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Lebenzon JE, Toxopeus J. Knock down to level up: Reframing RNAi for invertebrate ecophysiology. Comp Biochem Physiol A Mol Integr Physiol 2024; 297:111703. [PMID: 39029617 DOI: 10.1016/j.cbpa.2024.111703] [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: 02/21/2024] [Revised: 07/16/2024] [Accepted: 07/16/2024] [Indexed: 07/21/2024]
Abstract
Comparative ecophysiologists strive to understand physiological problems in non-model organisms, but molecular tools such as RNA interference (RNAi) are under-used in our field. Here, we provide a framework for invertebrate ecophysiologists to use RNAi to answer questions focused on physiological processes, rather than as a tool to investigate gene function. We specifically focus on non-model invertebrates, in which the use of other genetic tools (e.g., genetic knockout lines) is less likely. We argue that because RNAi elicits a temporary manipulation of gene expression, and resources to carry out RNAi are technically and financially accessible, it is an effective tool for invertebrate ecophysiologists. We cover the terminology and basic mechanisms of RNA interference as an accessible introduction for "non-molecular" physiologists, include a suggested workflow for identifying RNAi gene targets and validating biologically relevant gene knockdowns, and present a hypothesis-testing framework for using RNAi to answer common questions in the realm of invertebrate ecophysiology. This review encourages invertebrate ecophysiologists to use these tools and workflows to explore physiological processes and bridge genotypes to phenotypes in their animal(s) of interest.
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Affiliation(s)
- Jacqueline E Lebenzon
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4.
| | - Jantina Toxopeus
- Department of Biology, St. Francis Xavier University, 2321 Notre Dame Ave, Antigonish, NS, Canada B2G 2W5
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2
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Hashimshony T, Levin L, Fröbius AC, Dahan N, Chalifa-Caspi V, Hamo R, Gabai-Almog O, Blais I, Assaraf YG, Lubzens E. A transcriptomic examination of encased rotifer embryos reveals the developmental trajectory leading to long-term dormancy; are they "animal seeds"? BMC Genomics 2024; 25:119. [PMID: 38281016 PMCID: PMC10821554 DOI: 10.1186/s12864-024-09961-1] [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: 06/22/2023] [Accepted: 01/02/2024] [Indexed: 01/29/2024] Open
Abstract
BACKGROUND Organisms from many distinct evolutionary lineages acquired the capacity to enter a dormant state in response to environmental conditions incompatible with maintaining normal life activities. Most studied organisms exhibit seasonal or annual episodes of dormancy, but numerous less studied organisms enter long-term dormancy, lasting decades or even centuries. Intriguingly, many planktonic animals produce encased embryos known as resting eggs or cysts that, like plant seeds, may remain dormant for decades. Herein, we studied a rotifer Brachionus plicatilis as a model planktonic species that forms encased dormant embryos via sexual reproduction and non-dormant embryos via asexual reproduction and raised the following questions: Which genes are expressed at which time points during embryogenesis? How do temporal transcript abundance profiles differ between the two types of embryos? When does the cell cycle arrest? How do dormant embryos manage energy? RESULTS As the molecular developmental kinetics of encased embryos remain unknown, we employed single embryo RNA sequencing (CEL-seq) of samples collected during dormant and non-dormant embryogenesis. We identified comprehensive and temporal transcript abundance patterns of genes and their associated enriched functional pathways. Striking differences were uncovered between dormant and non-dormant embryos. In early development, the cell cycle-associated pathways were enriched in both embryo types but terminated with fewer nuclei in dormant embryos. As development progressed, the gene transcript abundance profiles became increasingly divergent between dormant and non-dormant embryos. Organogenesis was suspended in dormant embryos, concomitant with low transcript abundance of homeobox genes, and was replaced with an ATP-poor preparatory phase characterized by very high transcript abundance of genes encoding for hallmark dormancy proteins (e.g., LEA proteins, sHSP, and anti-ROS proteins, also found in plant seeds) and proteins involved in dormancy exit. Surprisingly, this period appeared analogous to the late maturation phase of plant seeds. CONCLUSIONS The study highlights novel divergent temporal transcript abundance patterns between dormant and non-dormant embryos. Remarkably, several convergent functional solutions appear during the development of resting eggs and plant seeds, suggesting a similar preparatory phase for long-term dormancy. This study accentuated the broad novel molecular features of long-term dormancy in encased animal embryos that behave like "animal seeds".
