1
|
García-Lozano M, Henzler C, Porras MÁG, Pons I, Berasategui A, Lanz C, Budde H, Oguchi K, Matsuura Y, Pauchet Y, Goffredi S, Fukatsu T, Windsor D, Salem H. Paleocene origin of a streamlined digestive symbiosis in leaf beetles. Curr Biol 2024; 34:1621-1634.e9. [PMID: 38377997 DOI: 10.1016/j.cub.2024.01.070] [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: 12/18/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/22/2024]
Abstract
Timing the acquisition of a beneficial microbe relative to the evolutionary history of its host can shed light on the adaptive impact of a partnership. Here, we investigated the onset and molecular evolution of an obligate symbiosis between Cassidinae leaf beetles and Candidatus Stammera capleta, a γ-proteobacterium. Residing extracellularly within foregut symbiotic organs, Stammera upgrades the digestive physiology of its host by supplementing plant cell wall-degrading enzymes. We observe that Stammera is a shared symbiont across tortoise and hispine beetles that collectively comprise the Cassidinae subfamily, despite differences in their folivorous habits. In contrast to its transcriptional profile during vertical transmission, Stammera elevates the expression of genes encoding digestive enzymes while in the foregut symbiotic organs, matching the nutritional requirements of its host. Despite the widespread distribution of Stammera across Cassidinae beetles, symbiont acquisition during the Paleocene (∼62 mya) did not coincide with the origin of the subfamily. Early diverging lineages lack the symbiont and the specialized organs that house it. Reconstructing the ancestral state of host-beneficial factors revealed that Stammera encoded three digestive enzymes at the onset of symbiosis, including polygalacturonase-a pectinase that is universally shared. Although non-symbiotic cassidines encode polygalacturonase endogenously, their repertoire of plant cell wall-degrading enzymes is more limited compared with symbiotic beetles supplemented with digestive enzymes from Stammera. Highlighting the potential impact of a symbiotic condition and an upgraded metabolic potential, Stammera-harboring beetles exploit a greater variety of plants and are more speciose compared with non-symbiotic members of the Cassidinae.
Collapse
Affiliation(s)
- Marleny García-Lozano
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Christine Henzler
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen 72076, Germany
| | | | - Inès Pons
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Aileen Berasategui
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen 72076, Germany; Amsterdam Institute for Life and Environment, Vrije Universiteit, Amsterdam 1081 HV, the Netherlands
| | - Christa Lanz
- Genome Center, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Heike Budde
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Kohei Oguchi
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan; Misaki Marine Biological Station, The University of Tokyo, Miura 238-0225, Japan
| | - Yu Matsuura
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan
| | - Yannick Pauchet
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Shana Goffredi
- Department of Biology, Occidental College, Los Angeles, CA 90041, USA
| | - Takema Fukatsu
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
| | - Donald Windsor
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama
| | - Hassan Salem
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen 72076, Germany; Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama.
| |
Collapse
|
2
|
Spencer N, Łukasik P, Meyer M, Veloso C, McCutcheon JP. No Transcriptional Compensation for Extreme Gene Dosage Imbalance in Fragmented Bacterial Endosymbionts of Cicadas. Genome Biol Evol 2023; 15:evad100. [PMID: 37267326 PMCID: PMC10287537 DOI: 10.1093/gbe/evad100] [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: 04/06/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/04/2023] Open
Abstract
Bacteria that form long-term intracellular associations with host cells lose many genes, a process that often results in tiny, gene-dense, and stable genomes. Paradoxically, the some of the same evolutionary processes that drive genome reduction and simplification may also cause genome expansion and complexification. A bacterial endosymbiont of cicadas, Hodgkinia cicadicola, exemplifies this paradox. In many cicada species, a single Hodgkinia lineage with a tiny, gene-dense genome has split into several interdependent cell and genome lineages. Each new Hodgkinia lineage encodes a unique subset of the ancestral unsplit genome in a complementary way, such that the collective gene contents of all lineages match the total found in the ancestral single genome. This splitting creates genetically distinct Hodgkinia cells that must function together to carry out basic cellular processes. It also creates a gene dosage problem where some genes are encoded by only a small fraction of cells while others are much more abundant. Here, by sequencing DNA and RNA of Hodgkinia from different cicada species with different amounts of splitting-along with its structurally stable, unsplit partner endosymbiont Sulcia muelleri-we show that Hodgkinia does not transcriptionally compensate to rescue the wildly unbalanced gene and genome ratios that result from lineage splitting. We also find that Hodgkinia has a reduced capacity for basic transcriptional control independent of the splitting process. Our findings reveal another layer of degeneration further pushing the limits of canonical molecular and cell biology in Hodgkinia and may partially explain its propensity to go extinct through symbiont replacement.
