration in bacterial cells, where genes are expressed in vivo, may be lower than in culture media. Therefore, the present study analyzed the effects of 50 and 500 µM of diaphorin on bacterial gene expression using the same analytical method. The result revealed that this concentration range of diaphorin, in contrast to 5-mM diaphorin, promotes the in vitro translation with the B. subtilis and E. coli ribosomes, suggesting that the positive effects of diaphorin on E. coli are due to its direct effects on translation. This study demonstrated for the first time that a pederin-type compound promotes gene expression, establishing a basis for utilizing its potential in pest management and industrial applications.IMPORTANCEThis study revealed that a limited concentration range of diaphorin, a secondary metabolite produced by a bacterial symbiont of an agricultural pest, promotes cell-free gene expression utilizing substrates and proteins purified from bacteria. The unique property of diaphorin, which is inhibitory to various eukaryotes and Bacillus subtilis but promotes the growth and metabolic activity of Escherichia coli, may affect the microbial flora of the pest insect, potentially influencing the transmission of devastating plant pathogens. Moreover, the activity may be exploited to improve the efficacy of industrial production by E. coli, which is often used to produce various important materials, including pharmaceuticals, enzymes, amino acids, and biofuels. This study elucidated a part of the mechanism by which the unique activity of diaphorin is expressed, constructing a foundation for applying the distinct property to pest management and industrial use.
Collapse
Affiliation(s)
- Rena Takasu
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi, Japan
| | - Takashi Izu
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi, Japan
| | - Atsushi Nakabachi
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi, Japan
- Research Center for Agrotechnology and Biotechnology, Toyohashi University of Technology, Toyohashi, Aichi, Japan
| |
Collapse
|
3
|
Aguirre-Carvajal K, Munteanu CR, Armijos-Jaramillo V. Database Bias in the Detection of Interdomain Horizontal Gene Transfer Events in Pezizomycotina. BIOLOGY 2024; 13:469. [PMID: 39056664 PMCID: PMC11273514 DOI: 10.3390/biology13070469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 07/28/2024]
Abstract
Horizontal gene transfer (HGT) is a widely acknowledged phenomenon in prokaryotes for generating genetic diversity. However, the impact of this process in eukaryotes, particularly interdomain HGT, is a topic of debate. Although there have been observed biases in interdomain HGT detection, little exploration has been conducted on the effects of imbalanced databases. In our study, we conducted experiments to assess how different databases affect the detection of interdomain HGT using proteomes from the Pezizomycotina fungal subphylum as our focus group. Our objective was to simulate the database imbalance commonly found in public biological databases, where bacterial and eukaryotic sequences are unevenly represented, and demonstrate that an increase in uploaded eukaryotic sequences leads to a decrease in predicted HGTs. For our experiments, four databases with varying proportions of eukaryotic sequences but consistent proportions of bacterial sequences were utilized. We observed a significant reduction in detected interdomain HGT candidates as the proportion of eukaryotes increased within the database. Our data suggest that the imbalance in databases bias the interdomain HGT detection and highlights challenges associated with confirming the presence of interdomain HGT among Pezizomycotina fungi and potentially other groups within Eukarya.
Collapse
Affiliation(s)
- Kevin Aguirre-Carvajal
- Department of Computer Science and Information Technologies, Faculty of Computer Science, University of A Coruña, Campus Elviña s/n, 15071 Coruña, Spain; (K.A.-C.); (C.R.M.)
- Bio-Cheminformatics Research Group, Universidad de Las Américas, Quito 170513, Ecuador
| | - Cristian R. Munteanu
- Department of Computer Science and Information Technologies, Faculty of Computer Science, University of A Coruña, Campus Elviña s/n, 15071 Coruña, Spain; (K.A.-C.); (C.R.M.)
| | - Vinicio Armijos-Jaramillo
- Bio-Cheminformatics Research Group, Universidad de Las Américas, Quito 170513, Ecuador
- Carrera de Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito 170513, Ecuador
| |
Collapse
|
4
|
Becchimanzi A, Nicoletti R, Di Lelio I, Russo E. Immune Gene Repertoire of Soft Scale Insects (Hemiptera: Coccidae). Int J Mol Sci 2024; 25:4922. [PMID: 38732132 PMCID: PMC11084805 DOI: 10.3390/ijms25094922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 04/25/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
Insects possess an effective immune system, which has been extensively characterized in several model species, revealing a plethora of conserved genes involved in recognition, signaling, and responses to pathogens and parasites. However, some taxonomic groups, characterized by peculiar trophic niches, such as plant-sap feeders, which are often important pests of crops and forestry ecosystems, have been largely overlooked regarding their immune gene repertoire. Here we annotated the immune genes of soft scale insects (Hemiptera: Coccidae) for which omics data are publicly available. By using immune genes of aphids and Drosophila to query the genome of Ericerus pela, as well as the transcriptomes of Ceroplastes cirripediformis and Coccus sp., we highlight the lack of peptidoglycan recognition proteins, galectins, thaumatins, and antimicrobial peptides in Coccidae. This work contributes to expanding our knowledge about the evolutionary trajectories of immune genes and offers a list of promising candidates for developing new control strategies based on the suppression of pests' immunity through RNAi technologies.
Collapse
Affiliation(s)
- Andrea Becchimanzi
- Department of Agricultural Sciences, University of Naples Federico II, 80126 Naples, Italy; (A.B.); (I.D.L.); (E.R.)
- BAT Center—Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Naples Federico II, 80126 Naples, Italy
| | - Rosario Nicoletti
- Department of Agricultural Sciences, University of Naples Federico II, 80126 Naples, Italy; (A.B.); (I.D.L.); (E.R.)
- Research Centre for Olive, Fruit and Citrus Crops, Council for Agricultural Research and Economics, 81100 Caserta, Italy
| | - Ilaria Di Lelio
- Department of Agricultural Sciences, University of Naples Federico II, 80126 Naples, Italy; (A.B.); (I.D.L.); (E.R.)
- BAT Center—Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Naples Federico II, 80126 Naples, Italy
| | - Elia Russo
- Department of Agricultural Sciences, University of Naples Federico II, 80126 Naples, Italy; (A.B.); (I.D.L.); (E.R.)
| |
Collapse
|
5
|
Nakabachi A, Suzaki T. Ultrastructure of the bacteriome and bacterial symbionts in the Asian citrus psyllid, Diaphorina citri. Microbiol Spectr 2024; 12:e0224923. [PMID: 38047691 PMCID: PMC10783097 DOI: 10.1128/spectrum.02249-23] [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: 05/30/2023] [Accepted: 11/04/2023] [Indexed: 12/05/2023] Open
Abstract
IMPORTANCE Omics analyses suggested a mutually indispensable tripartite association among the host D. citri and organelle-like bacteriome associates, Carsonella and Profftella, which are vertically transmitted through host generations. This relationship is based on the metabolic complementarity among these organisms, which is partly enabled by horizontal gene transfer between partners. However, little was known about the fine morphology of the symbionts and the bacteriome, the interface among these organisms. As a first step to address this issue, the present study performed transmission electron microscopy, which revealed previously unrecognized ultrastructures, including aggregations of ribosomes in Carsonella, numerous tubes and occasional protrusions of Profftella, apparently degrading Profftella, and host organelles with different abundance and morphology in distinct cell types. These findings provide insights into the behaviors of the symbionts and host cells to maintain the symbiotic relationship in D. citri.
Collapse
Affiliation(s)
- Atsushi Nakabachi
- Research Center for Agrotechnology and Biotechnology, Toyohashi University of Technology, Toyohashi, Aichi, Japan
| | | |
Collapse
|
6
|
Takasu R, Yasuda Y, Izu T, Nakabachi A. Diaphorin, a polyketide produced by a bacterial endosymbiont of the Asian citrus psyllid, adversely affects the in vitro gene expression with ribosomes from Escherichia coli and Bacillus subtilis. PLoS One 2023; 18:e0294360. [PMID: 37963163 PMCID: PMC10645341 DOI: 10.1371/journal.pone.0294360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023] Open
Abstract
Diaphorin is a polyketide produced by "Candidatus Profftella armatura" (Gammaproteobacteria), an obligate mutualist of an important agricultural pest, the Asian citrus psyllid Diaphorina citri (Hemiptera). Our previous study demonstrated that diaphorin, at physiological concentrations in D. citri, inhibits the growth and cell division of Bacillus subtilis (Firmicutes) but promotes the growth and metabolic activity of Escherichia coli (Gammaproteobacteria). This unique property of diaphorin may aid microbial mutualism in D. citri, potentially affecting the transmission of "Candidatus Liberibacter spp." (Alphaproteobacteria), the pathogens of the most destructive citrus disease Huanglongbing. Moreover, this property may be exploited to promote microbes' efficiency in producing industrial materials. However, the mechanism underlying this activity is unknown. Diaphorin belongs to the family of pederin-type compounds, which inhibit protein synthesis in eukaryotes by binding to eukaryotic ribosomes. Therefore, as a first step to assess diaphorin's direct influence on bacterial gene expression, this study examined the effect of diaphorin on the in vitro translation using ribosomes of B. subtilis and E. coli, quantifying the production of the green fluorescent protein. The results showed that the gene expression involving B. subtilis and E. coli ribosomes along with five millimolar diaphorin was 29.6% and 13.1%, respectively, less active than the control. This suggests that the diaphorin's adverse effects on B. subtilis are attributed to, at least partly, its inhibitory effects on gene expression. Moreover, as ingredients of the translation system were common other than ribosomes, the greater inhibitory effects observed with the B. subtilis ribosome imply that the ribosome is among the potential targets of diaphorin. On the other hand, the results also imply that diaphorin's positive effects on E. coli are due to targets other than the core machinery of transcription and translation. This study demonstrated for the first time that a pederin congener affects bacterial gene expression.