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Affiliation(s)
- Tamar Hashimshony
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Liron Levin
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Andreas C Fröbius
- Molecular Andrology, Biomedical Research Center Seltersberg (BFS), Justus Liebig University Gießen, Gießen, Germany.
| | - Nitsan Dahan
- Interdisciplinary Center for Life Sciences and Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Vered Chalifa-Caspi
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Reini Hamo
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Oshri Gabai-Almog
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Idit Blais
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and IVF, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Esther Lubzens
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
- (Retired) Israel Oceanographic and Limnological Research, Haifa, Israel.
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Grewal HS, Yoshinaga T, Ehsan H, Yu E, Kaneko G. A genome-wide screening of the 70 kDa heat shock protein (HSP70) genes in the rotifer Brachionus plicatilis sensu stricto with a characterization of two heat-inducible HSP70 genes. Cell Stress Chaperones 2023; 28:583-594. [PMID: 35147924 PMCID: PMC10468477 DOI: 10.1007/s12192-022-01260-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/26/2022] [Accepted: 02/01/2022] [Indexed: 12/16/2022] Open
Abstract
The 70 kDa heat shock proteins (HSP70s) and the constitutive members of the HSP70 family (heat shock cognates; HSC70s) play essential roles in various biological processes. The number of hsp70/hsc70 in the database is rapidly increasing because of their importance and the automatic annotation of newly sequenced genomes. However, accumulating evidence indicates that neither hsp70 nor hsc70 forms a monophyletic gene family, raising the need to reconsider the annotation strategy based on the traditional concept of the inducible HSP70 and constitutive HSC70s. The main aim of this study is to establish a systematic scheme to annotate hsp70-like genes taking the latest phylogenetic insights into account. We cloned two hsp70s from the rotifer Brachionus plicatilis sensu stricto (s.s.), an emerging model in evolutionary genetics, and conducted a genome-wide screening of B. plicatilis s.s. hsp70s using the two sequences as queries. A total of 15 hsp70-like genes were found, and 7 of them encoded distant members of the HSP70 family, the function of which largely remains unknown. Eight canonical hsp70s were annotated according to a recently proposed nomenclature based on the molecular evolution: e.g., HSP70cA1/B1 for the cytosolic lineage, HSP70er1 for the endoplasmic reticulum lineage, and HSP70m1 for the mitochondrial lineage. The two cloned hsp70s, HSP70cB1 and HSP70cB2, ubiquitously increased their mRNA levels up to 7.5 times after heat treatment as assessed by semi-quantitative PCR, real-time PCR, and in situ hybridization. This systematic screening incorporating a reasonable update to the annotation strategy would provide a useful example for future HSP70 studies, especially those in non-traditional model organisms.
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Affiliation(s)
- Harmanpreet S Grewal
- College of Natural and Applied Science, University of Houston-Victoria, Victoria, TX, USA
| | | | - Hashimul Ehsan
- College of Natural and Applied Science, University of Houston-Victoria, Victoria, TX, USA
| | - Ermeng Yu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute of CAFS, Guangzhou, China.
| | - Gen Kaneko
- College of Natural and Applied Science, University of Houston-Victoria, Victoria, TX, USA.
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RNAi Silencing of the Biomineralization Gene Perlucin Impairs Oyster Ability to Cope with Ocean Acidification. Int J Mol Sci 2023; 24:ijms24043661. [PMID: 36835072 PMCID: PMC9961701 DOI: 10.3390/ijms24043661] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
Calcifying marine organisms, including the eastern oyster (Crassostrea virginica), are vulnerable to ocean acidification (OA) because it is more difficult to precipitate calcium carbonate (CaCO3). Previous investigations of the molecular mechanisms associated with resilience to OA in C. virginica demonstrated significant differences in single nucleotide polymorphism and gene expression profiles among oysters reared under ambient and OA conditions. Converged evidence generated by both of these approaches highlighted the role of genes related to biomineralization, including perlucins. Here, gene silencing via RNA interference (RNAi) was used to evaluate the protective role of a perlucin gene under OA stress. Larvae were exposed to short dicer-substrate small interfering RNA (DsiRNA-perlucin) to silence the target gene or to one of two control treatments (control DsiRNA or seawater) before cultivation under OA (pH ~7.3) or ambient (pH ~8.2) conditions. Two transfection experiments were performed in parallel, one during fertilization and one during early larval development (6 h post-fertilization), before larval viability, size, development, and shell mineralization were monitored. Silenced oysters under acidification stress were the smallest, had shell abnormalities, and had significantly reduced shell mineralization, thereby suggesting that perlucin significantly helps larvae mitigate the effects of OA.