Collapse
Affiliation(s)
- Noah Spencer
- Biodesign Center for Mechanisms of Evolution and School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Piotr Łukasik
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Mariah Meyer
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Claudio Veloso
- Department of Ecological Sciences, Science Faculty, University of Chile, Santiago, Chile
| | - John P McCutcheon
- Biodesign Center for Mechanisms of Evolution and School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| |
Collapse
|
3
|
Salem H, Kirsch R, Pauchet Y, Berasategui A, Fukumori K, Moriyama M, Cripps M, Windsor D, Fukatsu T, Gerardo NM. Symbiont Digestive Range Reflects Host Plant Breadth in Herbivorous Beetles. Curr Biol 2020; 30:2875-2886.e4. [PMID: 32502409 DOI: 10.1016/j.cub.2020.05.043] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 04/05/2020] [Accepted: 05/12/2020] [Indexed: 02/07/2023]
Abstract
Numerous adaptations are gained in light of a symbiotic lifestyle. Here, we investigated the obligate partnership between tortoise leaf beetles (Chrysomelidae: Cassidinae) and their pectinolytic Stammera symbionts to detail how changes to the bacterium's streamlined metabolic range can shape the digestive physiology and ecological opportunity of its herbivorous host. Comparative genomics of 13 Stammera strains revealed high functional conservation, highlighted by the universal presence of polygalacturonase, a primary pectinase targeting nature's most abundant pectic class, homogalacturonan (HG). Despite this conservation, we unexpectedly discovered a disparate distribution for rhamnogalacturonan lyase, a secondary pectinase hydrolyzing the pectic heteropolymer, rhamnogalacturonan I (RG-I). Consistent with the annotation of rhamnogalacturonan lyase in Stammera, cassidines are able to depolymerize RG-I relative to beetles whose symbionts lack the gene. Given the omnipresence of HG and RG-I in foliage, Stammera that encode pectinases targeting both substrates allow their hosts to overcome a greater diversity of plant cell wall polysaccharides and maximize access to the nutritionally rich cytosol. Possibly facilitated by their symbionts' expanded digestive range, cassidines additionally endowed with rhamnogalacturonan lyase appear to utilize a broader diversity of angiosperms than those beetles whose symbionts solely supplement polygalacturonase. Our findings highlight how symbiont metabolic diversity, in concert with host adaptations, may serve as a potential source of evolutionary innovations for herbivorous lineages.
Collapse
Affiliation(s)
- Hassan Salem
- Department of Biology, Emory University, Atlanta, GA 30322, USA; National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA; Mutualisms Research Group, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany.
| | - Roy Kirsch
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Yannick Pauchet
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | | | - Kayoko Fukumori
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
| | - Minoru Moriyama
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
| | - Michael Cripps
- AgResearch, Lincoln Research Centre, Lincoln 7608, New Zealand
| | - Donald Windsor
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama
| | - Takema Fukatsu
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
| | | |
Collapse
|
4
|
Abstract
Bacteria participate in a wide diversity of symbiotic associations with eukaryotic hosts that require precise interactions for bacterial recognition and persistence. Most commonly, host-associated bacteria interfere with host gene expression to modulate the immune response to the infection. However, many of these bacteria also interfere with host cellular differentiation pathways to create a hospitable niche, resulting in the formation of novel cell types, tissues, and organs. In both of these situations, bacterial symbionts must interact with eukaryotic regulatory pathways. Here, we detail what is known about how bacterial symbionts, from pathogens to mutualists, control host cellular differentiation across the central dogma, from epigenetic chromatin modifications, to transcription and mRNA processing, to translation and protein modifications. We identify four main trends from this survey. First, mechanisms for controlling host gene expression appear to evolve from symbionts co-opting cross-talk between host signaling pathways. Second, symbiont regulatory capacity is constrained by the processes that drive reductive genome evolution in host-associated bacteria. Third, the regulatory mechanisms symbionts exhibit correlate with the cost/benefit nature of the association. And, fourth, symbiont mechanisms for interacting with host genetic regulatory elements are not bound by native bacterial capabilities. Using this knowledge, we explore how the ubiquitous intracellular Wolbachia symbiont of arthropods and nematodes may modulate host cellular differentiation to manipulate host reproduction. Our survey of the literature on how infection alters gene expression in Wolbachia and its hosts revealed that, despite their intermediate-sized genomes, different strains appear capable of a wide diversity of regulatory manipulations. Given this and Wolbachia's diversity of phenotypes and eukaryotic-like proteins, we expect that many symbiont-induced host differentiation mechanisms will be discovered in this system.
Collapse
Affiliation(s)
- Shelbi L Russell
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.
| | | |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Minimal fermentative metabolism fuels extracellular symbiont in a leaf beetle. ISME JOURNAL 2019; 14:866-870. [PMID: 31796934 DOI: 10.1038/s41396-019-0562-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 11/13/2019] [Accepted: 11/17/2019] [Indexed: 12/21/2022]
Abstract
While genome erosion is extensively studied in intracellular symbionts, the metabolic implications of reductive evolution in microbes subsisting extracellularly remain poorly understood. Stammera capleta-an extracellular symbiont in leaf beetles-possesses an extremely reduced genome (0.27 Mb), enabling the study of drastic reductive evolution in the absence of intracellularity. Here, we outline the genomic and transcriptomic profiles of Stammera and its host to elucidate host-symbiont metabolic interactions. Given the symbiont's substantial demands for nutrients and membrane components, the host's symbiotic organ shows repurposing of internal resources by upregulating nutrient transporters and cuticle-processing genes targeting epithelial chitin. Facilitated by this supplementation and its localization, Stammera exhibits a highly streamlined gene expression profile and a fermentation pathway for energy conversion, sharply contrasting the respiratory metabolism retained by most intracellular symbionts. Our results provide insights into a tightly regulated and metabolically integrated extracellular symbiosis, expanding our understanding of the minimal metabolism required to sustain life outside of a host cell.
Collapse
|