1
|
Ren QQ, Long GY, Yang H, Zhou C, Yang XB, Yan Y, Yan X. Conserved microRNAs miR-8-3p and miR-2a-3 targeting chitin biosynthesis to regulate the molting process of Sogatella furcifera (Horváth)(Hemiptera: Delphacidae). JOURNAL OF ECONOMIC ENTOMOLOGY 2024:toae123. [PMID: 38894631 DOI: 10.1093/jee/toae123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/24/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024]
Abstract
Molting is a key solution to growth restriction in insects. The periodic synthesis and degradation of chitin, one of the major components of the insect epidermis, is necessary for insect growth. MicroRNA (miRNA) have been implicated in molting regulation, yet their involvement in the interplay interaction between the chitin synthesis pathway and 20-hydroxyecdysone signaling remains poorly understood. In this study, soluble trehalase (Tre1) and phosphoacetylglucosamine mutase (PAGM) were identified as targets of conserved miR-8-3p and miR-2a-3, respectively. The expression profiles of miR-8-3p-SfTre1 and miR-2a-3-SfPAGM exhibited an opposite pattern during the different developmental stages, indicating a negative regulatory relationship between them. This relationship was confirmed by an in vitro dual-luciferase reporter system. Overexpression of miR-8-3p and miR-2a-3 by injection of mimics inhibited the expression of their respective target genes and increased mortality, leading to death in the pre-molting, and molting death phenomena. They also caused a decrease in chitin content and expression levels of key genes in the chitin synthesis pathway (SfTre1, SfTre2, SfHK, SfG6PI, SfGFAT, SfGNA, SfPAGM, SfUAP, SfCHS1, SfCHS1a, and SfCHS1b). Conversely, the injection of miRNA inhibitors resulted in the upregulation of the expression levels of these genes. Following 20E treatment, the expression levels of miR-8-3p and miR-2a-3 decreased significantly, while their corresponding target genes increased significantly. These results indicate that miR-8-3p and miR-2a-3 play a regulatory role in the molting of Sogatella furcifera by targeting SfTre1 and SfPAGM, respectively. These findings provide new potential targets for the development of subsequent new control strategies.
Collapse
Affiliation(s)
- Qian-Qian Ren
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, China
| | - Gui-Yun Long
- School of Chinese Ethnic Medicine, Key Laboratory of Guizhou Ethnic Medicine Resource Development and Utilization in Guizhou Minzu, Guizhou Minzu University, Guiyang, 550025, China
| | - Hong Yang
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, China
| | - Cao Zhou
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing, China
| | - Xi-Bin Yang
- Plant Protection and Quarantine Station, Department of Agriculture and Rural Affairs of Guizhou, Guiyang, 550001, China
| | - Yi Yan
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, China
| | - Xin Yan
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, China
| |
Collapse
|
2
|
Menzies JAC, Maia Chagas A, Baden T, Alonso CR. A microRNA that controls the emergence of embryonic movement. eLife 2024; 13:RP95209. [PMID: 38869942 PMCID: PMC11175612 DOI: 10.7554/elife.95209] [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] [Indexed: 06/14/2024] Open
Abstract
Movement is a key feature of animal systems, yet its embryonic origins are not fully understood. Here, we investigate the genetic basis underlying the embryonic onset of movement in Drosophila focusing on the role played by small non-coding RNAs (microRNAs, miRNAs). To this end, we first develop a quantitative behavioural pipeline capable of tracking embryonic movement in large populations of fly embryos, and using this system, discover that the Drosophila miRNA miR-2b-1 plays a role in the emergence of movement. Through the combination of spectral analysis of embryonic motor patterns, cell sorting and RNA in situs, genetic reconstitution tests, and neural optical imaging we define that miR-2b-1 influences the emergence of embryonic movement by exerting actions in the developing nervous system. Furthermore, through the combination of bioinformatics coupled to genetic manipulation of miRNA expression and phenocopy tests we identify a previously uncharacterised (but evolutionarily conserved) chloride channel encoding gene - which we term Movement Modulator (Motor) - as a genetic target that mechanistically links miR-2b-1 to the onset of movement. Cell-specific genetic reconstitution of miR-2b-1 expression in a null miRNA mutant background, followed by behavioural assays and target gene analyses, suggest that miR-2b-1 affects the emergence of movement through effects in sensory elements of the embryonic circuitry, rather than in the motor domain. Our work thus reports the first miRNA system capable of regulating embryonic movement, suggesting that other miRNAs are likely to play a role in this key developmental process in Drosophila as well as in other species.
Collapse
Affiliation(s)
- Jonathan AC Menzies
- Department of Neuroscience, Sussex Neuroscience, School of Life Sciences, University of SussexBrightonUnited Kingdom
| | - André Maia Chagas
- Department of Neuroscience, Sussex Neuroscience, School of Life Sciences, University of SussexBrightonUnited Kingdom
| | - Tom Baden
- Department of Neuroscience, Sussex Neuroscience, School of Life Sciences, University of SussexBrightonUnited Kingdom
| | - Claudio R Alonso
- Department of Neuroscience, Sussex Neuroscience, School of Life Sciences, University of SussexBrightonUnited Kingdom
| |
Collapse
|
3
|
Roberts KT, Steward RA, Süess P, Lehmann P, Wheat CW. A time course analysis through diapause reveals dynamic temporal patterns of microRNAs associated with endocrine regulation in the butterfly Pieris napi. Mol Ecol 2024:e17348. [PMID: 38597329 DOI: 10.1111/mec.17348] [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: 11/30/2023] [Revised: 03/13/2024] [Accepted: 03/27/2024] [Indexed: 04/11/2024]
Abstract
Organisms inhabiting highly seasonal environments must cope with a wide range of environmentally induced challenges. Many seasonal challenges require extensive physiological modification to survive. In winter, to survive extreme cold and limited resources, insects commonly enter diapause, which is an endogenously derived dormant state associated with minimized cellular processes and low energetic expenditure. Due to the high degree of complexity involved in diapause, substantial cellular regulation is required, of which our understanding primarily derives from the transcriptome via messenger RNA expression dynamics. Here we aim to advance our understanding of diapause by investigating microRNA (miRNA) expression in diapausing and direct developing pupae of the butterfly Pieris napi. We identified coordinated patterns of miRNA expression throughout diapause in both head and abdomen tissues of pupae, and via miRNA target identification, found several expression patterns to be enriched for relevant diapause-related physiological processes. We also identified two candidate miRNAs, miR-14-5p and miR-2a-3p, that are likely involved in diapause progression through their activity in the ecdysone pathway, a critical regulator of diapause termination. miR-14-5p targets phantom, a gene in the ecdysone synthesis pathway, and is upregulated early in diapause. miR-2a-3p has been found to be expressed in response to ecdysone, and is upregulated during diapause termination. Together, the expression patterns of these two miRNAs match our current understanding of the timing of hormonal regulation of diapause in P. napi and provide interesting candidates to further explore the mechanistic role of microRNAs in diapause regulation.
Collapse
Affiliation(s)
- Kevin T Roberts
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | - Rachel A Steward
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Department of Biology, Lund University, Lund, Sweden
| | - Philip Süess
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Philipp Lehmann
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | | |
Collapse
|
4
|
Zhang J, Liu M, Wen L, Hua Y, Zhang R, Li S, Zafar J, Pang R, Xu H, Xu X, Jin F. MiR-2b-3p Downregulated PxTrypsin-9 Expression in the Larval Midgut to Decrease Cry1Ac Susceptibility of the Diamondback Moth, Plutella xylostella (L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:2263-2276. [PMID: 38235648 DOI: 10.1021/acs.jafc.3c07678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Crystal (Cry) toxins, produced by Bacillus thuringiensis, are widely used as effective biological pesticides in agricultural production. However, insects always quickly evolve adaptations against Cry toxins within a few generations. In this study, we focused on the Cry1Ac protoxin activated by protease. Our results identified PxTrypsin-9 as a trypsin gene that plays a key role in Cry1Ac virulence in Plutella xylostella larvae. In addition, P. xylostella miR-2b-3p, a member of the micoRNA-2 (miR-2) family, was significantly upregulated by Cry1Ac protoxin and targeted to PxTrypsin-9 downregulated its expression. The mRNA level of PxTrypsin-9, regulated by miR-2b-3p, revealed an increased tolerance of P. xylostella larvae to Cry1Ac at the post-transcriptional level. Considering that miR-2b and trypsin genes are widely distributed in various pest species, our study provides the basis for further investigation of the roles of miRNAs in the regulation of the resistance to Cry1Ac and other insecticides.