Collapse
Affiliation(s)
- Rena Takasu
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi, Japan
| | - Yuka Yasuda
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi, Japan
| | - Takashi Izu
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi, Japan
| | - Atsushi Nakabachi
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi, Japan
- Research Center for Agrotechnology and Biotechnology, Toyohashi University of Technology, Toyohashi, Aichi, Japan
| |
Collapse
|
7
|
Gilbert C, Maumus F. Sidestepping Darwin: horizontal gene transfer from plants to insects. CURRENT OPINION IN INSECT SCIENCE 2023; 57:101035. [PMID: 37061183 DOI: 10.1016/j.cois.2023.101035] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 05/06/2023]
Abstract
Horizontal transfer of genetic material (HT) is the passage of DNA between organisms by means other than reproduction. Increasing numbers of HT are reported in insects, with bacteria, fungi, plants, and insects acting as the main sources of these transfers. Here, we provide a detailed account of plant-to-insect HT events. At least 14 insect species belonging to 6 orders are known to have received plant genetic material through HT. One of them, the whitefly Bemisia tabaci (Middle East Asia Minor 1), concentrates most of these transfers, with no less than 28 HT events yielding 55 plant-derived genes in this species. Several plant-to-insect HT events reported so far involve gene families known to play a role in plant-parasite interactions. We highlight methodological approaches that may further help characterize these transfers. We argue that plant-to-insect HT is likely more frequent than currently appreciated and that in-depth studies of these transfers will shed new light on plant-insect interactions.
Collapse
Affiliation(s)
- Clément Gilbert
- Université Paris-Saclay, CNRS, IRD, UMR Evolution, Génomes, Comportement et Ecologie, Gif-sur-Yvette, France.
| | - Florian Maumus
- Université Paris-Saclay, INRAE, URGI, Versailles, France
| |
Collapse
|
8
|
Maruyama J, Inoue H, Hirose Y, Nakabachi A. 16S rRNA Gene Sequencing of Six Psyllid Species of the Family Carsidaridae Identified Various Bacteria Including Symbiopectobacterium. Microbes Environ 2023; 38:ME23045. [PMID: 37612118 PMCID: PMC10522848 DOI: 10.1264/jsme2.me23045] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 06/23/2023] [Indexed: 08/25/2023] Open
Abstract
Psyllids (Hemiptera: Sternorrhyncha: Psylloidea) are plant sap-sucking insects that are closely associated with various microbes. To obtain a more detailed understanding of the ecological and evolutionary behaviors of microbes in Psylloidea, the bacterial populations of six psyllid species, belonging to the family Carsidaridae, were analyzed using high-throughput amplicon sequencing of the 16S rRNA gene. The majority of the secondary symbionts identified in the present study were gammaproteobacteria, particularly those of the order Enterobacterales, including Arsenophonus and Sodalis, which are lineages found in a wide variety of insect hosts. Additionally, Symbiopectobacterium, another Enterobacterales lineage, which has recently been recognized and increasingly shown to be vertically transmitted and mutualistic in various invertebrates, was identified for the first time in Psylloidea. This lineage is closely related to Pectobacterium spp., which are plant pathogens, but forms a distinct clade exhibiting no pathogenicity to plants. Non-Enterobacterales gammaproteobacteria found in the present study were Acinetobacter, Pseudomonas (both Pseudomonadales), Delftia, Comamonas (both Burkholderiales), and Xanthomonas (Xanthomonadales), a putative plant pathogen. Regarding alphaproteobacteria, three Wolbachia (Rickettsiales) lineages belonging to supergroup B, the major group in insect lineages, were detected in four psyllid species. In addition, a Wolbachia lineage of supergroup O, a minor group recently found for the first time in Psylloidea, was detected in one psyllid species. These results suggest the pervasive transfer of bacterial symbionts among animals and plants, providing deeper insights into the evolution of the interactions among these organisms.
Collapse
Affiliation(s)
- Junnosuke Maruyama
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1–1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441–8580, Japan
| | - Hiromitsu Inoue
- Institute for Plant Protection, National Agriculture and Food Research Organization, Higashihiroshima, Hiroshima 739–2494, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1–1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441–8580, Japan
| | - Atsushi Nakabachi
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1–1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441–8580, Japan
- Research Institute for Technological Science and Innovation, Toyohashi University of Technology, 1–1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441–8580, Japan
| |
Collapse
|
9
|
Diaphorin, a Polyketide Produced by a Bacterial Symbiont of the Asian Citrus Psyllid, Inhibits the Growth and Cell Division of Bacillus subtilis but Promotes the Growth and Metabolic Activity of Escherichia coli. Microbiol Spectr 2022; 10:e0175722. [PMID: 35894614 PMCID: PMC9430481 DOI: 10.1128/spectrum.01757-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Diaphorin is a polyketide produced by “Candidatus Profftella armatura” (Gammaproteobacteria: Burkholderiales), an obligate symbiont of a notorious agricultural pest, the Asian citrus psyllid Diaphorina citri (Hemiptera: Psyllidae). Diaphorin belongs to the pederin family of bioactive agents found in various host-symbiont systems, including beetles, lichens, and sponges, harboring phylogenetically diverse bacterial producers. Previous studies showed that diaphorin, which is present in D. citri at concentrations of 2 to 20 mM, has inhibitory effects on various eukaryotes, including the natural enemies of D. citri. However, little is known about its effects on prokaryotic organisms. To address this issue, the present study assessed the biological activities of diaphorin on two model prokaryotes, Escherichia coli (Gammaproteobacteria: Enterobacterales) and Bacillus subtilis (Firmicutes: Bacilli). Their growth and morphological features were analyzed using spectrophotometry, optical microscopy followed by image analysis, and transmission electron microscopy. The metabolic activity of E. coli was further assessed using the β-galactosidase assay. The results revealed that physiological concentrations of diaphorin inhibit the growth and cell division of B. subtilis but promote the growth and metabolic activity of E. coli. This finding implies that diaphorin functions as a defensive agent of the holobiont (host plus symbionts) against some bacterial lineages but is metabolically beneficial for others, which potentially include obligate symbionts of D. citri. IMPORTANCE Certain secondary metabolites, including antibiotics, evolve to mediate interactions among organisms. These molecules have distinct spectra for microorganisms and are often more effective against Gram-positive bacteria than Gram-negative ones. However, it is rare that a single molecule has completely opposite activities on distinct bacterial lineages. The present study revealed that a secondary metabolite synthesized by an organelle-like bacterial symbiont of psyllids inhibits the growth of Gram-positive Bacillus subtilis but promotes the growth of Gram-negative Escherichia coli. This finding not only provides insights into the evolution of microbiomes in animal hosts but also may potentially be exploited to promote the effectiveness of industrial material production by microorganisms.
Collapse
|
10
|
Rafiqi AM, Polo PG, Milat NS, Durmuş ZÖ, Çolak-Al B, Alarcón ME, Çağıl FZ, Rajakumar A. Developmental Integration of Endosymbionts in Insects. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.846586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In endosymbiosis, two independently existing entities are inextricably intertwined such that they behave as a single unit. For multicellular hosts, the endosymbiont must be integrated within the host developmental genetic network to maintain the relationship. Developmental integration requires innovations in cell type, gene function, gene regulation, and metabolism. These innovations are contingent upon the existing ecological interactions and may evolve mutual interdependence. Recent studies have taken significant steps toward characterizing the proximate mechanisms underlying interdependence. However, the study of developmental integration is only in its early stages of investigation. Here, we review the literature on mutualistic endosymbiosis to explore how unicellular endosymbionts developmentally integrate into their multicellular hosts with emphasis on insects as a model. Exploration of this process will help gain a more complete understanding of endosymbiosis. This will pave the way for a better understanding of the endosymbiotic theory of evolution in the future.
