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Nell LA, Weng YM, Phillips JS, Botsch JC, Book KR, Einarsson Á, Ives AR, Schoville SD. Shared Features Underlying Compact Genomes and Extreme Habitat Use in Chironomid Midges. Genome Biol Evol 2024; 16:evae086. [PMID: 38662498 PMCID: PMC11076180 DOI: 10.1093/gbe/evae086] [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] [Accepted: 04/21/2024] [Indexed: 05/09/2024] Open
Abstract
Nonbiting midges (family Chironomidae) are found throughout the world in a diverse array of aquatic and terrestrial habitats, can often tolerate harsh conditions such as hypoxia or desiccation, and have consistently compact genomes. Yet we know little about the shared molecular basis for these attributes and how they have evolved across the family. Here, we address these questions by first creating high-quality, annotated reference assemblies for Tanytarsus gracilentus (subfamily Chironominae, tribe Tanytarsini) and Parochlus steinenii (subfamily Podonominae). Using these and other publicly available assemblies, we created a time-calibrated phylogenomic tree for family Chironomidae with outgroups from order Diptera. We used this phylogeny to test for features associated with compact genomes, as well as examining patterns of gene family evolution and positive selection that may underlie chironomid habitat tolerances. Our results suggest that compact genomes evolved in the common ancestor of Chironomidae and Ceratopogonidae and that this occurred mainly through reductions in noncoding regions (introns, intergenic sequences, and repeat elements). Significantly expanded gene families in Chironomidae included biological processes that may relate to tolerance of stressful environments, such as temperature homeostasis, carbohydrate transport, melanization defense response, and trehalose transport. We identified several positively selected genes in Chironomidae, notably sulfonylurea receptor, CREB-binding protein, and protein kinase D. Our results improve our understanding of the evolution of small genomes and extreme habitat use in this widely distributed group.
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Affiliation(s)
- Lucas A Nell
- Department of Integrative Biology, University of Wisconsin, Madison, WI 53706, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Yi-Ming Weng
- Department of Entomology, University of Wisconsin, Madison, WI 53706, USA
- McGuire Center for Lepidoptera & Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Joseph S Phillips
- Department of Integrative Biology, University of Wisconsin, Madison, WI 53706, USA
- Department of Biology, Creighton University, Omaha, NE 68178, USA
| | - Jamieson C Botsch
- Department of Integrative Biology, University of Wisconsin, Madison, WI 53706, USA
- North Central Agricultural Research Laboratory, USDA-ARS, Brookings, SD 57006, USA
| | - K Riley Book
- Department of Integrative Biology, University of Wisconsin, Madison, WI 53706, USA
| | | | - Anthony R Ives
- Department of Integrative Biology, University of Wisconsin, Madison, WI 53706, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin, Madison, WI 53706, USA
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Mizutani K, Yoshida Y, Nakanishi E, Miyata Y, Tokumoto S, Fuse H, Gusev O, Kikuta S, Kikawada T. A sodium-dependent trehalose transporter contributes to anhydrobiosis in insect cell line, Pv11. Proc Natl Acad Sci U S A 2024; 121:e2317254121. [PMID: 38551840 PMCID: PMC10998604 DOI: 10.1073/pnas.2317254121] [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: 10/05/2023] [Accepted: 02/13/2024] [Indexed: 04/02/2024] Open
Abstract
Pv11 is the only animal cell line that, when preconditioned with a high concentration of trehalose, can be preserved in the dry state at room temperature for more than one year while retaining the ability to resume proliferation. This extreme desiccation tolerance is referred to as anhydrobiosis. Here, we identified a transporter that contributes to the recovery of Pv11 cells from anhydrobiosis. In general, the solute carrier 5 (SLC5)-type secondary active transporters cotransport Na+ and carbohydrates including glucose. The heterologous expression systems showed that the transporter belonging to the SLC5 family, whose expression increases upon rehydration, exhibits Na+-dependent trehalose transport activity. Therefore, we named it STRT1 (sodium-ion trehalose transporter 1). We report an SLC5 family member that transports a naturally occurring disaccharide, such as trehalose. Knockout of the Strt1 gene significantly reduced the viability of Pv11 cells upon rehydration after desiccation. During rehydration, when intracellular trehalose is no longer needed, Strt1-knockout cells released the disaccharide more slowly than the parental cell line. During rehydration, Pv11 cells became roughly spherical due to osmotic pressure changes, but then returned to their original spindle shape after about 30 min. Strt1-knockout cells, however, required about 50 min to adopt their normal morphology. STRT1 probably regulates intracellular osmolality by releasing unwanted intracellular trehalose with Na+, thereby facilitating the recovery of normal cell morphology during rehydration. STRT1 likely improves the viability of dried Pv11 cells by rapidly alleviating the significant physical stresses that arise during rehydration.