Collapse
Affiliation(s)
- Jie Zhang
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Mingyou Liu
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Liang Wen
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Yanyan Hua
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Ruonan Zhang
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - ShuZhong Li
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Junaid Zafar
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Rui Pang
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Hanhong Xu
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoxia Xu
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Fengliang Jin
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| |
Collapse
|
5
|
Huang S, Yoshitake K, Kinoshita S, Asakawa S. Transcriptional landscape of small non-coding RNAs reveals diversity of categories and functions in molluscs. RNA Biol 2024; 21:1-13. [PMID: 38693614 PMCID: PMC11067994 DOI: 10.1080/15476286.2024.2348893] [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: 12/07/2022] [Indexed: 05/03/2024] Open
Abstract
Small non-coding RNAs (sncRNAs) are non-coding RNA molecules that play various roles in metazoans. Among the sncRNAs, microRNAs (miRNAs) guide post-translational gene regulation during cellular development, proliferation, apoptosis, and differentiation, while PIWI-interacting RNAs (piRNAs) suppress transposon activity to safeguard the genome from detrimental insertion mutagenesis. While an increasing number of piRNAs are being identified in the soma and germlines of various organisms, they are scarcely reported in molluscs. To unravel the small RNA (sRNA) expression patterns and genomic function in molluscs, we generated a comprehensive sRNA dataset by sRNA sequencing (sRNA-seq) of eight mollusc species. Abundant miRNAs were identified and characterized in all investigated molluscs, and ubiquitous piRNAs were discovered in both somatic and gonadal tissues in six of the investigated molluscs, which are more closely associated with transposon silencing. Tens of piRNA clusters were also identified based on the genomic mapping results, which varied among different tissues and species. Our dataset serves as important reference data for future genomic and genetic studies on sRNAs in these molluscs and related species, especially in elucidating the ancestral state of piRNAs in bilaterians.
Collapse
Affiliation(s)
- Songqian Huang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, Japan
| | - Kazutoshi Yoshitake
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, Japan
| | - Shigeharu Kinoshita
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
6
|
Farsi NR, Naghipour B, Shahabi P, Safaralizadeh R, Hajiasgharzadeh K, Dastmalchi N, Alipour MR. The role of microRNAs in hepatocellular carcinoma: Therapeutic targeting of tumor suppressor and oncogenic genes. Clin Exp Hepatol 2023; 9:307-319. [PMID: 38774201 PMCID: PMC11103798 DOI: 10.5114/ceh.2023.131669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/31/2023] [Indexed: 05/24/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is a severe malignant liver cancer with a poor prognosis and a high mortality rate. This carcinoma is a multistage process that begins with chronic hepatitis and progresses to cirrhosis, dysplastic nodules, and eventually HCC. However, the exact molecular etiology remains unclear. MicroRNAs (miRs) are small non-coding RNAs that modulate the expression of numerous genes. These molecules have become significant participants in several functions, including cell proliferation, differentiation, development, and tumorrelated properties. They have a pivotal role in carcinogenesis as oncogenes or tumor suppressor genes. Furthermore, some investigations have shown that particular miRs might be used as predictive or diagnostic markers and therapeutic targets in HCC therapy. This review study summarizes the current level of knowledge on the role of miRs in the initiation and progression of HCC.
Collapse
Affiliation(s)
- Nasim Rahimi Farsi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Biology, University College of Nabi Akram, Tabriz, Iran
| | - Bahman Naghipour
- Department of Anesthesiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parviz Shahabi
- Department of Physiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Safaralizadeh
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | | | - Narges Dastmalchi
- Department of Biology, University College of Nabi Akram, Tabriz, Iran
| | - Mohammad Reza Alipour
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Physiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
7
|
Vasiliev GV, Ovchinnikov VY, Lisachev PD, Bondar NP, Grinkevich LN. The Expression of miRNAs Involved in Long-Term Memory Formation in the CNS of the Mollusk Helix lucorum. Int J Mol Sci 2022; 24:ijms24010301. [PMID: 36613744 PMCID: PMC9820140 DOI: 10.3390/ijms24010301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Mollusks are unique animals with a relatively simple central nervous system (CNS) containing giant neurons with identified functions. With such simple CNS, mollusks yet display sufficiently complex behavior, thus ideal for various studies of behavioral processes, including long-term memory (LTM) formation. For our research, we use the formation of the fear avoidance reflex in the terrestrial mollusk Helix lucorum as a learning model. We have shown previously that LTM formation in Helix requires epigenetic modifications of histones leading to both activation and inactivation of the specific genes. It is known that microRNAs (miRNAs) negatively regulate the expression of genes; however, the role of miRNAs in behavioral regulation has been poorly investigated. Currently, there is no miRNAs sequencing data being published on Helix lucorum, which makes it impossible to investigate the role of miRNAs in the memory formation of this mollusk. In this study, we have performed sequencing and comparative bioinformatics analysis of the miRNAs from the CNS of Helix lucorum. We have identified 95 different microRNAs, including microRNAs belonging to the MIR-9, MIR-10, MIR-22, MIR-124, MIR-137, and MIR-153 families, known to be involved in various CNS processes of vertebrates and other species, particularly, in the fear behavior and LTM. We have shown that in the CNS of Helix lucorum MIR-10 family (26 miRNAs) is the most representative one, including Hlu-Mir-10-S5-5p and Hlu-Mir-10-S9-5p as top hits. Moreover, we have shown the involvement of the MIR-10 family in LTM formation in Helix. The expression of 17 representatives of MIR-10 differentially changes during different periods of LTM consolidation in the CNS of Helix. In addition, using comparative analysis of microRNA expression upon learning in normal snails and snails with deficient learning abilities with dysfunction of the serotonergic system, we identified a number of microRNAs from several families, including MIR-10, which expression changes only in normal animals. The obtained data can be used for further fundamental and applied behavioral research.
Collapse
Affiliation(s)
- Gennady V. Vasiliev
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 10 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Vladimir Y. Ovchinnikov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 10 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Pavel D. Lisachev
- Federal Research Center for Information and Computational Technologies, 6 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Natalia P. Bondar
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 10 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Larisa N. Grinkevich
- The Federal State Budget Scientific Institution Pavlov Institute of Physiology, Russian Academy of Sciences, 6 nab. Makarova, St. Petersburg 199034, Russia
- Correspondence:
| |
Collapse
|
8
|
Yang XB, Zhou C, Yang JP, Gong MF, Yang H, Long GY, Jin DC. Identification and profiling of Sogatella furcifera microRNAs and their potential roles in regulating the developmental transitions of nymph-adult. INSECT MOLECULAR BIOLOGY 2022; 31:798-809. [PMID: 35899838 DOI: 10.1111/imb.12805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 07/24/2022] [Indexed: 06/15/2023]
Abstract
Sogatella furcifera is one of the most serious insect pests that affect rice in Asia. One class of small RNAs (sRNAs; ~22 nt long) is miRNAs, which participate in various biological processes by regulating the expression of target genes in a spatiotemporal manner. However, the role of miRNAs in nymph-to-adult transition in S. furcifera remains unknown. In this study, we sequenced sRNA libraries of S. furcifera prepared from individuals at three different developmental stages (pre-moult, moulting and early adult). A total of 253 miRNAs (134 known and 119 novel) were identified, of which 12 were differentially expressed during the nymph-to-adult developmental transition. Moreover, Real time quantitative PCR (RT-qPCR) analysis revealed that all 12 miRNAs were differentially expressed among five different nymph tissues and 14 different developmental stages (first to fifth instar nymphs and 1-day-old adults). Injection of miR-2a-2 mimic/antagomir and miR-305-5p-1 mimic/antagomir into 1-day-old fifth instar nymphs significantly increased the mortality rate. In addition, a defective moulting phenotype was observed in nymphs injected with miR-2a-2 and miR-305-5p-1, suggesting that these miRNAs are involved in S. furcifera nymph-adult transition. In conclusion, these results reveal the function of critical miRNAs in S. furcifera nymph-adult transition, and also provide novel potential targets of insecticides for the long-term sustainable management of S. furcifera.