Collapse
|
11
|
Xiong Q, Wan ATY, Liu X, Fung CSH, Xiao X, Malainual N, Hou J, Wang L, Wang M, Yang KY, Cui Y, Leung ELH, Nong W, Shin SK, Au SWN, Jeong KY, Chew FT, Hui JHL, Leung TF, Tungtrongchitr A, Zhong N, Liu Z, Tsui SKW. Comparative Genomics Reveals Insights into the Divergent Evolution of Astigmatic Mites and Household Pest Adaptations. Mol Biol Evol 2022; 39:6582989. [PMID: 35535514 PMCID: PMC9113151 DOI: 10.1093/molbev/msac097] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Highly diversified astigmatic mites comprise many medically important human household pests such as house dust mites causing ∼1–2% of all allergic diseases globally; however, their evolutionary origin and diverse lifestyles including reversible parasitism have not been illustrated at the genomic level, which hampers allergy prevention and our exploration of these household pests. Using six high-quality assembled and annotated genomes, this study not only refuted the monophyly of mites and ticks, but also thoroughly explored the divergence of Acariformes and the diversification of astigmatic mites. In monophyletic Acariformes, Prostigmata known as notorious plant pests first evolved, and then rapidly evolving Astigmata diverged from soil oribatid mites. Within astigmatic mites, a wide range of gene families rapidly expanded via tandem gene duplications, including ionotropic glutamate receptors, triacylglycerol lipases, serine proteases and UDP glucuronosyltransferases. Gene diversification after tandem duplications provides many genetic resources for adaptation to sensing environmental signals, digestion, and detoxification in rapidly changing household environments. Many gene decay events only occurred in the skin-burrowing parasitic mite Sarcoptes scabiei. Throughout the evolution of Acariformes, massive horizontal gene transfer events occurred in gene families such as UDP glucuronosyltransferases and several important fungal cell wall lytic enzymes, which enable detoxification and digestive functions and provide perfect drug targets for pest control. This comparative study sheds light on the divergent evolution and quick adaptation to human household environments of astigmatic mites and provides insights into the genetic adaptations and even control of human household pests.
Collapse
Affiliation(s)
- Qing Xiong
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - Angel Tsz-Yau Wan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - Xiaoyu Liu
- Shenzhen Key Laboratory of Allergy and Immunology, School of Medicine, Shenzhen University, China
| | - Cathy Sin-Hang Fung
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Xiaojun Xiao
- Shenzhen Key Laboratory of Allergy and Immunology, School of Medicine, Shenzhen University, China
| | - Nat Malainual
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jinpao Hou
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Centre for Microbial Genomics and Proteomics, The Chinese University of Hong Kong, Hong Kong
| | - Lingyi Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Mingqiang Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - Kevin Yi Yang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - Yubao Cui
- Department of Clinical Laboratory, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Elaine Lai-Han Leung
- Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau
| | - Wenyan Nong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Soo-Kyung Shin
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | | | - Kyoung Yong Jeong
- Institute of Allergy, Department of Internal Medicine, College of Medicine, Yonsei University, Seoul, Korea
| | - Fook-Tim Chew
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Jerome Ho-Lam Hui
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Ting-Fan Leung
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong
| | - Anchalee Tungtrongchitr
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhigang Liu
- Shenzhen Key Laboratory of Allergy and Immunology, School of Medicine, Shenzhen University, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong.,Centre for Microbial Genomics and Proteomics, The Chinese University of Hong Kong, Hong Kong
| |
Collapse
|
12
|
Nakabachi A, Inoue H, Hirose Y. Microbiome analyses of 12 psyllid species of the family Psyllidae identified various bacteria including Fukatsuia and Serratia symbiotica, known as secondary symbionts of aphids. BMC Microbiol 2022; 22:15. [PMID: 34996376 PMCID: PMC8740488 DOI: 10.1186/s12866-021-02429-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/20/2021] [Indexed: 01/04/2023] Open
Abstract
Background Psyllids (Hemiptera: Psylloidea) comprise a group of plant sap-sucking insects that includes important agricultural pests. They have close associations not only with plant pathogens, but also with various microbes, including obligate mutualists and facultative symbionts. Recent studies are revealing that interactions among such bacterial populations are important for psyllid biology and host plant pathology. In the present study, to obtain further insight into the ecological and evolutionary behaviors of bacteria in Psylloidea, we analyzed the microbiomes of 12 psyllid species belonging to the family Psyllidae (11 from Psyllinae and one from Macrocorsinae), using high-throughput amplicon sequencing of the 16S rRNA gene. Results The analysis showed that all 12 psyllids have the primary symbiont, Candidatus Carsonella ruddii (Gammaproteobacteria: Oceanospirillales), and at least one secondary symbiont. The majority of the secondary symbionts were gammaproteobacteria, especially those of the family Enterobacteriaceae (order: Enterobacteriales). Among them, symbionts belonging to “endosymbionts3”, which is a genus-level monophyletic group assigned by the SILVA rRNA database, were the most prevalent and were found in 9 of 11 Psyllinae species. Ca. Fukatsuia symbiotica and Serratia symbiotica, which were recognized only as secondary symbionts of aphids, were also identified. In addition to other Enterobacteriaceae bacteria, including Arsenophonus, Sodalis, and “endosymbionts2”, which is another genus-level clade, Pseudomonas (Pseudomonadales: Pseudomonadaceae) and Diplorickettsia (Diplorickettsiales: Diplorickettsiaceae) were identified. Regarding Alphaproteobacteria, the potential plant pathogen Ca. Liberibacter europaeus (Rhizobiales: Rhizobiaceae) was detected for the first time in Anomoneura mori (Psyllinae), a mulberry pest. Wolbachia (Rickettsiales: Anaplasmataceae) and Rickettsia (Rickettsiales: Rickettsiaceae), plausible host reproduction manipulators that are potential tools to control pest insects, were also detected. Conclusions The present study identified various bacterial symbionts including previously unexpected lineages in psyllids, suggesting considerable interspecific transfer of arthropod symbionts. The findings provide deeper insights into the evolution of interactions among insects, bacteria, and plants, which may be exploited to facilitate the control of pest psyllids in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02429-2.
Collapse
Affiliation(s)
- Atsushi Nakabachi
- Electronics-Inspired Interdisciplinary Research Institute (EIIRIS), Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan. .,Department of Applied Chemistry and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan.
| | - Hiromitsu Inoue
- Institute for Plant Protection, National Agriculture and Food Research Organization, Higashihiroshima, Hiroshima, 739-2494, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan
| |
Collapse
|
13
|
Han Z, Sieriebriennikov B, Susoy V, Lo WS, Igreja C, Dong C, Berasategui A, Witte H, Sommer RJ. Horizontally acquired cellulases assist the expansion of dietary range in Pristionchus nematodes. Mol Biol Evol 2022; 39:6493351. [PMID: 34978575 PMCID: PMC8826503 DOI: 10.1093/molbev/msab370] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Horizontal gene transfer (HGT) enables the acquisition of novel traits via non-Mendelian inheritance of genetic material. HGT plays a prominent role in the evolution of prokaryotes, whereas in animals, HGT is rare and its functional significance is often uncertain. Here, we investigate horizontally acquired cellulase genes in the free-living nematode model organism Pristionchus pacificus. We show that these cellulase genes 1) are likely of eukaryotic origin, 2) are expressed, 3) have protein products that are secreted and functional, and 4) result in endo-cellulase activity. Using CRISPR/Cas9, we generated an octuple cellulase mutant, which lacks all eight cellulase genes and cellulase activity altogether. Nonetheless, this cellulase-null mutant is viable and therefore allows a detailed analysis of a gene family that was horizontally acquired. We show that the octuple cellulase mutant has associated fitness costs with reduced fecundity and slower developmental speed. Furthermore, by using various Escherichia coli K-12 strains as a model for cellulosic biofilms, we demonstrate that cellulases facilitate the procurement of nutrients from bacterial biofilms. Together, our analysis of cellulases in Pristionchus provides comprehensive evidence from biochemistry, genetics, and phylogeny, which supports the integration of horizontally acquired genes into the complex life history strategy of this soil nematode.