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Affiliation(s)
- Kosuke Mizutani
- Department of Integrated Biosciences, Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Chiba277-8562, Japan
| | - Yuki Yoshida
- Division of Biomaterial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8634, Japan
| | - Eita Nakanishi
- Department of Integrated Biosciences, Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Chiba277-8562, Japan
| | - Yugo Miyata
- Department of Medical Chemistry, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo113-8510, Japan
| | - Shoko Tokumoto
- Division of Biomaterial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8634, Japan
- Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Bunkyo-ku, Tokyo113-8421, Japan
| | - Hiroto Fuse
- Department of Integrated Biosciences, Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Chiba277-8562, Japan
| | - Oleg Gusev
- Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Bunkyo-ku, Tokyo113-8421, Japan
| | - Shingo Kikuta
- Department of Regional and Comprehensive Agriculture, College of Agriculture, Ibaraki University, Ami, Ibaraki300-0393, Japan
| | - Takahiro Kikawada
- Department of Integrated Biosciences, Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Chiba277-8562, Japan
- Division of Biomaterial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8634, Japan
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Fuse H, Kikawada T, Cornette R. Effective methods for immobilization of non-adherent Pv11 cells while maintaining their desiccation tolerance. Cytotechnology 2023; 75:491-503. [PMID: 37841960 PMCID: PMC10575823 DOI: 10.1007/s10616-023-00592-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/24/2023] [Indexed: 10/17/2023] Open
Abstract
Pv11 was derived from embryos of the sleeping chironomid Polypedilum vanderplanki, which displays an extreme form of desiccation tolerance known as anhydrobiosis. Pre-treatment with a high concentration of trehalose allows Pv11 cells to enter anhydrobiosis. In the dry state, Pv11 cells preserve transgenic luciferase while retaining its activity. Thus, these cells could be utilized for dry-preserving antibodies, enzymes, signaling proteins or other valuable biological materials without denaturation. However, Pv11 cells grow in suspension, which limits their applicability; for instance, they cannot be integrated into microfluidic devices or used in devices such as sensor chips. Therefore, in this paper, we developed an effective immobilization system for Pv11 cells that, crucially, allows them to maintain their anhydrobiotic potential even when immobilized. Pv11 cells exhibited a very high adhesion rate with both biocompatible anchor for membrane (BAM) and Cell-Tak coatings, which have been reported to be effective on other cultured cells. We also found that Pv11 cells immobilized well to uncoated glass if handled in serum-free medium. Interestingly, Pv11 cells showed desiccation tolerance when trehalose treatment was done prior to immobilization of the cells. In contrast, trehalose treatment after immobilization of Pv11 cells resulted in a significant decrease in desiccation tolerance. Thus, it is important to induce anhydrobiosis before immobilization. In summary, we report the successful development of a protocol for the dry preservation of immobilized Pv11 cells. Supplementary Information The online version contains supplementary material available at 10.1007/s10616-023-00592-0.