Collapse
Affiliation(s)
- Xi-Bin Yang
- Institute of Entomology, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Guiyang, China
- Scientific Observing and Experimental Station of Crop Pests in Guiyang, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang, China
| | - Cao Zhou
- College of Life Science, Chongqing Normal University, Chongqing, China
| | - Jia-Peng Yang
- Institute of Entomology, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Guiyang, China
- Scientific Observing and Experimental Station of Crop Pests in Guiyang, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang, China
| | - Ming-Fu Gong
- Institute of Entomology, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Guiyang, China
- Scientific Observing and Experimental Station of Crop Pests in Guiyang, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang, China
| | - Hong Yang
- Institute of Entomology, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Guiyang, China
- Scientific Observing and Experimental Station of Crop Pests in Guiyang, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang, China
- College of Tobacco Science of Guizhou University, Guiyang, China
| | - Gui-Yun Long
- Institute of Entomology, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Guiyang, China
- Scientific Observing and Experimental Station of Crop Pests in Guiyang, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang, China
| | - Dao-Chao Jin
- Institute of Entomology, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Guiyang, China
- Scientific Observing and Experimental Station of Crop Pests in Guiyang, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang, China
| |
Collapse
|
9
|
A transcriptomic (RNA-seq) analysis of Drosophila melanogaster adult testes overexpressing microRNA-2b-1. Data Brief 2022; 45:108748. [DOI: 10.1016/j.dib.2022.108748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 11/14/2022] Open
|
10
|
Gaeta AL, Nourse JB, Willicott K, McKay LE, Keogh CM, Peter K, Russell SN, Hamamichi S, Berkowitz LA, Caldwell KA, Caldwell GA. Systemic RNA Interference Defective (SID) genes modulate dopaminergic neurodegeneration in C. elegans. PLoS Genet 2022; 18:e1010115. [PMID: 35984862 PMCID: PMC9432717 DOI: 10.1371/journal.pgen.1010115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 08/31/2022] [Accepted: 08/01/2022] [Indexed: 02/02/2023] Open
Abstract
The fine-tuning of gene expression is critical for all cellular processes; aberrations in this activity can lead to pathology, and conversely, resilience. As their role in coordinating organismal responses to both internal and external factors have increasingly come into focus, small non-coding RNAs have emerged as an essential component to disease etiology. Using Systemic RNA interference Defective (SID) mutants of the nematode Caenorhabditis elegans, deficient in gene silencing, we examined the potential consequences of dysfunctional epigenomic regulation in the context of Parkinson's disease (PD). Specifically, the loss of either the sid-1 or sid-3 genes, which encode a dsRNA transporter and an endocytic regulatory non-receptor tyrosine kinase, respectively, conferred neuroprotection to dopaminergic (DA) neurons in an established transgenic C. elegans strain wherein overexpression of human α-synuclein (α-syn) from a chromosomally integrated multicopy transgene causes neurodegeneration. We further show that knockout of a specific microRNA, mir-2, attenuates α-syn neurotoxicity; suggesting that the native targets of mir-2-dependent gene silencing represent putative neuroprotective modulators. In support of this, we demonstrated that RNAi knockdown of multiple mir-2 targets enhanced α-syn-induced DA neurodegeneration. Moreover, we demonstrate that mir-2 overexpression originating in the intestine can induce neurodegeneration of DA neurons, an effect that was reversed by pharmacological inhibition of SID-3 activity. Interestingly, sid-1 mutants retained mir-2-induced enhancement of neurodegeneration. Transcriptomic analysis of α-syn animals with and without a sid-1 mutation revealed 27 differentially expressed genes with human orthologs related to a variety of diseases, including PD. Among these was pgp-8, encoding a P-glycoprotein-related ABC transporter. Notably, sid-1; pgp-8 double mutants abolished the neurodegeneration resulting from intestinal mir-2 overexpression. This research positions known regulators of small RNA-dependent gene silencing within a framework that facilitates mechanistic evaluation of epigenetic responses to exogenous and endogenous factors influencing DA neurodegeneration, revealing a path toward new targets for therapeutic intervention of PD.
Collapse
Affiliation(s)
- Anthony L. Gaeta
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - J. Brucker Nourse
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Karolina Willicott
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Luke E. McKay
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Candice M. Keogh
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Kylie Peter
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Shannon N. Russell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Shusei Hamamichi
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Laura A. Berkowitz
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Kim A. Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
- Center for Convergent Bioscience and Medicine, The University of Alabama, Tuscaloosa, Alabama, United States of America
- Alabama Research Institute on Aging, The University of Alabama, Tuscaloosa, Alabama, United States of America
- Departments of Neurology and Neurobiology, Center for Neurodegeneration and Experimental Therapeutics, Nathan Shock Center of Excellence for Basic Research in the Biology of Aging, University of Alabama at Birmingham, Heersink School of Medicine, Birmingham, Alabama, United States of America
| | - Guy A. Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
- Center for Convergent Bioscience and Medicine, The University of Alabama, Tuscaloosa, Alabama, United States of America
- Departments of Neurology and Neurobiology, Center for Neurodegeneration and Experimental Therapeutics, Nathan Shock Center of Excellence for Basic Research in the Biology of Aging, University of Alabama at Birmingham, Heersink School of Medicine, Birmingham, Alabama, United States of America
| |
Collapse
|
11
|
Van den Brande S, Gijbels M, Wynant N, Peeters P, Gansemans Y, Van Nieuwerburgh F, Santos D, Vanden Broeck J. Identification and profiling of stable microRNAs in hemolymph of young and old Locusta migratoria fifth instars. CURRENT RESEARCH IN INSECT SCIENCE 2022; 2:100041. [PMID: 36003267 PMCID: PMC9387440 DOI: 10.1016/j.cris.2022.100041] [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: 12/30/2021] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Since the discovery of the first microRNA (miRNA) in the nematode Caenorhabditis elegans, numerous novel miRNAs have been identified which can regulate presumably every biological process in a wide range of metazoan species. In accordance, several insect miRNAs have been identified and functionally characterized. While regulatory RNA pathways are traditionally described at an intracellular level, studies reporting on the presence and potential role of extracellular (small) sRNAs have been emerging in the last decade, mainly in mammalian systems. Interestingly, evidence in several species indicates the functional transfer of extracellular RNAs between donor and recipient cells, illustrating RNA-based intercellular communication. In insects, however, reports on extracellular small RNAs are emerging but the number of detailed studies is still very limited. Here, we demonstrate the presence of stable sRNAs in the hemolymph of the migratory locust, Locusta migratoria. Moreover, the levels of several extracellular miRNAs (ex-miRNAs) present in locust hemolymph differed significantly between young and old fifth nymphal instars. In addition, we performed a 'proof of principle' experiment which suggested that extracellularly delivered miRNA molecules are capable of affecting the locusts' development.
Collapse
Affiliation(s)
- Stijn Van den Brande
- Research group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Zoological Institute, Naamsestraat 59 box 2465, 3000 Leuven, Belgium
| | - Marijke Gijbels
- Research group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Zoological Institute, Naamsestraat 59 box 2465, 3000 Leuven, Belgium
| | - Niels Wynant
- Research group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Zoological Institute, Naamsestraat 59 box 2465, 3000 Leuven, Belgium
| | - Paulien Peeters
- Research group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Zoological Institute, Naamsestraat 59 box 2465, 3000 Leuven, Belgium
| | - Yannick Gansemans
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Dulce Santos
- Research group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Zoological Institute, Naamsestraat 59 box 2465, 3000 Leuven, Belgium
| | - Jozef Vanden Broeck
- Research group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Zoological Institute, Naamsestraat 59 box 2465, 3000 Leuven, Belgium
| |
Collapse
|
12
|
Hebbar S, Panzade G, Vashisht AA, Wohlschlegel JA, Veksler-Lublinsky I, Zinovyeva AY. Functional identification of microRNA-centered complexes in C. elegans. Sci Rep 2022; 12:7133. [PMID: 35504914 PMCID: PMC9065084 DOI: 10.1038/s41598-022-10771-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/08/2022] [Indexed: 02/02/2023] Open
Abstract
microRNAs (miRNAs) are crucial for normal development and physiology. To identify factors that might coordinate with miRNAs to regulate gene expression, we used 2'O-methylated oligonucleotides to precipitate Caenorhabditis elegans let-7, miR-58, and miR-2 miRNAs and the associated proteins. A total of 211 proteins were identified through mass-spectrometry analysis of miRNA co-precipitates, which included previously identified interactors of key miRNA pathway components. Gene ontology analysis of the identified interactors revealed an enrichment for RNA binding proteins, suggesting that we captured proteins that may be involved in mRNA lifecycle. To determine which miRNA interactors are important for miRNA activity, we used RNAi to deplete putative miRNA co-factors in animals with compromised miRNA activity and looked for alterations of the miRNA mutant phenotypes. Depletion of 25 of 39 tested genes modified the miRNA mutant phenotypes in three sensitized backgrounds. Modulators of miRNA phenotypes ranged from RNA binding proteins RBD-1 and CEY-1 to metabolic factors such as DLST-1 and ECH-5, among others. The observed functional interactions suggest widespread coordination of these proteins with miRNAs to ultimately regulate gene expression. This study provides a foundation for future investigations aimed at deciphering the molecular mechanisms of miRNA-mediated gene regulation.