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Gribble KE. Brachionus rotifers as a model for investigating dietary and metabolic regulators of aging. ACTA ACUST UNITED AC 2021; 6:1-15. [PMID: 33709041 PMCID: PMC7903245 DOI: 10.3233/nha-200104] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Because every species has unique attributes relevant to understanding specific aspects of aging, using a diversity of study systems and a comparative biology approach for aging research has the potential to lead to novel discoveries applicable to human health. Monogonont rotifers, a standard model for studies of aquatic ecology, evolutionary biology, and ecotoxicology, have also been used to study lifespan and healthspan for nearly a century. However, because much of this work has been published in the ecology and evolutionary biology literature, it may not be known to the biomedical research community. In this review, we provide an overview of Brachionus rotifers as a model to investigate nutritional and metabolic regulators of aging, with a focus on recent studies of dietary and metabolic pathway manipulation. Rotifers are microscopic, aquatic invertebrates with many advantages as a system for studying aging, including a two-week lifespan, easy laboratory culture, direct development without a larval stage, sexual and asexual reproduction, easy delivery of pharmaceuticals in liquid culture, and transparency allowing imaging of cellular morphology and processes. Rotifers have greater gene homology with humans than do established invertebrate models for aging, and thus rotifers may be used to investigate novel genetic mechanisms relevant to human lifespan and healthspan. The research on caloric restriction; dietary, pharmaceutical, and genetic interventions; and transcriptomics of aging using rotifers provide insights into the metabolic regulators of lifespan and health and suggest future directions for aging research. Capitalizing on the unique biology of Brachionus rotifers, referencing the vast existing literature about the influence of diet and drugs on rotifer lifespan and health, continuing the development of genetic tools for rotifers, and growing the rotifer research community will lead to new discoveries a better understanding of the biology of aging.
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García-Roger EM, Lubzens E, Fontaneto D, Serra M. Facing Adversity: Dormant Embryos in Rotifers. THE BIOLOGICAL BULLETIN 2019; 237:119-144. [PMID: 31714860 DOI: 10.1086/705701] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
An in-depth look at the basic aspects of dormancy in cyclic parthenogenetic organisms is now possible thanks to research efforts conducted over the past two decades with rotifer dormant embryos. In this review, we assemble and compose the current knowledge on four central themes: (1) distribution of dormancy in animals, with an overview on the phylogenetic distribution of embryo dormancy in metazoans, and (2) physiological and cellular processes involved in dormancy, with a strong emphasis on the dormant embryos of cyclically parthenogenetic monogonont rotifers; and discussions of (3) the selective pressures and (4) the evolutionary and population implications of dormancy in these animals. Dormancy in metazoans is a widespread phenomenon with taxon-specific features, and rotifers are among the animals in which dormancy is an intrinsic feature of their life cycle. Our review shows that embryo dormancy in rotifers shares common functional pathways with other taxa at the molecular and cellular level, despite the independent evolution of dormancy across phyla. These pathways include the arrest of similar metabolic routes and the usage of common metabolites for the stabilization of cellular structures and to confer stress resistance. We conclude that specific features of recurrent harsh environmental conditions are a powerful selective pressure for the fine-tuning of dormancy patterns in rotifers. We hypothesize that similar mechanisms at the organism level will lead to similar adaptive consequences at the population level across taxa, among which the formation of egg banks, the coexistence of species, and the possibility of differentiation among populations and local adaptation stand out. Our review shows how studies of rotifers have contributed to improved knowledge of all of these aspects.
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Congeneric variability in lifespan extension and onset of senescence suggest active regulation of aging in response to low temperature. Exp Gerontol 2018; 114:99-106. [PMID: 30399408 PMCID: PMC6336457 DOI: 10.1016/j.exger.2018.10.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/28/2018] [Accepted: 10/30/2018] [Indexed: 01/26/2023]
Abstract
Lifespan extension under low temperature is well conserved across both endothermic and exothermic taxa, but the mechanism underlying this change in aging is poorly understood. Low temperature is thought to decrease metabolic rate, thus slowing the accumulation of cellular damage from reactive oxygen species, although recent evidence suggests involvement of specific cold-sensing biochemical pathways. We tested the effect of low temperature on aging in 11 strains of Brachionus rotifers, with the hypothesis that if the mechanism of lifespan extension is purely thermodynamic, all strains should have a similar increase in lifespan. We found differences in change in median lifespan ranging from a 6% decrease to a 100% increase, as well as differences in maximum and relative lifespan extension and in mortality rate. Low temperature delays reproductive senescence in most strains, suggesting an extension of healthspan, even in strains with little to no change in lifespan. The combination of low temperature and caloric restriction in one strain resulted in an additive lifespan increase, indicating these interventions may work via non- or partially-overlapping pathways. The known low temperature sensor TRPA1 is present in the rotifer genome, but chemical TRPA1 agonists did not affect lifespan, suggesting that this gene may be involved in low temperature sensation but not in chemoreception in rotifers. The congeneric variability in response to low temperature suggests that the mechanism of low temperature lifespan extension is an active genetic process rather than a passive thermodynamic one and is dependent upon genotype.
