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Duncan RP, Anderson CMH, Thwaites DT, Luetje CW, Wilson ACC. Co-option of a conserved host glutamine transporter facilitates aphid/ Buchnera metabolic integration. Proc Natl Acad Sci U S A 2023; 120:e2308448120. [PMID: 37844224 PMCID: PMC10614625 DOI: 10.1073/pnas.2308448120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 09/14/2023] [Indexed: 10/18/2023] Open
Abstract
Organisms across the tree of life colonize novel environments by partnering with bacterial symbionts. These symbioses are characterized by intimate integration of host/endosymbiont biology at multiple levels, including metabolically. Metabolic integration is particularly important for sap-feeding insects and their symbionts, which supplement nutritionally unbalanced host diets. Many studies reveal parallel evolution of host/endosymbiont metabolic complementarity in amino acid biosynthesis, raising questions about how amino acid metabolism is regulated, how regulatory mechanisms evolve, and the extent to which similar mechanisms evolve in different systems. In the aphid/Buchnera symbiosis, the transporter ApGLNT1 (Acyrthosiphon pisum glutamine transporter 1) supplies glutamine, an amino donor in transamination reactions, to bacteriocytes (where Buchnera reside) and is competitively inhibited by Buchnera-supplied arginine-consistent with a role regulating amino acid metabolism given host demand for Buchnera-produced amino acids. We examined how ApGLNT1 evolved a regulatory role by functionally characterizing orthologs in insects with and without endosymbionts. ApGLNT1 orthologs are functionally similar, and orthology searches coupled with homology modeling revealed that GLNT1 is ancient and structurally conserved across insects. Our results indicate that the ApGLNT1 symbiotic regulatory role is derived from its ancestral role and, in aphids, is likely facilitated by loss of arginine biosynthesis through the urea cycle. Given consistent loss of host arginine biosynthesis and retention of endosymbiont arginine supply, we hypothesize that GLNT1 is a general mechanism regulating amino acid metabolism in sap-feeding insects. This work fills a gap, highlighting the broad importance of co-option of ancestral proteins to novel contexts in the evolution of host/symbiont systems.
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Affiliation(s)
| | - Catriona M. H. Anderson
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon TyneNE1 7RU, United Kingdom
| | - David T. Thwaites
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
| | - Charles W. Luetje
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL33136
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2
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Mongiardino Koch N, Thompson JR, Hiley AS, McCowin MF, Armstrong AF, Coppard SE, Aguilera F, Bronstein O, Kroh A, Mooi R, Rouse GW. Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record. eLife 2022; 11:72460. [PMID: 35315317 PMCID: PMC8940180 DOI: 10.7554/elife.72460] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 03/03/2022] [Indexed: 12/25/2022] Open
Abstract
Echinoids are key components of modern marine ecosystems. Despite a remarkable fossil record, the emergence of their crown group is documented by few specimens of unclear affinities, rendering their early history uncertain. The origin of sand dollars, one of its most distinctive clades, is also unclear due to an unstable phylogenetic context. We employ 18 novel genomes and transcriptomes to build a phylogenomic dataset with a near-complete sampling of major lineages. With it, we revise the phylogeny and divergence times of echinoids, and place their history within the broader context of echinoderm evolution. We also introduce the concept of a chronospace - a multidimensional representation of node ages - and use it to explore methodological decisions involved in time calibrating phylogenies. We find the choice of clock model to have the strongest impact on divergence times, while the use of site-heterogeneous models and alternative node prior distributions show minimal effects. The choice of loci has an intermediate impact, affecting mostly deep Paleozoic nodes, for which clock-like genes recover dates more congruent with fossil evidence. Our results reveal that crown group echinoids originated in the Permian and diversified rapidly in the Triassic, despite the relative lack of fossil evidence for this early diversification. We also clarify the relationships between sand dollars and their close relatives and confidently date their origins to the Cretaceous, implying ghost ranges spanning approximately 50 million years, a remarkable discrepancy with their rich fossil record.