Collapse
Affiliation(s)
- Ziduan Han
- Max-Planck Institute for Developmental Biology, Tuebingen, 72076, Germany
| | | | - Vladislav Susoy
- Max-Planck Institute for Developmental Biology, Tuebingen, 72076, Germany
| | - Wen-Sui Lo
- Max-Planck Institute for Developmental Biology, Tuebingen, 72076, Germany
| | - Catia Igreja
- Max-Planck Institute for Developmental Biology, Tuebingen, 72076, Germany
| | - Chuanfu Dong
- Max-Planck Institute for Developmental Biology, Tuebingen, 72076, Germany
| | | | - Hanh Witte
- Max-Planck Institute for Developmental Biology, Tuebingen, 72076, Germany
| | - Ralf J Sommer
- Max-Planck Institute for Developmental Biology, Tuebingen, 72076, Germany
| |
Collapse
|
14
|
Nakabachi A, Inoue H, Hirose Y. High-resolution Microbiome Analyses of Nine Psyllid Species of the Family Triozidae Identified Previously Unrecognized but Major Bacterial Populations, including Liberibacter and Wolbachia of Supergroup O. Microbes Environ 2022; 37:ME22078. [PMID: 36476840 PMCID: PMC9763047 DOI: 10.1264/jsme2.me22078] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Psyllids (Hemiptera: Sternorrhyncha: Psylloidea) are plant sap-sucking insects that include important agricultural pests. To obtain insights into the ecological and evolutionary behaviors of microbes, including plant pathogens, in Psylloidea, high-resolution ana-lyses of the microbiomes of nine psyllid species belonging to the family Triozidae were performed using high-throughput amplicon sequencing of the 16S rRNA gene. Analyses identified various bacterial populations, showing that all nine psyllids have at least one secondary symbiont, along with the primary symbiont "Candidatus Carsonella ruddii" (Gammaproteobacteria: Oceanospirillales: Halomonadaceae). The majority of the secondary symbionts were gammaproteobacteria, particularly those of the order Enterobacterales, which included Arsenophonus and Serratia symbiotica, a bacterium formerly recognized only as a secondary symbiont of aphids (Hemiptera: Sternorrhyncha: Aphidoidea). The non-Enterobacterales gammaproteobacteria identified in the present study were Diplorickettsia (Diplorickettsiales: Diplorickettsiaceae), a potential human pathogen, and Carnimonas (Oceanospirillales: Halomonadaceae), a lineage detected for the first time in Psylloidea. Regarding alphaproteobacteria, the potential plant pathogen "Ca. Liberibacter europaeus" (Rhizobiales: Rhizobiaceae) was detected for the first time in Epitrioza yasumatsui, which feeds on the Japanese silverberry Elaeagnus umbellata (Elaeagnaceae), an aggressive invasive plant in the United States and Europe. Besides the detection of Wolbachia (Rickettsiales: Anaplasmataceae) of supergroup B in three psyllid species, a lineage belonging to supergroup O was identified for the first time in Psylloidea. These results suggest the rampant transfer of bacterial symbionts among animals and plants, thereby providing deeper insights into the evolution of interkingdom interactions among multicellular organisms and bacteria, which will facilitate the control of pest psyllids.
Collapse
Affiliation(s)
- Atsushi Nakabachi
- Electronics-Inspired Interdisciplinary Research Institute (EIIRIS), Toyohashi University of Technology, 1–1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441–8580, Japan,Department of Applied Chemistry and Life Sciences, Toyohashi University of Technology, 1–1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441–8580, Japan, Corresponding author. E-mail: ; Tel: +81–532–44–6901
| | - Hiromitsu Inoue
- Institute for Plant Protection, National Agriculture and Food Research Organization, Higashihiroshima, Hiroshima 739–2494, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Sciences, Toyohashi University of Technology, 1–1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441–8580, Japan
| |
Collapse
|
15
|
Horizontal-Acquisition of a Promiscuous Peptidoglycan-Recycling Enzyme Enables Aphids To Influence Symbiont Cell Wall Metabolism. mBio 2021; 12:e0263621. [PMID: 34933456 PMCID: PMC8689515 DOI: 10.1128/mbio.02636-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
During evolution, enzymes can undergo shifts in preferred substrates or in catalytic activities. An intriguing question is how enzyme function changes following horizontal gene transfer, especially for bacterial genes that have moved to animal genomes. Some insects have acquired genes that encode enzymes for the biosynthesis of bacterial cell wall components and that appear to function to support or control their obligate endosymbiotic bacteria. In aphids, the bacterial endosymbiont Buchnera aphidicola provides essential amino acids for aphid hosts but lacks most genes for remodeling of the bacterial cell wall. The aphid genome has acquired seven genes with putative functions in cell wall metabolism that are primarily expressed in the aphid cells harboring Buchnera. In analyses of aphid homogenates, we detected peptidoglycan (PGN) muropeptides indicative of the reactions of PGN hydrolases encoded by horizontally acquired aphid genes but not by Buchnera genes. We produced one such host enzyme, ApLdcA, and characterized its activity with both cell wall derived and synthetic PGN. Both ApLdcA and the homologous enzyme in Escherichia coli, which functions as an l,d-carboxypeptidase in the cytoplasmic PGN recycling pathway, exhibit turnover of PGN substrates containing stem pentapeptides and cross-linkages via l,d-endopeptidase activity, consistent with a potential role in cell wall remodeling. Our results suggest that ApLdcA derives its functions from the promiscuous activities of an ancestral LdcA enzyme, whose acquisition by the aphid genome may have enabled hosts to influence Buchnera cell wall metabolism as a means to control symbiont growth and division. IMPORTANCE Most enzymes are capable of performing biologically irrelevant side reactions. During evolution, promiscuous enzyme activities may acquire new biological roles, especially after horizontal gene transfer to new organisms. Pea aphids harbor obligate bacterial symbionts called Buchnera and encode horizontally acquired bacterial genes with putative roles in cell wall metabolism. Though Buchnera lacks cell wall endopeptidase genes, we found evidence of endopeptidase activity among peptidoglycan muropeptides purified from aphids. We characterized a multifunctional, aphid-encoded enzyme, ApLdcA, which displays l,d-endopeptidase activities considered promiscuous for the Escherichia coli homolog, for which these activities do not contribute to its native role in peptidoglycan recycling. These results exemplify the roles of enzyme promiscuity and horizontal gene transfer in enzyme evolution and demonstrate how aphids influence symbiont cell wall metabolism.
Collapse
|
16
|
Parisot N, Vargas-Chávez C, Goubert C, Baa-Puyoulet P, Balmand S, Beranger L, Blanc C, Bonnamour A, Boulesteix M, Burlet N, Calevro F, Callaerts P, Chancy T, Charles H, Colella S, Da Silva Barbosa A, Dell'Aglio E, Di Genova A, Febvay G, Gabaldón T, Galvão Ferrarini M, Gerber A, Gillet B, Hubley R, Hughes S, Jacquin-Joly E, Maire J, Marcet-Houben M, Masson F, Meslin C, Montagné N, Moya A, Ribeiro de Vasconcelos AT, Richard G, Rosen J, Sagot MF, Smit AFA, Storer JM, Vincent-Monegat C, Vallier A, Vigneron A, Zaidman-Rémy A, Zamoum W, Vieira C, Rebollo R, Latorre A, Heddi A. The transposable element-rich genome of the cereal pest Sitophilus oryzae. BMC Biol 2021; 19:241. [PMID: 34749730 PMCID: PMC8576890 DOI: 10.1186/s12915-021-01158-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/27/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions. RESULTS We sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino acids required for insect development and cuticle biosynthesis. CONCLUSIONS Here we present the genome of an agricultural pest beetle, which may act as a foundation for pest control. In addition, S. oryzae may be a useful model for endosymbiosis, and studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.