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8
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Waldron FM, Stone GN, Obbard DJ. Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes. PLoS Genet 2018; 14:e1007533. [PMID: 30059538 PMCID: PMC6085071 DOI: 10.1371/journal.pgen.1007533] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 08/09/2018] [Accepted: 07/04/2018] [Indexed: 11/24/2022] Open
Abstract
RNA interference (RNAi)-related pathways target viruses and transposable element (TE) transcripts in plants, fungi, and ecdysozoans (nematodes and arthropods), giving protection against infection and transmission. In each case, this produces abundant TE and virus-derived 20-30nt small RNAs, which provide a characteristic signature of RNAi-mediated defence. The broad phylogenetic distribution of the Argonaute and Dicer-family genes that mediate these pathways suggests that defensive RNAi is ancient, and probably shared by most animal (metazoan) phyla. Indeed, while vertebrates had been thought an exception, it has recently been argued that mammals also possess an antiviral RNAi pathway, although its immunological relevance is currently uncertain and the viral small RNAs (viRNAs) are not easily detectable. Here we use a metagenomic approach to test for the presence of viRNAs in five species from divergent animal phyla (Porifera, Cnidaria, Echinodermata, Mollusca, and Annelida), and in a brown alga-which represents an independent origin of multicellularity from plants, fungi, and animals. We use metagenomic RNA sequencing to identify around 80 virus-like contigs in these lineages, and small RNA sequencing to identify viRNAs derived from those viruses. We identified 21U small RNAs derived from an RNA virus in the brown alga, reminiscent of plant and fungal viRNAs, despite the deep divergence between these lineages. However, contrary to our expectations, we were unable to identify canonical (i.e. Drosophila- or nematode-like) viRNAs in any of the animals, despite the widespread presence of abundant micro-RNAs, and somatic transposon-derived piwi-interacting RNAs. We did identify a distinctive group of small RNAs derived from RNA viruses in the mollusc. However, unlike ecdysozoan viRNAs, these had a piRNA-like length distribution but lacked key signatures of piRNA biogenesis. We also identified primary piRNAs derived from putatively endogenous copies of DNA viruses in the cnidarian and the echinoderm, and an endogenous RNA virus in the mollusc. The absence of canonical virus-derived small RNAs from our samples may suggest that the majority of animal phyla lack an antiviral RNAi response. Alternatively, these phyla could possess an antiviral RNAi response resembling that reported for vertebrates, with cryptic viRNAs not detectable through simple metagenomic sequencing of wild-type individuals. In either case, our findings show that the antiviral RNAi responses of arthropods and nematodes, which are highly divergent from each other and from that of plants and fungi, are also highly diverged from the most likely ancestral metazoan state.
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Affiliation(s)
- Fergal M. Waldron
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
| | - Graham N. Stone
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
| | - Darren J. Obbard
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
- Centre for Immunity Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
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9
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Johnston RK, Snell TW. Moderately lower temperatures greatly extend the lifespan of Brachionus manjavacas (Rotifera): Thermodynamics or gene regulation? Exp Gerontol 2016; 78:12-22. [PMID: 26939542 PMCID: PMC4841702 DOI: 10.1016/j.exger.2016.02.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 02/19/2016] [Accepted: 02/25/2016] [Indexed: 01/30/2023]
Abstract
Environmental temperature greatly affects lifespan in a wide variety of animals, but the exact mechanisms underlying this effect are still largely unknown. A moderate temperature decrease from 22°C to 16°C extends the lifespan of the monogonont rotifer Brachionus manjavacas by up to 163%. Thermodynamic effects on metabolism contribute to this increase in longevity, but are not the only cause. When rotifers are exposed to 16°C for four days and then transfered to 22°C, they survive until day 13 at nearly identical rates as rotifers maintained at 16°C continuously. This persistence of the higher survival for nine days after transfer to 22°C suggests that low temperature exposure alters the expression of genes that affect the rate of aging. The relative persistence of the gene regulation effect suggests that it may play an even larger role in slowing aging than the thermodynamic effects. The life extending effects of these short-term low temperature treatments are largest when the exposure happens early in the life cycle, demonstrating the importance of early development. There is no advantage to lowering the temperature below 16°C to 11° or 5°C. Rotifers exposed to 16°C also displayed increased resistance to heat, starvation, oxidative and osmotic stress. Reproductive rates at 16°C were lower than those at 22°C, but because they reproduce longer, there is no significant change in the lifetime fecundity of females. To investigate which genes contribute to these effects, the expression of specific temperature sensing genes was knocked down using RNAi. Of 12 genes tested, RNAi knockdown of four eliminated the survival enhancing effects of the four-day cold treatment: TRP7, forkhead box C, Y-box factor, and ribosomal protein S6. This demonstrates that active gene regulation is an important factor in temperature mediated life extension, and that these particular genes play an integral role in these pathways. As a thermoresponsive sensor, TRP7 may be responsible for triggering the signaling cascade contributing to temperature mediated life extension. The TRP genes may also provide especially promising candidates for targeted gene manipulations or pharmacological interventions capable of mimicking the effects of low temperature exposure. These results support recent theories of aging that claim rate of aging is determined by an actively regulated genetic mechanism rather than an accumulation of molecular damage.