Collapse
Affiliation(s)
- Shilpa Hebbar
- Division of Biology, Kansas State University, Manhattan, 66506, USA
| | - Ganesh Panzade
- Division of Biology, Kansas State University, Manhattan, 66506, USA
| | - Ajay A Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, 90095, USA
- Genomics Institute of the Novartis Research Foundation, San Diego, 92121, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, 90095, USA
| | - Isana Veksler-Lublinsky
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Anna Y Zinovyeva
- Division of Biology, Kansas State University, Manhattan, 66506, USA.
| |
Collapse
|
13
|
Huang S, Nishiumi S, Asaduzzaman M, Pan Y, Liu G, Yoshitake K, Maeyama K, Kinoshita S, Nagai K, Watabe S, Yoshida T, Asakawa S. Exosome-derived small non-coding RNAs reveal immune response upon grafting transplantation in Pinctada fucata (Mollusca). Open Biol 2022; 12:210317. [PMID: 35506205 PMCID: PMC9065966 DOI: 10.1098/rsob.210317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Exosomes, a subset of small extracellular vesicles, carry various nucleic acids, proteins, lipids, amino acids and metabolites. They function as a mode of intercellular communication and molecular transfer. Exosome cargo molecules, including small non-coding RNAs (sncRNAs), are involved in the immune response in various organisms. However, the role of exosome-derived sncRNAs in immune responses in molluscs remains unclear. Here, we aimed to reveal the sncRNAs involved in the immune response during grafting transplantation by the pearl oyster Pinctada fucata. Exosomes were successfully extracted from the P. fucata haemolymph during graft transplantation. Abundant microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs) were simultaneously discovered in P. fucata exosomes by small RNA sequencing. The expression patterns of the miRNAs and piRNAs at the grafting and initial stages were not substantially different, but varied significantly between the initial and later stages. Target prediction and functional analysis indicate that these miRNAs and piRNAs are related to immune response upon grafting transplantation, whereas piRNAs may also be associated with transposon silencing by targeting with genome transposon elements. This work provides the basis for a functional understanding of exosome-derived sncRNAs and helps to gain further insight into the PIWI/piRNA pathway function outside of germline cells in molluscs.
Collapse
Affiliation(s)
- Songqian Huang
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Shinya Nishiumi
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Md Asaduzzaman
- Department of Marine Bioresources Science, Faculty of Fisheries, Chittagong Veterinary and Animal Sciences University, Khulshi 4225, Chittagong, Bangladesh
| | - Yida Pan
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Guanting Liu
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kazutoshi Yoshitake
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kaoru Maeyama
- Mikimoto Pharmaceutical Co., Ltd., Kurose 1425, Ise, Mie 516-8581, Japan
| | - Shigeharu Kinoshita
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kiyohito Nagai
- Pearl Research Laboratory, K. Mikimoto & Co., Ltd., Osaki Hazako 923, Hamajima, Shima, Mie 517-0403, Japan
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University, Minami-ku, Sagamihara, Kanagawa 252-0313, Japan
| | - Tetsuhiko Yoshida
- Institute for Advanced Sciences, Toagosei Co., Ltd., Tsukuba, Ibaraki 300-2611, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| |
Collapse
|
14
|
Li X, Zhang F, Coates B, Wei C, Zhu X, Zhang Y, Zhou X. Temporal analysis of microRNAs associated with wing development in the English grain aphid, Sitobion avenae (F.) (Homoptera: Aphidiae). INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 142:103579. [PMID: 33894361 DOI: 10.1016/j.ibmb.2021.103579] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 06/12/2023]
Abstract
Molecular mechanisms underlying wing evolution and development have been a point of scientific inquiry for decades. Phloem-feeding aphids are one of the most devastating global insect pests, where dispersal of winged morphs lead to annual movements, migrations, and range expansions. Aphids show a polyphenic wing dimorphism trait, and offer a model to study the role of environment in determining morphological plasticity of a single genotype. Despite recent progresses in the genetic understanding of wing polyphenism, the influence of environmental cues remains unclear. To investigate the involvement of miRNAs in wing development, we sequenced small RNA libraries of the English grain aphid, Sitobion avenae (F.) across six different developmental stages. As a result, we identified 113 conserved and 193 S. avenae-specific miRNAs. Gene Ontology and KEGG pathway analyses of putative target mRNAs for the six differentially expressed miRNAs are enriched for wing development processes. Dietary uptake of miR-263a, miR-316, and miR-184a agomirs and antagomirs led to significantly higher mortality (>70%) and a lower proportion of winged morphs (<5%). On the other hand, wing malformation was observed in miR-2 and miR-306 agomirs and miR-2 and miR-14 antagomirs, respectively, suggesting their involvement in S. avenae wing morphogenesis. These combined results not only shed light on the regulatory role of miRNAs in wing dimorphism, but also provide potential novel targets for the long-term sustainable management of S. avenae, a devastating global grain pest.
Collapse
Affiliation(s)
- Xiangrui Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Fangmei Zhang
- Henan Provincial South Henan Crop Pest Green Prevention and Control Academician Workstation, Xinyang Agriculture and Forestry University, Xinyang, 46400, China
| | - Brad Coates
- United States Department of Agriculture, Agricultural Research Service, Corn Insects & Crop Genetics Research Unit, Ames, IA, 50011, USA
| | - Changping Wei
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xun Zhu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yunhui Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, KY, 40546-0091, USA.
| |
Collapse
|
15
|
Li G, Zhang J, Liu XY, Niu J, Wang JJ. De novo RNA-Seq and Annotation of Sesquiterpenoid and Ecdysteroid Biosynthesis Genes and MicroRNAs in a Spider Mite Eotetranychus kankitus. JOURNAL OF ECONOMIC ENTOMOLOGY 2021; 114:2543-2552. [PMID: 34668540 DOI: 10.1093/jee/toab166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Indexed: 06/13/2023]
Abstract
Eotetranychus kankitus is an important mite pest in citrus, but molecular data on the developmental processes of E. kankitus are lacking. The different development stages mix of E. kankitus was used to sequence for transcriptome and small RNAs to identify genes and predict miRNAs associated with sesquiterpenoid and ecdysteroid biosynthesis and signaling pathways. More than 36 million clean reads were assembled and 67,927 unigenes were generated. Of the unigenes, 19,300 were successfully annotated through annotation databases NR, SwissProt, COG, GO, KEGG, PFAM, and KOG. The transcripts were involved in sesquiterpenoid biosynthesis (11 genes) and ecdysteroid biosynthesis and signaling pathway (13 genes). Another, small RNA library was obtained and 31 conserved miRNAs were identified. Five most abundant miRNAs were Ek-miR-5735, Ek-miR-1, Ek-miR-263a, Ek-miR-184, and Ek-miR-8. The target genes related to sesquiterpenoid and ecdysteroid showed that 10 of the conserved miRNAs could potentially target the sesquiterpenoid and ecdysteroid pathway according to four-prediction software, sRNAT, miRanda, RNAhybrid, and Risearch2. Thus, the results of this study will provide bioinformatics information for further molecular studies of E. kankitus which may facilitate improved pest control strategies.