Collapse
Affiliation(s)
- Nicolas Parisot
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Carlos Vargas-Chávez
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Institute for Integrative Systems Biology (I2SySBio), Universitat de València and Spanish Research Council (CSIC), València, Spain
- Present Address: Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Clément Goubert
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, New York, 14853, USA
- Present Address: Human Genetics, McGill University, Montreal, QC, Canada
| | | | - Séverine Balmand
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Louis Beranger
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Caroline Blanc
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Aymeric Bonnamour
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Matthieu Boulesteix
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
| | - Nelly Burlet
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
| | - Federica Calevro
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Patrick Callaerts
- Department of Human Genetics, Laboratory of Behavioral and Developmental Genetics, KU Leuven, University of Leuven, B-3000, Leuven, Belgium
| | - Théo Chancy
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Hubert Charles
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- ERABLE European Team, INRIA, Rhône-Alpes, France
| | - Stefano Colella
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: LSTM, Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, CIRAD, INRAE, SupAgro, Univ Montpellier, Montpellier, France
| | - André Da Silva Barbosa
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Elisa Dell'Aglio
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Alex Di Genova
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
- ERABLE European Team, INRIA, Rhône-Alpes, France
- Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile
| | - Gérard Febvay
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Toni Gabaldón
- Life Sciences, Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Mechanisms of Disease, Institute for Research in Biomedicine (IRB), Barcelona, Spain
- Institut Catalan de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Alexandra Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Benjamin Gillet
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Lyon, France
| | | | - Sandrine Hughes
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Lyon, France
| | - Emmanuelle Jacquin-Joly
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Justin Maire
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Florent Masson
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Camille Meslin
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Nicolas Montagné
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Andrés Moya
- Institute for Integrative Systems Biology (I2SySBio), Universitat de València and Spanish Research Council (CSIC), València, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), València, Spain
| | | | - Gautier Richard
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653, Le Rheu, France
| | - Jeb Rosen
- Institute for Systems Biology, Seattle, WA, USA
| | - Marie-France Sagot
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
- ERABLE European Team, INRIA, Rhône-Alpes, France
| | | | | | | | - Agnès Vallier
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Aurélien Vigneron
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: Department of Evolutionary Ecology, Institute for Organismic and Molecular Evolution, Johannes Gutenberg University, 55128, Mainz, Germany
| | - Anna Zaidman-Rémy
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Waël Zamoum
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France.
- ERABLE European Team, INRIA, Rhône-Alpes, France.
| | - Rita Rebollo
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France.
| | - Amparo Latorre
- Institute for Integrative Systems Biology (I2SySBio), Universitat de València and Spanish Research Council (CSIC), València, Spain.
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), València, Spain.
| | - Abdelaziz Heddi
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France.
| |
Collapse
|
17
|
Prasad A, Chirom O, Prasad M. Insect herbivores benefit from horizontal gene transfer. TRENDS IN PLANT SCIENCE 2021; 26:1096-1097. [PMID: 34364793 DOI: 10.1016/j.tplants.2021.07.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/22/2021] [Accepted: 07/24/2021] [Indexed: 06/13/2023]
Abstract
Evidence suggests that horizontal gene transfer (HGT) is relatively common in eukaryotes, contrary to what was previously believed. For example, insects that feed on complex sugars and neutralize, degrade, and sequester toxic secondary metabolites have recently been shown to benefit by acquiring genes through HGT.
Collapse
Affiliation(s)
- Ashish Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Oceania Chirom
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; Department of Plant Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India.
| |
Collapse
|
18
|
Nakabachi A, Piel J, Malenovský I, Hirose Y. Comparative Genomics Underlines Multiple Roles of Profftella, an Obligate Symbiont of Psyllids: Providing Toxins, Vitamins, and Carotenoids. Genome Biol Evol 2021; 12:1975-1987. [PMID: 32797185 PMCID: PMC7643613 DOI: 10.1093/gbe/evaa175] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2020] [Indexed: 12/27/2022] Open
Abstract
The Asian citrus psyllid Diaphorina citri (Insecta: Hemiptera: Psylloidea), a serious pest of citrus species worldwide, harbors vertically transmitted intracellular mutualists, Candidatus Profftella armatura (Profftella_DC, Gammaproteobacteria: Burkholderiales) and Candidatus Carsonella ruddii (Carsonella_DC, Gammaproteobacteria: Oceanospirillales). Whereas Carsonella_DC is a typical nutritional symbiont, Profftella_DC is a unique defensive symbiont with organelle-like features, including intracellular localization within the host, perfect infection in host populations, vertical transmission over evolutionary time, and drastic genome reduction down to much less than 1 Mb. Large parts of the 460-kb genome of Profftella_DC are devoted to genes for synthesizing a polyketide toxin; diaphorin. To better understand the evolution of this unusual symbiont, the present study analyzed the genome of Profftella_Dco, a sister lineage to Profftella_DC, using Diaphorina cf. continua, a host psyllid congeneric with D. citri. The genome of coresiding Carsonella (Carsonella_Dco) was also analyzed. The analysis revealed nearly perfect synteny conservation in these genomes with their counterparts from D. citri. The substitution rate analysis further demonstrated genomic stability of Profftella which is comparable to that of Carsonella. Profftella_Dco and Profftella_DC shared all genes for the biosynthesis of diaphorin, hemolysin, riboflavin, biotin, and carotenoids, underlining multiple roles of Profftella, which may contribute to stabilizing symbiotic relationships with the host. However, acyl carrier proteins were extensively amplified in polyketide synthases DipP and DipT for diaphorin synthesis in Profftella_Dco. This level of acyl carrier protein augmentation, unprecedented in modular polyketide synthases of any known organism, is not thought to influence the polyketide structure but may improve the synthesis efficiency.
Collapse
Affiliation(s)
- Atsushi Nakabachi
- Electronics-Inspired Interdisciplinary Research Institute (EIIRIS), Toyohashi University of Technology, Japan.,Department of Applied Chemistry and Life Sciences, Toyohashi University of Technology, Japan
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland
| | - Igor Malenovský
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Yuu Hirose
- Department of Applied Chemistry and Life Sciences, Toyohashi University of Technology, Japan
| |
Collapse
|
19
|
Zhao C, Miao S, Yin Y, Zhu Y, Nabity P, Bansal R, Liu C. Tripartite parasitic and symbiotic interactions as a possible mechanism of horizontal gene transfer. Ecol Evol 2021; 11:7018-7028. [PMID: 34141272 PMCID: PMC8207144 DOI: 10.1002/ece3.7550] [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: 03/11/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 12/03/2022] Open
Abstract
Herbivory is a highly sophisticated feeding behavior that requires abilities of plant defense suppression, phytochemical detoxification, and plant macromolecule digestion. For plant-sucking insects, salivary glands (SGs) play important roles in herbivory by secreting and injecting proteins into plant tissues to facilitate feeding. Little is known on how insects evolved secretory SG proteins for such specialized functions. Here, we investigated the composition and evolution of secretory SG proteins in the brown marmorated stink bug (Halyomorpha halys) and identified a group of secretory SG phospholipase C (PLC) genes with highest sequence similarity to the bacterial homologs. Further analyses demonstrated that they were most closely related to PLCs of Xenorhabdus, a genus of Gammaproteobacteria living in symbiosis with insect-parasitizing nematodes. These suggested that H. halys might acquire these PLCs from Xenorhabdus through the mechanism of horizontal gene transfer (HGT), likely mediated by a nematode during its parasitizing an insect host. We also showed that the original HGT event was followed by gene duplication and expansion, leading to functional diversification of the bacterial-origin PLC genes in H. halys. Thus, this study suggested that an herbivore might enhance adaptation through gaining genes from an endosymbiont of its parasite in the tripartite parasitic and symbiotic interactions.
Collapse
Affiliation(s)
- Chaoyang Zhao
- Department of Botany and Plant SciencesUniversity of California RiversideRiversideCAUSA
| | - Shaoming Miao
- Sino‐American Biological Control LaboratoryInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Yanfang Yin
- Sino‐American Biological Control LaboratoryInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Yanjuan Zhu
- Sino‐American Biological Control LaboratoryInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Paul Nabity
- Department of Botany and Plant SciencesUniversity of California RiversideRiversideCAUSA
| | - Raman Bansal
- USDA‐ARSSan Joaquin Valley Agricultural Sciences CenterParlierCAUSA
| | - Chenxi Liu
- Sino‐American Biological Control LaboratoryInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| |
Collapse
|
20
|
Kett S, Pathak A, Turillazzi S, Cavalieri D, Marvasi M. Antifungals, arthropods and antifungal resistance prevention: lessons from ecological interactions. Proc Biol Sci 2021; 288:20202716. [PMID: 33529557 DOI: 10.1098/rspb.2020.2716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Arthropods can produce a wide range of antifungal compounds, including specialist proteins, cuticular products, venoms and haemolymphs. In spite of this, many arthropod taxa, particularly eusocial insects, make use of additional antifungal compounds derived from their mutualistic association with microbes. Because multiple taxa have evolved such mutualisms, it must be assumed that, under certain ecological circumstances, natural selection has favoured them over those relying upon endogenous antifungal compound production. Further, such associations have been shown to persist versus specific pathogenic fungal antagonists for more than 50 million years, suggesting that compounds employed have retained efficacy in spite of the pathogens' capacity to develop resistance. We provide a brief overview of antifungal compounds in the arthropods' armoury, proposing a conceptual model to suggest why their use remains so successful. Fundamental concepts embedded within such a model may suggest strategies by which to reduce the rise of antifungal resistance within the clinical milieu.