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Affiliation(s)
- Rachel K Johnston
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA.
| | - Terry W Snell
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA
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Zhang G, He LS, Wong YH, Yu L, Qian PY. siRNA transfection in the barnacle Amphibalanus amphitrite larvae. J Exp Biol 2015; 218:2505-9. [DOI: 10.1242/jeb.120113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 06/15/2015] [Indexed: 01/20/2023]
Abstract
RNA interference (RNAi) provides an efficient and specific technique for functional genomic studies. Yet, no successful application of RNAi has been reported in barnacles. In this study, siRNA against p38 MAPK was synthesized and then transfected into A. amphitrite larvae at either nauplius or cyprid stage, or both. Effects of siRNA transfection on p38 MAPK level were hardly detectable in the cyprids that their corresponding nauplii were transfected. In contrast, larvae that were transfected at cyprid stage showed lower level of p38 MAPK than the blank and reagent controls. However, significantly decreased level of phosphorylated p38 MAPK (pp38 MAPK) and reduced settlement rate were observed only in the “Double Transfection”, in which larvae were exposed to siRNA solution at both the nauplius and cyprid stages. Relatively longer transfection time and more cells of the larvae exposed to siRNA directly might explain the higher efficiency in the “Double Transfection”.
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Affiliation(s)
- Gen Zhang
- Environmental Science Programs, School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- KAUST Global Collaborative Research Program, Division of Life Science, School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Li-sheng He
- KAUST Global Collaborative Research Program, Division of Life Science, School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- Sanya Institute of Deep-sea Science and Engineering, Chinese Academy of Science, No. 62, Fenghuang Road, Sanya City, Hainan Province, China, 572000
| | - Yue Him Wong
- KAUST Global Collaborative Research Program, Division of Life Science, School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Li Yu
- Environmental Science Programs, School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- KAUST Global Collaborative Research Program, Division of Life Science, School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Pei-yuan Qian
- Environmental Science Programs, School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- KAUST Global Collaborative Research Program, Division of Life Science, School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
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Barreto FS, Schoville SD, Burton RS. Reverse genetics in the tide pool: knock-down of target gene expression via RNA interference in the copepodTigriopus californicus. Mol Ecol Resour 2014; 15:868-79. [DOI: 10.1111/1755-0998.12359] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 12/02/2014] [Accepted: 12/05/2014] [Indexed: 01/02/2023]
Affiliation(s)
- Felipe S. Barreto
- Marine Biology Research Division; Scripps Institution of Oceanography; University of California; San Diego La Jolla CA 92037 USA
| | - Sean D. Schoville
- Department of Entomology; University of Wisconsin-Madison; Madison WI 53706 USA
| | - Ronald S. Burton
- Marine Biology Research Division; Scripps Institution of Oceanography; University of California; San Diego La Jolla CA 92037 USA
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12
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Snell TW, Johnston RK, Rabeneck B, Zipperer C, Teat S. Joint inhibition of TOR and JNK pathways interacts to extend the lifespan of Brachionus manjavacas (Rotifera). Exp Gerontol 2014; 52:55-69. [PMID: 24486130 PMCID: PMC3970784 DOI: 10.1016/j.exger.2014.01.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Revised: 01/17/2014] [Accepted: 01/20/2014] [Indexed: 12/30/2022]
Abstract
The TOR kinase pathway is central in modulating aging in a variety of animal models. The target of rapamycin (TOR) integrates a complex network of signals from growth conditions, nutrient availability, energy status, and physiological stresses and matches an organism's growth rate to the resource environment. Important remaining problems are the identification of the pathways that interact with TOR and their characterization as additive or synergistic. One of the most versatile stress sensors in metazoans is the Jun-N-terminal kinase (JNK) signaling pathway. JNK is an evolutionarily conserved stress-activated protein kinase that is induced by a range of stressors, including UV irradiation, reactive oxygen species, DNA damage, heat, and bacterial antigens. JNK is thought to interact with the TOR pathway, but its effects on TOR are poorly understood. We used the rotifer