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Affiliation(s)
- Hiroto Fuse
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwa, Chiba 277-8562 Japan
| | - Takahiro Kikawada
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwa, Chiba 277-8562 Japan
- Division of Biomaterial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-0851 Japan
| | - Richard Cornette
- Division of Biomaterial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-0851 Japan
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Shaikhutdinov NM, Klink GV, Garushyants SK, Kozlova OS, Cherkasov AV, Kikawada T, Okuda T, Pemba D, Shagimardanova EI, Penin AA, Deviatiiarov RM, Gazizova GR, Cornette R, Gusev OA, Bazykin GA. Population Genomics of Two Closely Related Anhydrobiotic Midges Reveals Differences in Adaptation to Extreme Desiccation. Genome Biol Evol 2023; 15:evad169. [PMID: 37708413 PMCID: PMC10558213 DOI: 10.1093/gbe/evad169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 09/16/2023] Open
Abstract
The sleeping chironomid Polypedilum vanderplanki is capable of anhydrobiosis, a striking example of adaptation to extreme desiccation. Tolerance to complete desiccation in this species is associated with emergence of multiple paralogs of protective genes. One of the gene families highly expressed under anhydrobiosis and involved in this process is protein-L-isoaspartate (D-aspartate) O-methyltransferases (PIMTs). Recently, another closely related midge was discovered, Polypedilum pembai, which is able not only to tolerate desiccation but also to survive multiple desiccation-rehydration cycles. To investigate the evolution of anhydrobiosis in these species, we sequenced and assembled the genome of P. pembai and compared it with P. vanderplanki and also performed a population genomics analysis of several populations of P. vanderplanki and one population of P. pembai. We observe positive selection and radical changes in the genetic architecture of the PIMT locus between the two species, including its amplification in the P. pembai lineage. In particular, PIMT-4, the most highly expressed of these PIMTs, is present in six copies in the P. pembai; these copies differ in expression profiles, suggesting possible sub- or neofunctionalization. The nucleotide diversity of the genomic region carrying these new genes is decreased in P. pembai, but not in the orthologous region carrying the ancestral gene in P. vanderplanki, providing evidence for a selective sweep associated with postduplication adaptation in the former. Overall, our results suggest an extensive relatively recent and likely ongoing adaptation of the mechanisms of anhydrobiosis.
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Affiliation(s)
- Nurislam M Shaikhutdinov
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Galya V Klink
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
| | - Sofya K Garushyants
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
| | - Olga S Kozlova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Alexander V Cherkasov
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Takahiro Kikawada
- National Agriculture and Food Research Organization (NARO), Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | | | - Dylo Pemba
- Vectorborne Diseases Laboratory, University of Malawi Chancellor College, Zomba, Malawi
| | - Elena I Shagimardanova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Aleksey A Penin
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
| | - Ruslan M Deviatiiarov
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Guzel R Gazizova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Richard Cornette
- National Agriculture and Food Research Organization (NARO), Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Oleg A Gusev
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
- Life Improvement by Future Technologies (LIFT) Center, Moscow, Russia
- Intractable Disease Research Center, School of Medicine, Juntendo University, Tokyo, Japan
| | - Georgii A Bazykin
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
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Deciphering the Biological Enigma-Genomic Evolution Underlying Anhydrobiosis in the Phylum Tardigrada and the Chironomid Polypedilum vanderplanki. INSECTS 2022; 13:insects13060557. [PMID: 35735894 PMCID: PMC9224920 DOI: 10.3390/insects13060557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/13/2022] [Accepted: 06/17/2022] [Indexed: 02/04/2023]
Abstract
Anhydrobiosis, an ametabolic dehydrated state triggered by water loss, is observed in several invertebrate lineages. Anhydrobiotes revive when rehydrated, and seem not to suffer the ultimately lethal cell damage that results from severe loss of water in other organisms. Here, we review the biochemical and genomic evidence that has revealed the protectant molecules, repair systems, and maintenance pathways associated with anhydrobiosis. We then introduce two lineages in which anhydrobiosis has evolved independently: Tardigrada, where anhydrobiosis characterizes many species within the phylum, and the genus Polypedilum, where anhydrobiosis occurs in only two species. Finally, we discuss the complexity of the evolution of anhydrobiosis within invertebrates based on current knowledge, and propose perspectives to enhance the understanding of anhydrobiosis.
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