Collapse
Affiliation(s)
- Steve Kett
- Department of Natural Sciences, Middlesex University London, London, UK
| | - Ayush Pathak
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
| | - Stefano Turillazzi
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy.,Insect Pharma Entomotherapy S.r.l, Sesto Fiorentino, Florence, Italy
| | - Duccio Cavalieri
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Massimiliano Marvasi
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
| |
Collapse
|
21
|
Li HS, Tang XF, Huang YH, Xu ZY, Chen ML, Du XY, Qiu BY, Chen PT, Zhang W, Ślipiński A, Escalona HE, Waterhouse RM, Zwick A, Pang H. Horizontally acquired antibacterial genes associated with adaptive radiation of ladybird beetles. BMC Biol 2021; 19:7. [PMID: 33446206 PMCID: PMC7807722 DOI: 10.1186/s12915-020-00945-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/22/2020] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Horizontal gene transfer (HGT) has been documented in many herbivorous insects, conferring the ability to digest plant material and promoting their remarkable ecological diversification. Previous reports suggest HGT of antibacterial enzymes may have contributed to the insect immune response and limit bacterial growth. Carnivorous insects also display many evolutionary successful lineages, but in contrast to the plant feeders, the potential role of HGTs has been less well-studied. RESULTS Using genomic and transcriptomic data from 38 species of ladybird beetles, we identified a set of bacterial cell wall hydrolase (cwh) genes acquired by this group of beetles. Infection with Bacillus subtilis led to upregulated expression of these ladybird cwh genes, and their recombinantly produced proteins limited bacterial proliferation. Moreover, RNAi-mediated cwh knockdown led to downregulation of other antibacterial genes, indicating a role in antibacterial immune defense. cwh genes are rare in eukaryotes, but have been maintained in all tested Coccinellinae species, suggesting that this putative immune-related HGT event played a role in the evolution of this speciose subfamily of predominant predatory ladybirds. CONCLUSION Our work demonstrates that, in a manner analogous to HGT-facilitated plant feeding, enhanced immunity through HGT might have played a key role in the prey adaptation and niche expansion that promoted the diversification of carnivorous beetle lineages. We believe that this represents the first example of immune-related HGT in carnivorous insects with an association with a subsequent successful species radiation.
Collapse
Affiliation(s)
- Hao-Sen Li
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xue-Fei Tang
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yu-Hao Huang
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Ze-Yu Xu
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Mei-Lan Chen
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
- School of Environment and Life Science, Nanning Normal University, Nanning, 530001, China
| | - Xue-Yong Du
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Bo-Yuan Qiu
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Pei-Tao Chen
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Wei Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Adam Ślipiński
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Hermes E Escalona
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Hong Pang
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China.
| |
Collapse
|
22
|
Nakabachi A, Malenovský I, Gjonov I, Hirose Y. 16S rRNA Sequencing Detected Profftella, Liberibacter, Wolbachia, and Diplorickettsia from Relatives of the Asian Citrus Psyllid. MICROBIAL ECOLOGY 2020; 80:410-422. [PMID: 32052099 DOI: 10.1007/s00248-020-01491-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 01/31/2020] [Indexed: 06/10/2023]
Abstract
The Asian citrus psyllid Diaphorina citri (Hemiptera: Psylloidea) is a serious pest of citrus species worldwide because it transmits Candidatus Liberibacter spp. (Alphaproteobacteria: Rhizobiales), the causative agents of the incurable citrus disease, huanglongbing or greening disease. Diaphorina citri possesses a specialized organ called a bacteriome, which harbors vertically transmitted intracellular mutualists, Ca. Carsonella ruddii (Gammaproteobacteria: Oceanospirillales) and Ca. Profftella armatura (Gammaproteobacteria: Betaproteobacteriales). Whereas Carsonella is a typical nutritional symbiont, Profftella is an unprecedented type of toxin-producing defensive symbiont, unusually sharing organelle-like features with nutritional symbionts. Additionally, many D. citri strains are infected with Wolbachia, which manipulate reproduction in various arthropod hosts. In the present study, in an effort to obtain insights into the evolution of symbioses between Diaphorina and bacteria, microbiomes of psyllids closely related to D. citri were investigated. Bacterial populations of Diaphorina cf. continua and Diaphorina lycii were analyzed using Illumina sequencing of 16S rRNA gene amplicons and compared with data obtained from D. citri. The analysis revealed that all three Diaphorina spp. harbor Profftella as well as Carsonella lineages, implying that Profftella is widespread within the genus Diaphorina. Moreover, the analysis identified Ca. Liberibacter europaeus and Diplorickettsia sp. (Gammaproteobacteria: Diplorickettsiales) in D. cf. continua, and a total of four Wolbachia (Alphaproteobacteria: Rickettsiales) lineages in the three psyllid species. These results provide deeper insights into the interactions among insects, bacteria, and plants, which would eventually help to better manage horticulture.
Collapse
Affiliation(s)
- Atsushi Nakabachi
- Electronics-Inspired Interdisciplinary Research Institute (EIIRIS), Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan.
- Department of Applied Chemistry and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan.
| | - Igor Malenovský
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37, Brno, Czech Republic
| | - Ilia Gjonov
- Department of Zoology and Anthropology, Faculty of Biology, Sofia University, Dragan Tzankov 8, 1164, Sofia, Bulgaria
| | - Yuu Hirose
- Department of Applied Chemistry and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580, Japan
| |
Collapse
|
23
|
Lapadula WJ, Marcet PL, Taracena ML, Lenhart A, Juri Ayub M. Characterization of horizontally acquired ribotoxin encoding genes and their transcripts in Aedes aegypti. Gene 2020; 754:144857. [PMID: 32512159 DOI: 10.1016/j.gene.2020.144857] [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: 04/20/2020] [Revised: 06/01/2020] [Accepted: 06/04/2020] [Indexed: 10/24/2022]
Abstract
Ribosome Inactivating Proteins (RIPs) are RNA N-glycosidases that depurinate a specific adenine residue in the conserved sarcin/ricin loop of the 28S rRNA. The occurrence of RIP genes has been described in a wide range of plant taxa, as well as in several species of bacteria and fungi. A remarkable case is the presence of these genes in metazoans belonging to the Culicinae subfamily. We reported that these genes are derived from a single horizontal gene transfer event, most likely from a bacterial donor species. Moreover, we have shown evidence that mosquito RIP genes are evolving under purifying selection, suggesting that these toxins have acquired a functional role in these organisms. In the present work, we characterized the intra-specific sequence variability of Aedes aegypti RIP genes (RIPAe1, RIPAe2, and RIPAe3) and tested their expression at the mRNA level. Our results show that RIPAe2 and RIPAe3 are transcribed and polyadenylated, and their expression levels are modulated across the developmental stages. Varibility among genes was observed, including the existence of null alleles for RIPAe1 and RIPAe2, with variants showing partial deletions. These results further support the existence of a physiological function for these foreign genes in mosquitoes. The possible nature of this functionality is discussed.
Collapse
Affiliation(s)
- Walter J Lapadula
- Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, IMIBIO-SL-CONICET and Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejercito de Los Andes, 950, D5700HHW San Luis, Argentina
| | - Paula L Marcet
- Centers for Disease Control and Prevention, Division of Parasitic Diseases and Malaria, Entomology Branch. 1600 Clifton Road, Atlanta, GA 30333, USA.
| | - Mabel L Taracena
- Centers for Disease Control and Prevention, Division of Parasitic Diseases and Malaria, Entomology Branch. 1600 Clifton Road, Atlanta, GA 30333, USA
| | - Audrey Lenhart
- Centers for Disease Control and Prevention, Division of Parasitic Diseases and Malaria, Entomology Branch. 1600 Clifton Road, Atlanta, GA 30333, USA
| | - Maximiliano Juri Ayub
- Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, IMIBIO-SL-CONICET and Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejercito de Los Andes, 950, D5700HHW San Luis, Argentina.