Brachionus manjavacas as a model animal to probe the regulation of TOR and JNK pathways and explore their interaction. The effect of various chemical inhibitors was examined in life table and stressor challenge experiments. A survey of 12 inhibitors revealed two, rapamycin and JNK inhibitor, that significantly extended lifespan of B. manjavacas. At 1 μM concentration, exposure to rapamycin or JNK inhibitor extended mean rotifer lifespan by 35% and maximum lifespan by 37%. Exposure to both rapamycin and JNK inhibitor simultaneously extended mean rotifer lifespan by 65% more than either alone. Exposure to a combination of rapamycin and JNK inhibitors conveyed greater protection to starvation, UV and osmotic stress than either inhibitor alone. RNAi knockdown of TOR and JNK gene expression was investigated for its ability to extend rotifer lifespan. RNAi knockdown of the TOR gene resulted in 29% extension of the mean lifespan compared to control and knockdown of the JNK gene resulted in 51% mean lifespan extension. In addition to the lifespan, we quantified mitochondria activity using the fluorescent marker MitoTracker and lysosome activity using LysoTracker. Treatment of rotifers with JNK inhibitor enhanced mitochondria activity nearly 3-fold, whereas rapamycin treatment had no significant effect. Treatment of rotifers with rapamycin or JNK inhibitor reduced lysosome activity in 1, 3 and 8 day old animals, but treatment with both inhibitors did not produce any additive effect. We conclude that inhibition of TOR and JNK pathways significantly extends the lifespan of B. manjavacas. These pathways interact so that inhibition of both simultaneously acts additively to extend rotifer lifespan more than the inhibition of either alone.
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Affiliation(s)
- Terry W Snell
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA.
| | - Rachel K Johnston
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA
| | - Brett Rabeneck
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA
| | - Cody Zipperer
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA
| | - Stephanie Teat
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA
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13
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Snell TW. Rotifers as models for the biology of aging. INTERNATIONAL REVIEW OF HYDROBIOLOGY 2014; 99:84-95. [PMID: 24791148 PMCID: PMC4004354 DOI: 10.1002/iroh.201301707] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
It has been two decades since 1993 when research on the biology of rotifer aging was last reviewed by Enesco. Much has transpired during this time as rotifer biologists have adapted to the "omics" revolution and incorporated these techniques into the experimental analysis of rotifers. Rotifers are amenable to many of these approaches and getting adequate quantities of DNA, RNA, and protein from rotifers is not difficult. Analysis of rotifer genomes, transcriptomes, and proteomes is rapidly yielding candidate genes that likely regulate a variety of features of rotifer biology. Parallel developments in aging biology have recognized the limitations of standard animal models like worms and flies and that comparative aging research has essentially ignored a large fraction of animal phylogeny in the lophotrochozoans. As experimentally tractable members of this group, rotifers have attracted interest as models of aging. In this paper, I review advances over the past 20 years in the biology of aging in rotifers, with emphasis on the unique contributions of rotifer models for understanding aging. The majority of experimental work has manipulated rotifer diet and followed changes in survival and reproductive dynamics like mean lifespan, maximum lifespan, reproductive lifespan, and mortality rate doubling time. The main dietary manipulation has been some form of caloric restriction, withholding food for some period or feeding continuously at low levels. There have been comparative studies of several rotifer species, with some species responding to caloric restriction with life extension, but others not, at least under the tested food regimens. Other aspects of diet are less explored, like nutritional properties of different algae species and their capacity to extend rotifer lifespan. Several descriptive studies have reported many genes involved in rotifer aging by comparing gene expression in young and old individuals. Classes of genes up or down-regulated during aging have become prime targets for rotifer aging investigations. Alterations of gene expression by exposure to specific inhibitors or RNAi knockdown will probably yield valuable insights into the cellular mechanisms of rotifer life extension. I highlight major experimental contributions in each of these areas and indicate opportunities where I believe additional investigation is likely to be profitable.