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Affiliation(s)
- Nicolás Mongiardino Koch
- Department of Earth & Planetary Sciences, Yale University, New Haven, United States.,Scripps Institution of Oceanography, University of California San Diego, La Jolla, United States
| | - Jeffrey R Thompson
- Department of Earth Sciences, Natural History Museum, London, United Kingdom.,University College London Center for Life's Origins and Evolution, London, United Kingdom
| | - Avery S Hiley
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, United States
| | - Marina F McCowin
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, United States
| | - A Frances Armstrong
- Department of Invertebrate Zoology and Geology, California Academy of Sciences, San Francisco, United States
| | - Simon E Coppard
- Bader International Study Centre, Queen's University, Herstmonceux Castle, East Sussex, United Kingdom
| | - Felipe Aguilera
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Omri Bronstein
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.,Steinhardt Museum of Natural History, Tel-Aviv, Israel
| | - Andreas Kroh
- Department of Geology and Palaeontology, Natural History Museum Vienna, Vienna, Austria
| | - Rich Mooi
- Department of Invertebrate Zoology and Geology, California Academy of Sciences, San Francisco, United States
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, United States
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3
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Banfill CR, Wilson ACC, Lu HL. Further evidence that mechanisms of host/symbiont integration are dissimilar in the maternal versus embryonic Acyrthosiphon pisum bacteriome. EvoDevo 2020; 11:23. [PMID: 33292476 PMCID: PMC7654044 DOI: 10.1186/s13227-020-00168-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/29/2020] [Indexed: 03/29/2023] Open
Abstract
Background Host/symbiont integration is a signature of evolutionarily ancient, obligate endosymbioses. However, little is known about the cellular and developmental mechanisms of host/symbiont integration at the molecular level. Many insects possess obligate bacterial endosymbionts that provide essential nutrients. To advance understanding of the developmental and metabolic integration of hosts and endosymbionts, we track the localization of a non-essential amino acid transporter, ApNEAAT1, across asexual embryogenesis in the aphid, Acyrthosiphon pisum. Previous work in adult bacteriomes revealed that ApNEAAT1 functions to exchange non-essential amino acids at the A. pisum/Buchnera aphidicola symbiotic interface. Driven by amino acid concentration gradients, ApNEAAT1 moves proline, serine, and alanine from A. pisum to Buchnera and cysteine from Buchnera to A. pisum. Here, we test the hypothesis that ApNEAAT1 is localized to the symbiotic interface during asexual embryogenesis. Results During A. pisum asexual embryogenesis, ApNEAAT1 does not localize to the symbiotic interface. We observed ApNEAAT1 localization to the maternal follicular epithelium, the germline, and, in late-stage embryos, to anterior neural structures and insect immune cells (hemocytes). We predict that ApNEAAT1 provisions non-essential amino acids to developing oocytes and embryos, as well as to the brain and related neural structures. Additionally, ApNEAAT1 may perform roles related to host immunity. Conclusions Our work provides further evidence that the embryonic and adult bacteriomes of asexual A. pisum are not equivalent. Future research is needed to elucidate the developmental time point at which the bacteriome reaches maturity.
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Affiliation(s)
- Celeste R Banfill
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Alex C C Wilson
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA.
| | - Hsiao-Ling Lu
- Department of Biotechnology, National Formosa University, Huwei, Taiwan.
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4
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Thairu MW, Hansen AK. It's a small, small world: unravelling the role and evolution of small RNAs in organelle and endosymbiont genomes. FEMS Microbiol Lett 2019; 366:5371121. [PMID: 30844054 DOI: 10.1093/femsle/fnz049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 03/05/2019] [Indexed: 12/19/2022] Open
Abstract
Organelles and host-restricted bacterial symbionts are characterized by having highly reduced genomes that lack many key regulatory genes and elements. Thus, it has been hypothesized that the eukaryotic nuclear genome is primarily responsible for regulating these symbioses. However, with the discovery of organelle- and symbiont-expressed small RNAs (sRNAs) there is emerging evidence that these sRNAs may play a role in gene regulation as well. Here, we compare the diversity of organelle and bacterial symbiont sRNAs recently identified using genome-enabled '-omic' technologies and discuss their potential role in gene regulation. We also discuss how the genome architecture of small genomes may influence the evolution of these sRNAs and their potential function. Additionally, these new studies suggest that some sRNAs are conserved within organelle and symbiont taxa and respond to changes in the environment and/or their hosts. In summary, these results suggest that organelle and symbiont sRNAs may play a role in gene regulation in addition to nuclear-encoded host mechanisms.