| |
Collapse
|
24
|
Nakabachi A, Fujikami M. Concentration and distribution of diaphorin, and expression of diaphorin synthesis genes during Asian citrus psyllid development. JOURNAL OF INSECT PHYSIOLOGY 2019; 118:103931. [PMID: 31442480 DOI: 10.1016/j.jinsphys.2019.103931] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/19/2019] [Accepted: 08/19/2019] [Indexed: 06/10/2023]
Abstract
The Asian citrus psyllid Diaphorina citri Kuwayama (Hemiptera: Sternorrhyncha: Psylloidea: Liviidae) is an important pest of citrus species worldwide because it transmits Candidatus Liberibacter spp. (Alphaproteobacteria); the causative agents of an incurable citrus disease known as huanglongbing or greening disease. D. citri possesses a vertically transmitted intracellular symbiont, Candidatus Profftella armatura (Betaproteobacteria), which produces diaphorin; a polyketide that is toxic to various eukaryotic organisms. Our previous study demonstrated that the total amount and average concentration of diaphorin in adult D. citri, when homogeneous distribution is assumed within the insect, are sufficient to exert inhibitory effects on fungi and insects, including the Asian lady beetle Harmonia axyridis (Coleoptera: Coccinellidae); one of the major predators of D. citri. However, diaphorin may be localized to a limited body area within D. citri, and its concentration may change during development. In the present study, to better understand the physiological and ecological function of diaphorin, we assessed the distribution of diaphorin within the D. citri body and analyzed concentrations of diaphorin in various developmental stages. Expression of genes involved in diaphorin synthesis was also analyzed. The results demonstrated that diaphorin is distributed widely in the D. citri body, which appears to be a prerequisite for effective deterrence of natural enemies. The concentration of diaphorin was shown to change significantly during the development of D. citri. It was highest in mature adults, followed by embryos and teneral adults, and lowest in nymphs. The lowest concentrations of diaphorin observed in nymphs are still presumed to be effective in deterring invasive natural enemies, including parasites, parasitoids, and entomopathogenic fungi. Quantitative RT-PCR indicated that amounts of transcripts for diaphorin synthesis genes dipP and dipT were at a minimum in embryos, increased during the nymphal period, and reached a maximum level just after adult eclosion. The alteration pattern of the amounts of transcripts for diaphorin synthesis genes appeared to partially disagree with that of the concentration of diaphorin. The present study provides new insights into the function of diaphorin, which is essential for further investigations that aim to improve the efficacy of D. citri biological control.
Collapse
Affiliation(s)
- Atsushi Nakabachi
- Electronics-Inspired Interdisciplinary Research Institute (EIIRIS), Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan; Department of Applied Chemistry and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan.
| | - Masaya Fujikami
- Department of Applied Chemistry and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan
| |
Collapse
|
25
|
Nakabachi A, Okamura K. Diaphorin, a polyketide produced by a bacterial symbiont of the Asian citrus psyllid, kills various human cancer cells. PLoS One 2019; 14:e0218190. [PMID: 31181122 PMCID: PMC6557518 DOI: 10.1371/journal.pone.0218190] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 05/28/2019] [Indexed: 12/15/2022] Open
Abstract
Diaphorin is a polyketide produced by Candidatus Profftella armatura (Betaproteobacteria), an organelle-like defensive symbiont harbored by a plant sap-sucking insect, Asian citrus psyllid Diaphorina citri (Hemiptera: Liviidae). Diaphorin belongs to the pederin family, a group of compounds that share much of their core structure with that of pederin, which is characterized by two dihydropyran rings bridged by an N-acyl aminal. Most members of this family have potent antitumor activity, making them promising anticancer drug candidates. The present study assessed the therapeutic potential of diaphorin for its antitumor activity against 39 human cancer cell lines including those from breast, brain, colon, lung, skin, ovary, kidney, stomach, and prostate. The results showed that diaphorin had inhibitory activity against all 39 cancer cell lines tested. The GI50, TGI, and LC50 values ranged from 0.28 μM- 2.4 μM, 1.6 μM -11 μM, and 7.5 μM-> 100 μM, respectively. These values are among the highest in the pederin family, indicating that the anticancer activity of diaphorin is milder than those of other pederin congeners. The inhibitory effects of diaphorin significantly differed among the distinct cancer types. The maximum difference was about 10-fold, which was similar to those of most other pederin congeners.
Collapse
Affiliation(s)
- Atsushi Nakabachi
- Electronics-Inspired Interdisciplinary Research Institute (EIIRIS), Toyohashi University of Technology, Toyohashi, Aichi, Japan
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Toyohashi, Aichi, Japan
| | - Keiko Okamura
- Electronics-Inspired Interdisciplinary Research Institute (EIIRIS), Toyohashi University of Technology, Toyohashi, Aichi, Japan
| |
Collapse
|
26
|
Yamada T, Hamada M, Floreancig P, Nakabachi A. Diaphorin, a polyketide synthesized by an intracellular symbiont of the Asian citrus psyllid, is potentially harmful for biological control agents. PLoS One 2019; 14:e0216319. [PMID: 31048920 PMCID: PMC6497295 DOI: 10.1371/journal.pone.0216319] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/19/2019] [Indexed: 12/03/2022] Open
Abstract
The Asian citrus psyllid Diaphorina citri Kuwayama (Hemiptera: Sternorrhyncha: Psylloidea: Liviidae) is an important pest of citrus species worldwide because it transmits Candidatus Liberibacter spp. (Alphaproteobacteria), the causative agents of an incurable citrus disease known as huanglongbing or greening disease. Diaphorina citri possesses a vertically-transmitted intracellular symbiont, Candidatus Profftella armatura (Betaproteobacteria), which produces diaphorin, a polyketide that is significantly toxic to mammalian cells. Diaphorin is an analog of pederin, a defensive polyketide in the body fluid of Paederus rove beetles (Coleoptera: Staphylinidae) that deters predators. In the present study, as a first step to assess the possibility that diaphorin is toxic to biological control agents, we assayed diaphorin activities against insects and fungi. The target cells and organisms were (a) the Sf9 cell line derived from the fall armyworm moth Spodoptera frugiperda (Lepidoptera: Noctuidae), (b) the pea aphid Acyrthosiphon pisum (Hemiptera: Sternorrhyncha: Aphidoidea: Aphididae), a phloem sap-sucking insect that is closely related to psyllids, (c) the Asian lady beetle Harmonia axyridis (Coleoptera: Coccinellidae), one of the major predators of D. citri, and (d) the budding yeast Saccharomyces cerevisiae (Ascomycota: Saccharomycetes) as a model of fungal pathogens. For a comparison, we also evaluated pederin activities. The results of our analyses revealed the following: (1) Diaphorin and pederin are significantly toxic to the tested insects and yeast; (2) Their toxicities vary widely among the target cells and organisms; (3) Diaphorin is generally less toxic than pederin; (4) The toxicities of diaphorin and pederin are considerably different in the Sf9 insect cell line and S. cerevisiae, but similar in A. pisum and H. axyridis; and (5) The amount of diaphorin contained in D. citri is toxic to all of the tested cells and organisms, suggesting that this polyketide is potentially harmful for biological control agents.
Collapse
Affiliation(s)
- Tomoko Yamada
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Toyohashi, Aichi, Japan
| | - Masato Hamada
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Toyohashi, Aichi, Japan
| | - Paul Floreancig
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Atsushi Nakabachi
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Toyohashi, Aichi, Japan
- Electronics-Inspired Interdisciplinary Research Institute (EIIRIS), Toyohashi University of Technology, Toyohashi, Aichi, Japan
| |
Collapse
|
27
|
Petersen M, Armisén D, Gibbs RA, Hering L, Khila A, Mayer G, Richards S, Niehuis O, Misof B. Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects. BMC Evol Biol 2019; 19:11. [PMID: 30626321 PMCID: PMC6327564 DOI: 10.1186/s12862-018-1324-9] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 12/11/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are a major component of metazoan genomes and are associated with a variety of mechanisms that shape genome architecture and evolution. Despite the ever-growing number of insect genomes sequenced to date, our understanding of the diversity and evolution of insect TEs remains poor. RESULTS Here, we present a standardized characterization and an order-level comparison of arthropod TE repertoires, encompassing 62 insect and 11 outgroup species. The insect TE repertoire contains TEs of almost every class previously described, and in some cases even TEs previously reported only from vertebrates and plants. Additionally, we identified a large fraction of unclassifiable TEs. We found high variation in TE content, ranging from less than 6% in the antarctic midge (Diptera), the honey bee and the turnip sawfly (Hymenoptera) to more than 58% in the malaria mosquito (Diptera) and the migratory locust (Orthoptera), and a possible relationship between the content and diversity of TEs and the genome size. CONCLUSION While most insect orders exhibit a characteristic TE composition, we also observed intraordinal differences, e.g., in Diptera, Hymenoptera, and Hemiptera. Our findings shed light on common patterns and reveal lineage-specific differences in content and evolution of TEs in insects. We anticipate our study to provide the basis for future comparative research on the insect TE repertoire.