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Affiliation(s)
- Terry W. Snell
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0230, USA
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Lifespan extension of rotifers by treatment with red algal extracts. Exp Gerontol 2013; 48:1420-7. [PMID: 24120568 DOI: 10.1016/j.exger.2013.09.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 09/20/2013] [Accepted: 09/30/2013] [Indexed: 01/29/2023]
Abstract
Aging results from an accumulation of damage to macromolecules inhibiting cellular replication, repair, and other necessary functions. Damage may be due to environmental stressors such as metal toxicity, oxidative stress caused by imperfections in electron transfer reactions, or other metabolic processes. In an effort to discover medical treatments that counteract this damage, we initiated a search for small molecule drugs from natural sources using life table experiments which, through their unbiased approach, present the opportunity to discover first-in-class molecules. We have identified marine red algae as a source of natural products that slow aging of the invertebrate rotifer Brachionus manjavacas. Rotifers are a promising model organism for life extension studies as they maintain a short, measurable lifespan while also having an extensive literature related to aging. Rotifer lifespan was increased 9-14% by exposure to three of a total of 200 screened red algal extracts. Bioassay guided fractionation led to semi-purified extracts composed primarily of lipids responsible for rotifer life extension. The life extending mixture from the red alga Acanthophora spicifera contained eicosanoic, octadecanoic, and hexadecanoic acids as well as several unidentified unsaturated fatty acids. The life extending effects of these small molecule mixtures are not a result of their direct antioxidant capacity; other unknown mechanisms of action are likely involved. An understanding of how these natural products interact with their molecular targets could lead to selective and effective treatments for slowing aging and reducing age related diseases.
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Liu BR, Liou JS, Chen YJ, Huang YW, Lee HJ. Delivery of nucleic acids, proteins, and nanoparticles by arginine-rich cell-penetrating peptides in rotifers. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2013; 15:584-95. [PMID: 23715807 DOI: 10.1007/s10126-013-9509-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 04/09/2013] [Indexed: 06/02/2023]
Abstract
Cell-penetrating peptides (CPPs) are a group of short, membrane-permeable cationic peptides that represent a nonviral technology for delivering nanomaterials and macromolecules into live cells. In this study, two arginine-rich CPPs, HR9 and IR9, were found to be capable of entering rotifers. CPPs were able to efficiently deliver noncovalently associated with cargoes, including plasmid DNAs, red fluorescent proteins (RFPs), and semiconductor quantum dots, into rotifers. The functional reporter gene assay demonstrated that HR9-delivered plasmid DNAs containing the enhanced green fluorescent protein and RFP coding sequences could be actively expressed in rotifers. The 1-(4,5-dimethylthiazol-2-yl)-3,5-diphenylformazan assay further confirmed that CPP-mediated cargo delivery was not toxic to rotifers. Thus, these two CPPs hold a great potential for the delivery of exogenous genes, proteins, and nanoparticles in rotifers.
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Affiliation(s)
- Betty Revon Liu
- Department of Natural Resources and Environmental Studies, National Dong Hwa University, 1, Sec. 2, Da-Hsueh Road, Shoufeng, Hualien, 97401, Taiwan
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Gribble KE, Mark Welch DB. The mate recognition protein gene mediates reproductive isolation and speciation in the Brachionus plicatilis cryptic species complex. BMC Evol Biol 2012; 12:134. [PMID: 22852831 PMCID: PMC3495898 DOI: 10.1186/1471-2148-12-134] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 07/23/2012] [Indexed: 12/15/2022] Open
Abstract
Background Chemically mediated prezygotic barriers to reproduction likely play an important role in speciation. In facultatively sexual monogonont rotifers from the Brachionus plicatilis cryptic species complex, mate recognition of females by males is mediated by the Mate Recognition Protein (MRP), a globular glycoprotein on the surface of females, encoded by the mmr-b gene family. In this study, we sequenced mmr-b copies from 27 isolates representing 11 phylotypes of the B. plicatilis species complex, examined the mode of evolution and selection of mmr-b, and determined the relationship between mmr-b genetic distance and mate recognition among isolates. Results Isolates of the B. plicatilis species complex have 1–4 copies of mmr-b, each composed of 2–9 nearly identical tandem repeats. The repeats within a gene copy are generally more similar than are gene copies among phylotypes, suggesting concerted evolution. Compared to housekeeping genes from the same isolates, mmr-b has accumulated only half as many synonymous differences but twice as many non-synonymous differences. Most of the amino acid differences between repeats appear to occur on the outer face of the protein, and these often result in changes in predicted patterns of phosphorylation. However, we found no evidence of positive selection driving these differences. Isolates with the most divergent copies were unable to mate with other isolates and rarely self-crossed. Overall the degree of mate recognition was significantly correlated with the genetic distance of mmr-b. Conclusions Discrimination of compatible mates in the B. plicatilis species complex is determined by proteins encoded by closely related copies of a single gene, mmr-b. While concerted evolution of the tandem repeats in mmr-b may function to maintain identity, it can also lead to the rapid spread of a mutation through all copies in the genome and thus to reproductive isolation. The mmr-b gene is evolving rapidly, and novel alleles may be maintained and increase in frequency via asexual reproduction. Our analyses indicate that mate recognition, controlled by MMR-B, may drive reproductive isolation and allow saltational sympatric speciation within the B. plicatilis cryptic species complex, and that this process may be largely neutral.