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Affiliation(s)
- Margaret W Thairu
- Department of Entomology, University of California, Riverside, Riverside, CA, USA
| | - Allison K Hansen
- Department of Entomology, University of California, Riverside, Riverside, CA, USA
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5
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Bisch G, Neuvonen MM, Pierce NE, Russell JA, Koga R, Sanders JG, Lukasik P, Andersson SGE. Genome Evolution of Bartonellaceae Symbionts of Ants at the Opposite Ends of the Trophic Scale. Genome Biol Evol 2018; 10:1687-1704. [PMID: 29982531 PMCID: PMC6044324 DOI: 10.1093/gbe/evy126] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2018] [Indexed: 12/17/2022] Open
Abstract
Many insects rely on bacterial symbionts to supply essential amino acids and vitamins that are deficient in their diets, but metabolic comparisons of closely related gut bacteria in insects with different dietary preferences have not been performed. Here, we demonstrate that herbivorous ants of the genus Dolichoderus from the Peruvian Amazon host bacteria of the family Bartonellaceae, known for establishing chronic or pathogenic infections in mammals. We detected these bacteria in all studied Dolichoderus species, and found that they reside in the midgut wall, that is, the same location as many previously described nutritional endosymbionts of insects. The genomic analysis of four divergent strains infecting different Dolichoderus species revealed genes encoding pathways for nitrogen recycling and biosynthesis of several vitamins and all essential amino acids. In contrast, several biosynthetic pathways have been lost, whereas genes for the import and conversion of histidine and arginine to glutamine have been retained in the genome of a closely related gut bacterium of the carnivorous ant Harpegnathos saltator. The broad biosynthetic repertoire in Bartonellaceae of herbivorous ants resembled that of gut bacteria of honeybees that likewise feed on carbohydrate-rich diets. Taken together, the broad distribution of Bartonellaceae across Dolichoderus ants, their small genome sizes, the specific location within hosts, and the broad biosynthetic capability suggest that these bacteria are nutritional symbionts in herbivorous ants. The results highlight the important role of the host nutritional biology for the genomic evolution of the gut microbiota-and conversely, the importance of the microbiota for the nutrition of hosts.
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Affiliation(s)
- Gaelle Bisch
- Cell and Molecular Biology, Science for Life Laboratory, Department of Molecular Evolution, Uppsala University, Sweden
| | - Minna-Maria Neuvonen
- Cell and Molecular Biology, Science for Life Laboratory, Department of Molecular Evolution, Uppsala University, Sweden
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology, Harvard University
| | | | - Ryuichi Koga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Jon G Sanders
- Department of Organismic and Evolutionary Biology, Harvard University.,Department of Pediatrics, University of California San Diego, La Jolla
| | - Piotr Lukasik
- Department of Biology, Drexel University.,Division of Biological Sciences, University of Montana
| | - Siv G E Andersson
- Cell and Molecular Biology, Science for Life Laboratory, Department of Molecular Evolution, Uppsala University, Sweden
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Feng H, Wang L, Wuchty S, Wilson ACC. microRNA regulation in an ancient obligate endosymbiosis. Mol Ecol 2018; 27:1777-1793. [PMID: 29271121 DOI: 10.1111/mec.14464] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/20/2017] [Accepted: 11/28/2017] [Indexed: 01/03/2023]
Abstract
Although many insects are associated with obligate bacterial endosymbionts, the mechanisms by which these host/endosymbiont associations are regulated remain mysterious. While microRNAs (miRNAs) have been recently identified as regulators of host/microbe interactions, including host/pathogen and host/facultative endosymbiont interactions, the role miRNAs may play in mediating host/obligate endosymbiont interactions is virtually unknown. Here, we identified conserved miRNAs that potentially mediate symbiotic interactions between aphids and their obligate endosymbiont, Buchnera aphidicola. Using small RNA sequence data from Myzus persicae and Acyrthosiphon pisum, we annotated 93 M. persicae and 89 A. pisum miRNAs, among which 69 were shared. We found 14 miRNAs that were either highly expressed in aphid bacteriome, the Buchnera-housing tissue, or differentially expressed in bacteriome