Collapse
Affiliation(s)
- Gang Li
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jun Zhang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Xun-Yan Liu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jinzhi Niu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| |
Collapse
|
16
|
Zafar J, Zhang Y, Huang J, Freed S, Shoukat RF, Xu X, Jin F. Spatio-Temporal Profiling of Metarhizium anisopliae-Responsive microRNAs Involved in Modulation of Plutella xylostella Immunity and Development. J Fungi (Basel) 2021; 7:942. [PMID: 34829229 PMCID: PMC8620415 DOI: 10.3390/jof7110942] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/30/2021] [Accepted: 11/01/2021] [Indexed: 02/06/2023] Open
Abstract
Metarhizium anisopliae, a ubiquitous pathogenic fungus, regulates a wide array of the insect pest population. The fungus has been employed to control Plutella xylostella, an insecticide-resistant destructive lepidopteran pest, which causes substantial economic losses in crops worldwide. Integration of modern gene-silencing technologies in pest control strategies has become more crucial to counter pesticide-resistant insects. MicroRNAs (miRNA) play essential roles in the various biological process via post-transcriptional gene regulation. In the present study, RNA-seq analysis of control (CK36h, CK72h) and fungal-infected (T36h, T72h) midguts was performed to reveal underlying molecular mechanisms occurring in larval midgut at different time courses. We aimed at exploring M. anisopliae-responsive miRNAs and their target genes involved in development and immunity. After data filtration, a combined set of 170 miRNAs were identified from all libraries. Interestingly, miR-281, miR-263, miR-1, miR-6094 and miR-8 were listed among the most abundantly expressed conserved miRNAs. Furthermore, we experimentally studied the role of differentially expressed miR-11912-5p in regulating corresponding target trypsin-like serine proteinase (Px_TLSP). The luciferase assay (in vitro) revealed that miRNA-11912-5p significantly downregulated its target gene, suggesting it might play a crucial role in defense mechanism of P. xylostella against M.+ anisopliae infection. We used synthetic miRNA mimic/inhibitor (in vivo), to overexpress/silence miRNA, which showed harmful effects on larval duration, survival and adult fecundity. Additionally, fungal application in the presence of mimics revealed enhanced sensitivity of P. xylostella to infection. Our finding provides an insight into the relatively obscure molecular mechanisms involved in insect midgut during the fungal infection.
Collapse
Affiliation(s)
- Junaid Zafar
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (Y.Z.); (J.H.); (R.F.S.)
| | - Yuxin Zhang
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (Y.Z.); (J.H.); (R.F.S.)
| | - Junlin Huang
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (Y.Z.); (J.H.); (R.F.S.)
| | - Shoaib Freed
- Laboratory of Insect Microbiology and Biotechnology, Department of Entomology, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan 66000, Pakistan;
| | - Rana Fartab Shoukat
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (Y.Z.); (J.H.); (R.F.S.)
| | - Xiaoxia Xu
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (Y.Z.); (J.H.); (R.F.S.)
| | - Fengliang Jin
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (Y.Z.); (J.H.); (R.F.S.)
| |
Collapse
|
17
|
Huang JH, Jiao YH, Li L, Li DW, Li HY, Yang WD. Small RNA analysis of Perna viridis after exposure to Prorocentrum lima, a DSP toxins-producing dinoflagellate. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 239:105950. [PMID: 34474269 DOI: 10.1016/j.aquatox.2021.105950] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
Diarrheic shellfish poisoning toxins (DSP toxins) are a set of the most important phycotoxins produced by some dinoflagellates. Studies have shown that DSP toxins have various toxicities such as genotoxicity, cytotoxicity, and immunotoxicity to bivalve mollusks. However, these toxicities appear decreasing with exposure time and concentration of DSP toxins. The underlying mechanism involved remains unclear. In this study, small RNA sequencing was performed in the digestive gland of the mussel Perna viridis after exposure to DSP toxins-producing dinoflagellate Prorocentrum lima for different time periods. The potential roles of miRNAs in response and detoxification to DSP toxins in the mussel were analyzed. Small RNA sequencing of 12 samples from 72 individuals was conducted by BGISEQ-500. A total of 123 mature miRNAs were identified, including 90 conserved miRNAs and 33 potential novel miRNAs. After exposure to P. lima, multiple important miRNAs displayed some alterations. Further miRNA target prediction revealed some important genes involved in cytoskeleton, apoptosis, complement system and immune stress. qPCR demonstrated that miR-71_5, miR-750_1 and novel_mir4 were significantly up-regulated at 6 h after exposure to P. lima, while miR-100_2 was significantly down-regulated after 96 h of exposure. Accordingly, putative target genes of these differentially expressed miRNAs experienced some changes. After 6 h of DSP toxins exposure, NHLRC2 and C1q-like were significantly down-regulated. After 96 h of DSP toxins exposure, NHLRC2 was significantly up-regulated. It is reasonable to speculate that the mussel P. viridis might respond to DSP toxins through miR-750_1, novel_mir4 and miR-71_5 regulating the expression of relevant target genes involved in apoptosis, cytoskeleton, and immune response, etc. This study might provide new clues to uncover the toxic response of bivalve to DSP toxins and lay a foundation for revealing the roles of miRNAs in the environmental adaptation in shellfish.
Collapse
Affiliation(s)
- Jia-Hui Huang
- College of Life Science and Technology, Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, Jinan University, Guangzhou 510632, China
| | - Yu-Hu Jiao
- College of Life Science and Technology, Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, Jinan University, Guangzhou 510632, China
| | - Li Li
- College of Life Science and Technology, Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, Jinan University, Guangzhou 510632, China
| | - Da-Wei Li
- College of Life Science and Technology, Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, Jinan University, Guangzhou 510632, China
| | - Hong-Ye Li
- College of Life Science and Technology, Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, Jinan University, Guangzhou 510632, China
| | - Wei-Dong Yang
- College of Life Science and Technology, Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, Jinan University, Guangzhou 510632, China.
| |
Collapse
|
18
|
Yang J, Xu X, Lin S, Chen S, Lin G, Song Q, Bai J, You M, Xie M. Profiling of MicroRNAs in Midguts of Plutella xylostella Provides Novel Insights Into the Bacillus thuringiensis Resistance. Front Genet 2021; 12:739849. [PMID: 34567090 PMCID: PMC8455949 DOI: 10.3389/fgene.2021.739849] [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: 07/12/2021] [Accepted: 08/20/2021] [Indexed: 01/03/2023] Open
Abstract
The diamondback moth (DBM), Plutella xylostella, one of the most destructive lepidopteran pests worldwide, has developed field resistance to Bacillus thuringiensis (Bt) Cry toxins. Although miRNAs have been reported to be involved in insect resistance to multiple insecticides, our understanding of their roles in mediating Bt resistance is limited. In this study, we constructed small RNA libraries from midguts of the Cry1Ac-resistant (Cry1S1000) strain and the Cry1Ac-susceptible strain (G88) using a high-throughput sequencing analysis. A total of 437 (76 known and 361 novel miRNAs) were identified, among which 178 miRNAs were classified into 91 miRNA families. Transcripts per million analysis revealed 12 differentially expressed miRNAs between the Cry1S1000 and G88 strains. Specifically, nine miRNAs were down-regulated and three up-regulated in the Cry1S1000 strain compared to the G88 strain. Next, we predicted the potential target genes of these differentially expressed miRNAs and carried out GO and KEGG pathway analyses. We found that the cellular process, metabolism process, membrane and the catalytic activity were the most enriched GO terms and the Hippo, MAPK signaling pathway might be involved in Bt resistance of DBM. In addition, the expression patterns of these miRNAs and their target genes were determined by RT-qPCR, showing that partial miRNAs negatively while others positively correlate with their corresponding target genes. Subsequently, novel-miR-240, one of the differentially expressed miRNAs with inverse correlation with its target genes, was confirmed to interact with Px017590 and Px007885 using dual luciferase reporter assays. Our study highlights the characteristics of differentially expressed miRNAs in midguts of the Cry1S1000 and G88 strains, paving the way for further investigation of miRNA roles in mediating Bt resistance.
Collapse
Affiliation(s)
- Jie Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.,Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuejiao Xu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.,Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sujie Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.,Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shiyao Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guifang Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.,Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO, United States
| | - Jianlin Bai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.,Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Minsheng You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.,Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Miao Xie
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China.,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.,Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China.,College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
19
|
Fonseca PLC, Mucherino M JJ, Porto JAM, Armache JN, de Almeida JPP, da Silva FF, Olmo RP, Faria IJDS, de Carvalho DS, Góes-Neto A, Corrêa RX, Pirovani CP, Pacheco LGC, Costa MA, Aguiar ERGR. Genome-wide identification of miRNAs and target regulatory network in the invasive ectoparasitic mite Varroa destructor. Genomics 2021; 113:2290-2303. [PMID: 34044154 DOI: 10.1016/j.ygeno.2021.05.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 04/21/2021] [Accepted: 05/23/2021] [Indexed: 12/29/2022]
Abstract
Varroa destructor is an ectoparasite mite that attacks bees leading to colony disorders worldwide. microRNAs (miRNAs) are key molecules used by eukaryotes to post-transcriptional control of gene expression. Nevertheless, still lack information aboutV. destructor miRNAs and its regulatory networks. Here, we used an integrative strategy to characterize the miRNAs in the V. destructor mite. We identified 310 precursors that give rise to 500 mature miRNAs, which 257 are likely mite-specific elements. miRNAs showed canonical length ranging between 18 and 25 nucleotides and 5' uracil preference. Top 10 elements concentrated over 80% of total miRNA expression, with bantam alone representing ~50%. We also detected non-templated bases in precursor-derived small RNAs, indicative of miRNA post-transcriptional regulatory mechanisms. Finally, we note that conserved miRNAs control similar processes in different organisms, suggesting a conservative role. Altogether, our findings contribute to the better understanding of the mite biology that can assist future studies on varroosis control.