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Affiliation(s)
- Kristin E Gribble
- Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA
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Snell TW, Fields AM, Johnston RK. Antioxidants can extend lifespan of Brachionus manjavacas (Rotifera), but only in a few combinations. Biogerontology 2012; 13:261-75. [PMID: 22270335 DOI: 10.1007/s10522-012-9371-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 01/04/2012] [Indexed: 12/21/2022]
Abstract
Animal cells are protected from oxidative damage by an antioxidant network operating as a coordinated system, with strong synergistic interactions. Lifespan studies with whole animals are expensive and laborious, so there has been little investigation of which antioxidant interactions might be useful for life extension. Animals in the phylum Rotifera are particularly promising models for aging studies because they are small (0.1-1 mm), have short, two-week lifespan, display typical patterns of animal aging, and have well characterized, easy to measure phenotypes of aging and senescence. One class of interventions that has consistently produced significant rotifer life extension is antioxidants. Although the mechanism of antioxidant effects on animal aging remains controversial, the ability of some antioxidant supplements to extend rotifer lifespan was unequivocal. We found that exposing rotifers to certain combinations of antioxidant supplements can produce up to about 20% longer lifespan, but that most antioxidants have no effect. We performed life table tests with 20 single antioxidants and none yielded significant rotifer life extension. We tested 60 two-way combinations of selected antioxidants and only seven (12%) produced significant rotifer life extension. None of the 20 three- and four-way antioxidant combinations tested yielded significant rotifer life extension. These observations suggest that dietary exposure of antioxidants can extend rotifer lifespan, but most antioxidants do not. We observed significant rotifer life extension only when antioxidants were paired with trolox, N-acetyl cysteine, L: -carnosine, or EUK-8. This illustrates that antioxidant treatments capable of rotifer life extension are patchily distributed in the parameter space, so large regions must be searched to find them. It furthermore underscores the value of the rotifer model to conduct rapid, facile life table experiments with many treatments, which makes such a search feasible. Although some antioxidants extended rotifer lifespan, they likely did so by another mechanism than direct antioxidation.
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Affiliation(s)
- Terry W Snell
- School of Biology, Georgia Institute of Technology, Atlanta, 30332-0230, USA.
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Kaneko G, Yoshinaga T, Yanagawa Y, Ozaki Y, Tsukamoto K, Watabe S. Calorie restriction‐induced maternal longevity is transmitted to their daughters in a rotifer. Funct Ecol 2010. [DOI: 10.1111/j.1365-2435.2010.01773.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Gen Kaneko
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113‐8657, Japan
| | - Tatsuki Yoshinaga
- School of Marine Biosciences, Kitasato University, Ofunato, Iwate 022‐0101, Japan
| | - Yoshiko Yanagawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113‐8657, Japan
| | - Yori Ozaki
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113‐8657, Japan
| | - Katsumi Tsukamoto
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277‐8564, Japan
| | - Shugo Watabe
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113‐8657, Japan
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Conservation of progesterone hormone function in invertebrate reproduction. Proc Natl Acad Sci U S A 2010; 107:11859-64. [PMID: 20547846 DOI: 10.1073/pnas.1006074107] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Steroids play fundamental roles regulating mammalian reproduction and development. Although sex steroids and their receptors are well characterized in vertebrates and several arthropod invertebrates, little is known about the hormones and receptors regulating reproduction in other invertebrate species. Evolutionary insights into ancient endocrine pathways can be gained by elucidating the hormones and receptors functioning in invertebrate reproduction. Using a combination of genomic analyses, receptor imaging, ligand identification, target elucidation, and exploration of function through receptor knockdown, we now show that comparable progesterone chemoreception exists in the invertebrate monogonont rotifer Brachionus manjavacas, suggesting an ancient origin of the signal transduction systems commonly associated with the development and integration of sexual behavior in mammals.
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