vs. gut, a non-Buchnera-housing tissue. Strikingly, 10 of these 14 miRNAs have been implicated previously in other host/microbe interaction studies. Investigating the interaction networks of these miRNAs using a custom computational pipeline, we identified 103 miRNA::mRNA interactions shared between M. persicae and A. pisum. Functional annotation of the shared mRNA targets revealed only two over-represented cluster of orthologous group categories: amino acid transport and metabolism, and signal transduction mechanisms. Our work supports a role for miRNAs in mediating host/symbiont interactions between aphids and their obligate endosymbiont Buchnera. In addition, our results highlight the probable importance of signal transduction mechanisms to host/endosymbiont coevolution.
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Affiliation(s)
- Honglin Feng
- Department of Biology, University of Miami, Coral Gables, FL, USA
| | - Lingyu Wang
- Department of Biology, University of Miami, Coral Gables, FL, USA
| | - Stefan Wuchty
- Department of Biology, University of Miami, Coral Gables, FL, USA.,Department of Computer Science, University of Miami, Coral Gables, FL, USA.,Center for Computational Science, University of Miami, Coral Gables, FL, USA.,Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Alex C C Wilson
- Department of Biology, University of Miami, Coral Gables, FL, USA
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7
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The challenges of integrating two genomes in one cell. Curr Opin Microbiol 2017; 41:89-94. [PMID: 29277086 DOI: 10.1016/j.mib.2017.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/26/2017] [Accepted: 12/10/2017] [Indexed: 11/22/2022]
Abstract
Mutualistic bacteria and mitochondria have small genomes that harbor host-essential genes. A major question is why a distinct bacterial or mitochondrial genome is needed to encode these functions. The dual location of genes demand two sets of information processing systems, coordination of gene expression and elaborate transport systems. A simpler solution would be to harbor all genes in a single genome. Functional gene transfers to the host nuclear genome is uncommon in mutualistic bacteria and lost gene functions are rather rescued by co-symbiotic bacteria. Recent findings suggest that the mitochondrial genome is retained to avoid conflicting signals between protein targeting pathways in the cell. However, if the selective pressure for oxygenic respiration is lost, the mitochondrial genome will start to deteriorate and soon be lost.
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8
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Skidmore IH, Hansen AK. The evolutionary development of plant-feeding insects and their nutritional endosymbionts. INSECT SCIENCE 2017; 24:910-928. [PMID: 28371395 DOI: 10.1111/1744-7917.12463] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 06/07/2023]
Abstract
Herbivorous insects have evolved diverse mechanisms enabling them to feed on plants with suboptimal nutrient availability. Low nutrient availability negatively impacts insect herbivore development and fitness. To overcome this obstacle numerous insect lineages have evolved intimate associations with nutritional endosymbionts. This is especially true for insects that specialize on nitrogen-poor substrates, as these insects are highly dependent on intracellular symbionts to provide nitrogen lacking in their insect host's diet. Emerging evidence in these systems suggest that the symbiont's and/or the insect's biosynthetic pathways are dynamically regulated throughout the insect's development to potentially cope with the insect's changing nutritional demands. In this review, we evaluate the evolutionary development of symbiotic insect cells (bacteriocytes) by comparing and contrasting genes and mechanisms involved in maintaining and regulating the nutritional symbiosis throughout insect development in a diversity of insect herbivore-endosymbiont associations. With new advances in genome sequencing and functional genomics, we evaluate to what extent nutritional symbioses are shaped by (i) the regulation of symbiont titer, (ii) the regulation of insect symbiosis genes, and (iii) the regulation of symbiont genes. We discuss how important these mechanisms are for the biosynthesis of essential amino acids and vitamins across insect life stages in divergent insect-symbiont systems. We conclude by suggesting future directions of research to further elucidate the evolutionary development of bacteriocytes and the impact of these nutritional symbioses on insect-plant interactions.