Collapse
Affiliation(s)
- Paula L C Fonseca
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Jonathan J Mucherino M
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil; Department of Forest Management, Facultad de Ciencias Forestales y Ambientales, Universidad de Los Andes, Mérida, Mérida 5101, Venezuela
| | - Joel A M Porto
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Juliana N Armache
- Bioinformatics Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - João Paulo P de Almeida
- Bioinformatics Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Felipe F da Silva
- Bioinformatics Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Roenick P Olmo
- Université de Strasbourg, CNRS UPR9022, Inserm, Strasbourg, France
| | - Isaque J da S Faria
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Daniel S de Carvalho
- Bioinformatics Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Aristóteles Góes-Neto
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil; Bioinformatics Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Ronan X Corrêa
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Carlos P Pirovani
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Luis G C Pacheco
- Institute of Health Sciences, Universidade Federal da Bahia, Salvador, BA, Brazil
| | - Marco Antônio Costa
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Eric R G R Aguiar
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil.
| |
Collapse
|
20
|
miRNAs of Aedes aegypti (Linnaeus 1762) conserved in six orders of the class Insecta. Sci Rep 2021; 11:10706. [PMID: 34021209 PMCID: PMC8139948 DOI: 10.1038/s41598-021-90095-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 04/05/2021] [Indexed: 11/08/2022] Open
Abstract
Aedes aegypti L. is the most important vector of arboviruses such as dengue, Zika, chikungunya, Mayaro, and yellow fever, which impact millions of people's health per year. MicroRNA profile has been described in some mosquito species as being important for biological processes such as digestion of blood, oviposition, sexual differentiation, insecticide resistance, and pathogens dissemination. We identified the miRNAs of Ae. aegypti females, males and eggs of a reference insecticide susceptible strain New Orleans and compared them with those other insects to determine miRNA fingerprint by new-generation sequencing. The sequences were analyzed using data mining tools and categorization, followed by differential expression analysis and conservation with other insects. A total of 55 conserved miRNAs were identified, of which 34 were of holometabolous insects and 21 shared with hemimetabolous insects. Of these miRNAs, 32 had differential expression within the stages analyzed. Three predominant functions of miRNA were related to embryonic development regulation, metamorphosis, and basal functions. The findings of this research describe new information on Ae. aegypti physiology which could be useful for the development of new control strategies, particularly in mosquito development and metamorphosis processes.
Collapse
|
21
|
Yang X, Fishilevich E, German MA, Gandra P, McEwan RE, Billion A, Knorr E, Vilcinskas A, Narva KE. Elucidation of the microRNA Transcriptome in Western Corn Rootworm Reveals Its Dynamic and Evolutionary Complexity. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:800-814. [PMID: 33607298 PMCID: PMC9170749 DOI: 10.1016/j.gpb.2019.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 11/21/2018] [Accepted: 03/28/2019] [Indexed: 11/25/2022]
Abstract
Diabrotica virgifera virgifera (western corn rootworm, WCR) is one of the most destructive agricultural insect pests in North America. It is highly adaptive to environmental stimuli and crop protection technologies. However, little is known about the underlying genetic basis of WCR behavior and adaptation. More specifically, the involvement of small RNAs (sRNAs), especially microRNAs (miRNAs), a class of endogenous small non-coding RNAs that regulate various biological processes, has not been examined, and the datasets of putative sRNA sequences have not previously been generated for WCR. To achieve a comprehensive collection of sRNA transcriptomes in WCR, we constructed, sequenced, and analyzed sRNA libraries from different life stages of WCR and northern corn rootworm (NCR), and identified 101 conserved precursor miRNAs (pre-miRNAs) in WCR and other Arthropoda. We also identified 277 corn rootworm specific pre-miRNAs. Systematic analyses of sRNA populations in WCR revealed that its sRNA transcriptome, which includes PIWI-interacting RNAs (piRNAs) and miRNAs, undergoes a dynamic change throughout insect development. Phylogenetic analysis of miRNA datasets from model species reveals that a large pool of species-specific miRNAs exists in corn rootworm; these are potentially evolutionarily transient. Comparisons of WCR miRNA clusters to other insect species highlight conserved miRNA-regulated processes that are common to insects. Parallel Analysis of RNA Ends (PARE) also uncovered potential miRNA-guided cleavage sites in WCR. Overall, this study provides a new resource for studying the sRNA transcriptome and miRNA-mediated gene regulation in WCR and other Coleopteran insects.
Collapse
Affiliation(s)
- Xiaozeng Yang
- Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; Corteva Agriscience™, Agriculture Division of DowDuPont™, Indiana, 46268, United States.
| | - Elane Fishilevich
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Indiana, 46268, United States; University of Nebraska-Lincoln, Department of Entomology, Nebraska, 68583, United States
| | - Marcelo A German
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Indiana, 46268, United States
| | - Premchand Gandra
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Indiana, 46268, United States
| | - Robert E McEwan
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Indiana, 46268, United States
| | - André Billion
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Department of Bioresources, Giessen, 35394, Germany
| | - Eileen Knorr
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Department of Bioresources, Giessen, 35394, Germany
| | - Andreas Vilcinskas
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Department of Bioresources, Giessen, 35394, Germany
| | - Kenneth E Narva
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Indiana, 46268, United States.
| |
Collapse
|
22
|
Huang S, Yoshitake K, Asaduzzaman M, Kinoshita S, Watabe S, Asakawa S. Discovery and functional understanding of MiRNAs in molluscs: a genome-wide profiling approach. RNA Biol 2021; 18:1702-1715. [PMID: 33356816 DOI: 10.1080/15476286.2020.1867798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Small non-coding RNAs play a pivotal role in gene regulation, repression of transposable element and viral activity in various organisms. Among the various categories of these small non-coding RNAs, microRNAs (miRNAs) guide post-translational gene regulation in cellular development, proliferation, apoptosis, oncogenesis, and differentiation. Here, we performed a genome-wide computational prediction of miRNAs to improve the understanding of miRNA observation and function in molluscs. As an initial step, hundreds of conserved miRNAs were predicted in 35 species of molluscs through genome scanning. Afterwards, the miRNAs' population, isoforms, organization, and function were characterized in detail. Furthermore, the key miRNA biogenesis factors, including AGO2, DGCR8, DICER, DROSHA, TRABP2, RAN, and XPO5, were elucidated based on homologue sequence searching. We also summarized the miRNAs' function in biomineralization, immune and stress response, as well as growth and development in molluscs. Because miRNAs play a vital role in various lifeforms, this study will provide insight into miRNA biogenesis and function in molluscs, as well as other invertebrates.