Collapse
Affiliation(s)
- Malte Petersen
- University of Bonn, Bonn, Germany
- Zoological Research Museum Alexander Koenig, Center for Molecular Biodiversity Research, Adenauerallee 160, Bonn, 53113 Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, Frankfurt, 60325 Germany
| | - David Armisén
- Université de Lyon, Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d’Italie, Lyon, 69364 France
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, 77030 TX USA
| | - Lars Hering
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, Kassel, 34132 Germany
| | - Abderrahman Khila
- Université de Lyon, Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d’Italie, Lyon, 69364 France
| | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, Kassel, 34132 Germany
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, 77030 TX USA
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute for Biology I (Zoology), University of Freiburg, Freiburg (Brsg.), 79104 Germany
| | - Bernhard Misof
- Zoological Research Museum Alexander Koenig, Center for Molecular Biodiversity Research, Adenauerallee 160, Bonn, 53113 Germany
| |
Collapse
|
28
|
Dan H, Ikeda N, Fujikami M, Nakabachi A. Behavior of bacteriome symbionts during transovarial transmission and development of the Asian citrus psyllid. PLoS One 2017; 12:e0189779. [PMID: 29240843 PMCID: PMC5730177 DOI: 10.1371/journal.pone.0189779] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 12/01/2017] [Indexed: 02/07/2023] Open
Abstract
The Asian citrus psyllid Diaphorina citri Kuwayama (Hemiptera: Liviidae) is a serious pest worldwide, transmitting Candidatus Liberibacter spp. (Alphaproteobacteria), the causative agents of a devastating citrus disease known as huanglongbing or greening disease. In a symbiotic organ called the bacteriome, D. citri possesses an organelle-like defensive symbiont, Candidatus Profftella armatura (Betaproteobacteria), and a nutritional symbiont, Ca. Carsonella ruddii (Gammaproteobacteria). Drastically reduced symbiont genomes and metabolic complementarity among the symbionts and D. citri indicate their mutually indispensable association. Moreover, horizontal gene transfer between the Profftella and Liberibacter lineages suggests ecological and evolutionary interactions between the bacteriome symbiont and the HLB pathogen. Using fluorescence in situ hybridization, we examined the behavior of Profftella and Carsonella during transovarial transmission and the development of D. citri. In the bacteriomes of sexually-mature female adults, symbionts transformed from an extremely elongated tubular form into spherical or short-rod forms, which migrated toward the ovary. The symbionts then formed mosaic masses, which entered at the posterior pole of the vitellogenic oocytes. After anatrepsis, Carsonella and Profftella migrated to the central and peripheral parts of the mass, respectively. Following the appearance of host nuclei, the mass cellularized, segregating Carsonella and Profftella in the central syncytium and peripheral uninucleate bacteriocytes, respectively. Subsequently, the uninucleate bacteriocytes harboring Profftella assembled at the posterior pole, while the syncytium, containing Carsonella, sat on the anterior side facing the germ band initiating katatrepsis. During dorsal closure, the syncytium was divided into uninuclear bacteriocytes, which surrounded the mass of bacteriocytes containing Profftella. Once fully surrounded, the bacteriocyte mass containing Profftella was fused into a syncytium. Prior to hatching, a pair of wing-like protrusions arose from both lateral sides of the bacteriome, which continued to grow throughout the nymphal stages. These findings provide a foundation for better understanding the intricate relationship between D. citri and its microbiota.
Collapse
Affiliation(s)
- Hiroki Dan
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Toyohashi, Aichi, Japan
| | - Naoya Ikeda
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Toyohashi, Aichi, Japan
| | - Masaya Fujikami
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Toyohashi, Aichi, Japan
| | - Atsushi Nakabachi
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Toyohashi, Aichi, Japan
- Electronics-Inspired Interdisciplinary Research Institute (EIIRIS), Toyohashi University of Technology, Toyohashi, Aichi, Japan
| |
Collapse
|
29
|
Sudakaran S, Kost C, Kaltenpoth M. Symbiont Acquisition and Replacement as a Source of Ecological Innovation. Trends Microbiol 2017; 25:375-390. [DOI: 10.1016/j.tim.2017.02.014] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 02/24/2017] [Accepted: 02/28/2017] [Indexed: 10/19/2022]
|
30
|
Nakao R, Abe T, Funayama S, Sugimoto C. Horizontally Transferred Genetic Elements in the Tsetse Fly Genome: An Alignment-Free Clustering Approach Using Batch Learning Self-Organising Map (BLSOM). BIOMED RESEARCH INTERNATIONAL 2016; 2016:3164624. [PMID: 28074180 PMCID: PMC5198169 DOI: 10.1155/2016/3164624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/26/2016] [Accepted: 11/08/2016] [Indexed: 12/02/2022]
Abstract
Tsetse flies (Glossina spp.) are the primary vectors of trypanosomes, which can cause human and animal African trypanosomiasis in Sub-Saharan African countries. The objective of this study was to explore the genome of Glossina morsitans morsitans for evidence of horizontal gene transfer (HGT) from microorganisms. We employed an alignment-free clustering method, that is, batch learning self-organising map (BLSOM), in which sequence fragments are clustered based on the similarity of oligonucleotide frequencies independently of sequence homology. After an initial scan of HGT events using BLSOM, we identified 3.8% of the tsetse fly genome as HGT candidates. The predicted donors of these HGT candidates included known symbionts, such as Wolbachia, as well as bacteria that have not previously been associated with the tsetse fly. We detected HGT candidates from diverse bacteria such as Bacillus and Flavobacteria, suggesting a past association between these taxa. Functional annotation revealed that the HGT candidates encoded loci in various functional pathways, such as metabolic and antibiotic biosynthesis pathways. These findings provide a basis for understanding the coevolutionary history of the tsetse fly and its microbes and establish the effectiveness of BLSOM for the detection of HGT events.
Collapse
Affiliation(s)
- Ryo Nakao
- Unit of Risk Analysis and Management, Hokkaido University Research Center for Zoonosis Control, Kita 20, Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0020, Japan
- Laboratory of Parasitology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Kita 18, Nishi 9, Kita-Ku, Sapporo, Hokkaido 060-0818, Japan
| | - Takashi Abe
- Graduate School of Science & Technology, Niigata University, No. 8050, Igarashi 2-no-cho, Nishi-ku, Niigata 950-2181, Japan
| | - Shunsuke Funayama
- Graduate School of Science & Technology, Niigata University, No. 8050, Igarashi 2-no-cho, Nishi-ku, Niigata 950-2181, Japan
| | - Chihiro Sugimoto
- Division of Collaboration and Education, Hokkaido University Research Center for Zoonosis Control, Kita 20, Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0020, Japan
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita 20, Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0020, Japan
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, P.O. Box 32379, Lusaka, Zambia
| |
Collapse
|
31
|
Linard B, Crampton-Platt A, Gillett CPDT, Timmermans MJTN, Vogler AP. Metagenome Skimming of Insect Specimen Pools: Potential for Comparative Genomics. Genome Biol Evol 2015; 7:1474-89. [PMID: 25979752 PMCID: PMC4494052 DOI: 10.1093/gbe/evv086] [Citation(s) in RCA: 30] [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] [Accepted: 05/09/2015] [Indexed: 01/08/2023] Open
Abstract
Metagenomic analyses are challenging in metazoans, but high-copy number and repeat regions can be assembled from low-coverage sequencing by "genome skimming," which is applied here as a new way of characterizing metagenomes obtained in an ecological or taxonomic context. Illumina shotgun sequencing on two pools of Coleoptera (beetles) of approximately 200 species each were assembled into tens of thousands of scaffolds. Repeated low-coverage sequencing recovered similar scaffold sets consistently, although approximately 70% of scaffolds could not be identified against existing genome databases. Identifiable scaffolds included mitochondrial DNA, conserved sequences with hits to expressed sequence tag and protein databases, and known repeat elements of high and low complexity, including numerous copies of rRNA and histone genes. Assemblies of histones captured a diversity of gene order and primary sequence in Coleoptera. Scaffolds with similarity to multiple sites in available coleopteran genome sequences for Dendroctonus and Tribolium revealed high specificity of scaffolds to either of these genomes, in particular for high-copy number repeats. Numerous "clusters" of scaffolds mapped to the same genomic site revealed intra- and/or intergenomic variation within a metagenome pool. In addition to effect of taxonomic composition of the metagenomes, the number of mapped scaffolds also revealed structural differences between the two reference genomes, although the significance of this striking finding remains unclear. Finally, apparently exogenous sequences were recovered, including potential food plants, fungal pathogens, and bacterial symbionts. The "metagenome skimming" approach is useful for capturing the genomic diversity of poorly studied, species-rich lineages and opens new prospects in environmental genomics.
Collapse
Affiliation(s)
- Benjamin Linard
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Alex Crampton-Platt
- Department of Life Sciences, Natural History Museum, London, United Kingdom Department of Genetics, Evolution and Environment, University College London, United Kingdom
| | | | - Martijn J T N Timmermans
- Department of Life Sciences, Natural History Museum, London, United Kingdom Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, United Kingdom
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, United Kingdom Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, United Kingdom
| |
Collapse
|