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Affiliation(s)
- Isabel H Skidmore
- Department of Entomology, University of Illinois, Urbana-Champaign, Illinois, USA
| | - Allison K Hansen
- Department of Entomology, University of Illinois, Urbana-Champaign, Illinois, USA
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9
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Lu HL, Chang CC, Wilson ACC. Amino acid transporters implicated in endocytosis of Buchnera during symbiont transmission in the pea aphid. EvoDevo 2016; 7:24. [PMID: 27895889 PMCID: PMC5117694 DOI: 10.1186/s13227-016-0061-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 11/04/2016] [Indexed: 12/29/2022] Open
Abstract
Background Many insects host their obligate, maternally transmitted symbiotic bacteria in specialized cells called bacteriocytes. One of the best-studied insect nutritional endosymbioses is that of the aphid and its endosymbiont, Buchnera aphidicola. Aphids and Buchnera are metabolically and developmentally integrated, but the molecular mechanisms underlying Buchnera transmission and coordination with aphid development remain largely unknown. Previous work using electron microscopy to study aphid asexual embryogenesis has revealed that Buchnera transmission involves exocytosis from a maternal bacteriocyte followed by endocytotic uptake by a blastula. While the importance of exo- and endocytic cellular processes for symbiont transmission is clear, the molecular mechanisms that regulate these processes are not known. Here, we shed light on the molecular mechanisms that regulate Buchnera transmission and developmental integration. Results We present the developmental atlas of ACYPI000536 and ACYPI008904 mRNAs during asexual embryogenesis in the pea aphid, Acyrthosiphon pisum. Immediately before Buchnera invasion, transcripts of both genes were detected by whole-mount in situ hybridization in the posterior syncytial nuclei of late blastula embryos. Following Buchnera invasion, expression of both genes was identified in the region occupied by Buchnera throughout embryogenesis. Notably during Buchnera migration, expression of both genes was not concomitant with the entirety of the bacterial mass but rather expression colocalized with Buchnera in the anterior region of the bacterial mass. In addition, we found that ACYPI000536 was expressed in nuclei at the leading edge of the bacterial mass, joining the bacterial mass in subsequent developmental stages. Finally, quantitative reverse transcription real-time PCR suggested that early in development both transcripts were maternally provisioned to embryos. Conclusions We venture that ACYPI000536 and ACYPI008904 function as nutrient sensors at the site of symbiont invasion to facilitate TOR-pathway-mediated endocytosis of Buchnera by the aphid blastula. Our data support earlier reports of bacteriocyte determination involving a two-step recruitment process but suggest that the second wave of recruitment occurs earlier than previously described. Finally, our work highlights that bacteriocyte-enriched amino acid transporter paralogs have additionally been retained to play novel developmental roles in both symbiont recruitment and bacteriome development. Electronic supplementary material The online version of this article (doi:10.1186/s13227-016-0061-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hsiao-Ling Lu
- Department of Biology, University of Miami, Coral Gables, FL 33146 USA ; Department of Entomology, College of Bioresources and Agriculture, National Taiwan University, Taipei, 10617 Taiwan ; Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, 10617 Taiwan
| | - Chun-Che Chang
- Department of Entomology, College of Bioresources and Agriculture, National Taiwan University, Taipei, 10617 Taiwan ; Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, 10617 Taiwan ; Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, 10617 Taiwan
| | - Alex C C Wilson
- Department of Biology, University of Miami, Coral Gables, FL 33146 USA
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