Collapse
Affiliation(s)
- Songqian Huang
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazutoshi Yoshitake
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Md Asaduzzaman
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shigeharu Kinoshita
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Shuichi Asakawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
23
|
Berkhout RP, Keijser R, Repping S, Lambalk CB, Afink GB, Mastenbroek S, Hamer G. High-quality human preimplantation embryos stimulate endometrial stromal cell migration via secretion of microRNA hsa-miR-320a. Hum Reprod 2020; 35:1797-1807. [PMID: 32644109 PMCID: PMC7398623 DOI: 10.1093/humrep/deaa149] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/22/2020] [Indexed: 01/18/2023] Open
Abstract
STUDY QUESTION How do high-quality human preimplantation embryos influence the endometrium to promote their own implantation? SUMMARY ANSWER High-quality human preimplantation embryos secrete a specific microRNA (miRNA), hsa-miR-320a, which promotes migration of human endometrial stromal cells (hESCs). WHAT IS KNOWN ALREADY We have previously shown that high-quality human preimplantation embryos excrete unknown factors that influence migration of hESCs. STUDY DESIGN, SIZE, DURATION Embryo excreted miRNAs, specifically those excreted by high-quality embryos, were identified and their effect on hESCs was determined by measuring the migration capacity and gene expression patterns of primary isolated hESCs. PARTICIPANTS/MATERIALS, SETTING, METHODS Embryo conditioned medium (ECM) from routine ICSI procedures was used to identify embryo excreted miRNAs. miRNome analyses were performed on ECM from individually cultured embryos with high morphological quality, with low morphological quality or empty control medium. MiRNA mimics and inhibitors were then used to further study the effect of miRNAs of interest on migration and gene expression of hESCs. Migration assays were performed using hESCs that were obtained from endometrial biopsies performed on hysterectomy specimens from women that received surgery for spotting due to a niche in a cesarean section scar. MAIN RESULTS AND THE ROLE OF CHANCE By using miRNA mimics and inhibitors, we showed that hsa-miR-320a alone can stimulate migration of decidualized hESCs, accurately resembling the response typically triggered only by high-quality embryos. Transcriptome analysis further demonstrated that this effect is very likely mediated via altered expression of genes involved in cell adhesion and cytoskeleton organization. LIMITATIONS, REASONS FOR CAUTION The effect of hsa-miR-320a on hESCs was measured in vitro. Further studies on the in vivo effect of hsa-miR-320a are warranted. WIDER IMPLICATIONS OF THE FINDINGS Implantation failure is one of the major success limiting factors in human reproduction. By secreting hsa-miR-320a, high-quality human preimplantation embryos directly influence hESCs, most likely to prime the endometrium at the implantation site for successful implantation. Together, our results indicate that hsa-miR-320a may be a promising target to further increase success rates in assisted reproduction. STUDY FUNDING/COMPETING INTEREST(S) The study was funded by the Amsterdam University Medical Centers and the Amsterdam Reproduction & Development Research Institute. R.P.B., G.H. and S.M. have a patent on the use of hsa-miR-320a in assisted reproduction treatments pending. TRIAL REGISTRATION NUMBER N/A.
Collapse
Affiliation(s)
- Robbert P Berkhout
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Obstetrics and Gynaecology, Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, VU University, Amsterdam, The Netherlands
| | - Remco Keijser
- Reproductive Biology Laboratory, Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Sjoerd Repping
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Cornelis B Lambalk
- Department of Obstetrics and Gynaecology, Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, VU University, Amsterdam, The Netherlands
| | - Gijs B Afink
- Reproductive Biology Laboratory, Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Sebastiaan Mastenbroek
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Geert Hamer
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
24
|
Cardoso TCDS, de Araújo CB, Portilho LG, Mendes LGA, Alves TC, Silva GC, Ribeiro THC, Gandolfi PE, Morais ER, do Amaral LR, Gomes MDS. Computational prediction and characterisation of miRNAs and their pathway genes in human schistosomiasis caused by Schistosoma haematobium. Mem Inst Oswaldo Cruz 2020; 115:e190378. [PMID: 32401998 PMCID: PMC7207159 DOI: 10.1590/0074-02760190378] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 03/03/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Key genes control the infectivity of the Schistosoma haematobium causing schistosomiasis. A method for understanding the regulation of these genes might help in developing new disease strategies to control schistosomiasis, such as the silencing mediated by microRNAs (miRNAs). The miRNAs have been studied in schistosome species and they play important roles in the post-transcriptional regulation of genes, and in parasite-host interactions. However, genome-wide identification and characterisation of novel miRNAs and their pathway genes and their gene expression have not been explored deeply in the genome and transcriptome of S. haematobium. OBJECTIVES Identify and characterise mature and precursor miRNAs and their pathway genes in the S. haematobium genome. METHODS Computational prediction and characterisation of miRNAs and genes involved in miRNA pathway from S. haematobium genome on SchistoDB. Conserved domain analysis was performed using PFAM and CDD databases. A robust algorithm was applied to identify mature miRNAs and their precursors. The characterisation of the precursor miRNAs was performed using RNAfold, RNAalifold and Perl scripts. FINDINGS We identified and characterised 14 putative proteins involved in miRNA pathway including ARGONAUTE and DICER in S. haematobium. Besides that, 149 mature miRNAs and 131 precursor miRNAs were identified in the genome including novel miRNAs. MAIN CONCLUSIONS miRNA pathway occurs in the S. haematobium, including endogenous miRNAs and miRNA pathway components, suggesting a role of this type of non-coding RNAs in gene regulation in the parasite. The results found in this work will open up a new avenue for studying miRNAs in the S. haematobium biology in helping to understand the mechanism of gene silencing in the human parasite Schistosome.
Collapse
Affiliation(s)
- Thaís Cunha de Sousa Cardoso
- Laboratório de Bioinformática e Análises Moleculares, Universidade Federal de Uberlândia, Patos de Minas, MG, Brazil
| | - Carlos Bruno de Araújo
- Laboratório de Bioinformática e Análises Moleculares, Universidade Federal de Uberlândia, Patos de Minas, MG, Brazil
| | - Laysa Gomes Portilho
- Laboratório de Bioinformática e Análises Moleculares, Universidade Federal de Uberlândia, Patos de Minas, MG, Brazil
| | - Luiz Guilherme Alves Mendes
- Laboratório de Bioinformática e Análises Moleculares, Universidade Federal de Uberlândia, Patos de Minas, MG, Brazil
| | - Tamires Caixeta Alves
- Laboratório de Bioinformática e Análises Moleculares, Universidade Federal de Uberlândia, Patos de Minas, MG, Brazil
| | - Gustavo Caetano Silva
- Laboratório de Bioinformática e Análises Moleculares, Universidade Federal de Uberlândia, Patos de Minas, MG, Brazil
| | - Thales Henrique Cherubino Ribeiro
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia, Setor de Fisiologia Vegetal, Universidade Federal de Lavras, Lavras, MG, Brasil
| | - Peterson Elizandro Gandolfi
- Laboratório de Bioinformática e Análises Moleculares, Universidade Federal de Uberlândia, Patos de Minas, MG, Brazil
| | - Enyara Rezende Morais
- Laboratório de Bioinformática e Análises Moleculares, Universidade Federal de Uberlândia, Patos de Minas, MG, Brazil
| | - Laurence Rodrigues do Amaral
- Laboratório de Bioinformática e Análises Moleculares, Universidade Federal de Uberlândia, Patos de Minas, MG, Brazil
| | - Matheus de Souza Gomes
- Laboratório de Bioinformática e Análises Moleculares, Universidade Federal de Uberlândia, Patos de Minas, MG, Brazil
| |
Collapse
|
25
|
Song J, Zhou S. Post-transcriptional regulation of insect metamorphosis and oogenesis. Cell Mol Life Sci 2020; 77:1893-1909. [PMID: 31724082 PMCID: PMC11105025 DOI: 10.1007/s00018-019-03361-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 10/18/2019] [Accepted: 10/30/2019] [Indexed: 12/17/2022]
Abstract
Metamorphic transformation from larvae to adults along with the high fecundity is key to insect success. Insect metamorphosis and reproduction are governed by two critical endocrines, juvenile hormone (JH), and 20-hydroxyecdysone (20E). Recent studies have established a crucial role of microRNA (miRNA) in insect metamorphosis and oogenesis. While miRNAs target genes involved in JH and 20E-signaling pathways, these two hormones reciprocally regulate miRNA expression, forming regulatory loops of miRNA with JH and 20E-signaling cascades. Insect metamorphosis and oogenesis rely on the coordination of hormones, cognate genes, and miRNAs for precise regulation. In addition, the alternative splicing of genes in JH and 20E-signaling pathways has distinct functions in insect metamorphosis and oogenesis. We, therefore, focus in this review on recent advances in post-transcriptional regulation, with the emphasis on the regulatory role of miRNA and alternative splicing, in insect metamorphosis and oogenesis. We will highlight important new findings of miRNA interactions with hormonal signaling and alternative splicing of JH receptor heterodimer gene Taiman.
Collapse
Affiliation(s)
- Jiasheng Song
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Shutang Zhou
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China.
| |
Collapse
|
26
|
MicroRNAs in Daphnia magna identified and characterized by deep sequencing, genome mapping and manual curation. Sci Rep 2019; 9:15945. [PMID: 31685896 PMCID: PMC6828783 DOI: 10.1038/s41598-019-52387-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 10/11/2019] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that function in RNA silencing and post-transcriptional regulation of gene expression in most organisms. The water flea, Daphnia magna is a key model to study phenotypic, physiological and genomic responses to environmental cues and miRNAs can potentially mediate these responses. By using deep sequencing, genome mapping and manual curations, we have characterised the miRNAome of D. magna. We identified 66 conserved miRNAs and 13 novel miRNAs; all of these were found in the three studied life stages of D. magna (juveniles, subadults, adults), but with variation in expression levels between stages. Forty-one of the miRNAs were clustered into 13 genome clusters also present in the D. pulex genome. Most miRNAs contained sequence variants (isomiRs). The highest expressed isomiRs were 3′ template variants with one nucleotide deletion or 3′ non-template variants with addition of A or U at the 3′ end. We also identified offset RNAs (moRs) and loop RNAs (loRs). Our work extends the base for further work on all species (miRNA, isomiRs, moRNAs, loRNAs) of the miRNAome of Daphnia as biomarkers in response to chemical substances and environment cues, and underline age dependency.
Collapse
|
27
|
Qiao H, Jiang S, Xiong Y, Fu H, Zhang W, Wang Y, Gong Y, Jin S, Wu Y. Integrated analysis of differentially expressed microRNAs and mRNAs to screen miRNAs and genes related to reproduction in Macrobrachium nipponense. 3 Biotech 2019; 9:327. [PMID: 31406649 PMCID: PMC6689314 DOI: 10.1007/s13205-019-1847-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/19/2019] [Indexed: 01/29/2023] Open
Abstract
Female Macrobrachium nipponense has the characteristic of short sexual maturity during the breeding season, which can increase breeding risk and lead to prevalent female individual miniaturization. In this study, we characterized micro (mi)RNA-seq data of the eyestalk (E) and cerebral ganglia (B) of female M. nipponense during breeding and non-breeding seasons. A total of 393 and 189 differentially expressed miRNAs (DE miRNAs) were identified in BSE vs. NBSE and BSB vs. NBSB, respectively. The most abundant up- and down-regulated DE miRNAs were miR-124, miR-14, and miR-7. Enrichment analysis showed that DE miRNA target genes were mainly involved in 'metabolic process' and 'binding', and were associated with 'neurohormonal regulation' and 'photoreceptor activity' signaling pathways. Integrated analysis of miRNA-mRNA expression showed that the most abundant DE miRNAs were miR-14 and miR-278 in BSE vs. NBSE and BSB vs. NBSB, respectively. Four pairs of DE miRNAs and their corresponding target annotated genes were selected from the DE miRNA-mRNA interaction network (bmo-miR-316-5p/opsin protein, ame-miR-125/skeletal muscle actin 8, dmo-miR-278/sugar transporter, and tca-miR-3885-5p/5-HT1 receptor). Gene expression analysis of these four pairs in different ovary development stages showed their potential regulatory roles in ovary maturation.
Collapse
Affiliation(s)
- Hui Qiao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081 People’s Republic of China
| | - Sufei Jiang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081 People’s Republic of China
| | - Yiwei Xiong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081 People’s Republic of China
| | - Hongtuo Fu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081 People’s Republic of China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081 People’s Republic of China
| | - Wenyi Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081 People’s Republic of China
| | - Yabing Wang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081 People’s Republic of China
| | - Yongsheng Gong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081 People’s Republic of China
| | - Shubo Jin
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081 People’s Republic of China
| | - Yan Wu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081 People’s Republic of China
| |
Collapse
|
28
|
Song J, Li W, Zhao H, Zhou S. Clustered miR-2, miR-13a, miR-13b and miR-71 coordinately target Notch gene to regulate oogenesis of the migratory locust Locusta migratoria. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 106:39-46. [PMID: 30453026 DOI: 10.1016/j.ibmb.2018.11.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 06/09/2023]
Abstract
MicroRNAs (miRNAs), ∼22-nt small noncoding RNAs with a crucial role in various biological processes of organisms, are usually clustered in the genome. However, little is known about the miRNA clusters involved in insect reproduction. By small RNA sequencing and quantification followed by qRT-PCR, we found that the expression of invertebrate-specific miR-2/13/71 cluster including miR-2, miR-13a, miR-13b and miR-71 significantly decreased after adult ecdysis of the migratory locust, Locusta migratoria. Luciferase reporter assay and RNA immunoprecipitation demonstrated that miR-2/13/71 bound to the protein coding sequence of Notch and downregulated its expression. Injection of miR-2/13/71 agomiRs led to significant decrease of Notch expression as well as markedly reduced levels of Vitellogenin mRNA, suppressed oocyte maturation and impaired ovarian growth. Moreover, the expression of miR-2/13/71 was repressed by juvenile hormone (JH). Our results thus point to a previously unidentified mechanism by which JH-repressed miR-2/13/71 coordinately downregulates Notch to modulate insect reproduction. The increase of JH and decrease of miR-2/13/71 expression in both previtellogenic and vitellogenic stages of adult females ensure a high level of Notch expression, critically contributing to JH-dependent vitellogenesis and oogenesis.
Collapse
Affiliation(s)
- Jiasheng Song
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Wanwan Li
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Haihong Zhao
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Shutang Zhou
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China.
| |
Collapse
|
29
|
Hoyeck MP, Hadj-Moussa H, Storey KB. Estivation-responsive microRNAs in a hypometabolic terrestrial snail. PeerJ 2019; 7:e6515. [PMID: 30809463 PMCID: PMC6387573 DOI: 10.7717/peerj.6515] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/25/2019] [Indexed: 01/01/2023] Open
Abstract
When faced with extreme environmental conditions, the milk snail (Otala lactea) enters a state of dormancy known as estivation. This is characterized by a strong reduction in metabolic rate to <30% of normal resting rate that is facilitated by various behavioural, physiological, and molecular mechanisms. Herein, we investigated the regulation of microRNA in the induction of estivation. Changes in the expression levels of 75 highly conserved microRNAs were analysed in snail foot muscle, of which 26 were significantly upregulated during estivation compared with controls. These estivation-responsive microRNAs were linked to cell functions that are crucial for long-term survival in a hypometabolic state including anti-apoptosis, cell-cycle arrest, and maintenance of muscle functionality. Several of the microRNA responses by snail foot muscle also characterize hypometabolism in other species and support the existence of a conserved suite of miRNA responses that regulate environmental stress responsive metabolic rate depression across phylogeny.
Collapse
Affiliation(s)
- Myriam P Hoyeck
- Institute of Biochemistry, Departments of Biology and Chemistry, Carleton University, Ottawa, Ontario, Canada
| | - Hanane Hadj-Moussa
- Institute of Biochemistry, Departments of Biology and Chemistry, Carleton University, Ottawa, Ontario, Canada
| | - Kenneth B Storey
- Institute of Biochemistry, Departments of Biology and Chemistry, Carleton University, Ottawa, Ontario, Canada
| |
Collapse
|
30
|
Burgos-Aceves MA, Cohen A, Smith Y, Faggio C. A potential microRNA regulation of immune-related genes in invertebrate haemocytes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 621:302-307. [PMID: 29190554 DOI: 10.1016/j.scitotenv.2017.11.285] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 11/24/2017] [Accepted: 11/24/2017] [Indexed: 06/07/2023]
Abstract
Bivalve mollusks have been employed as sentinel organisms in environmental health programs due to their sedentary lifestyle, filter-feeding behavior and their ability to accumulate pathogens or toxin molecules inside tissues. Endocrine disrupting chemicals (EDCs) can be up taken and bioaccumulated, and due to sensibility of mollusks to these EDCs, being able to cause immune alterations. Recently, microRNAs (miRNAs) were shown to be involved in modulation and buffering developmental processes against the effects of environmental alterations and pathogenic microorganisms. Moreover, it is suggested that this miRNAs are incorporated into the estrogen-controlled immune network, regulating mechanism of immune gene expression at the posttranscriptional level, modulating immune responses as phagocytosis, redox reaction and apoptosis in bivalve haemocytes. Thus, miRNAs can be used as biomarkers that specifically elucidate immunotoxic effects caused by exogenous biotic or abiotic factors, and can act as useful tools in integrated monitoring environmental health programs. In this review, we aim to describe the investigations that have been carried out on miRNAs in bivalve mollusks, especially those associated with immune responses against infectious agents and xenobiotic exposure.
Collapse
Affiliation(s)
- Mario Alberto Burgos-Aceves
- Centro de Investigaciones Biológicas del Noroeste, S.C., Mar Bermejo 195, Col. Playa Palo de Sta. Rita, La Paz, BCS 23096, Mexico
| | - Amit Cohen
- Genomic Data Analysis Unit, The Hebrew University of Jerusalem-Hadassah Medical School, P.O. Box 12272, Jerusalem 91120, Israel
| | - Yoav Smith
- Genomic Data Analysis Unit, The Hebrew University of Jerusalem-Hadassah Medical School, P.O. Box 12272, Jerusalem 91120, Israel
| | - Caterina Faggio
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres, 31, 98166 Messina, Italy.
| |
Collapse
|
31
|
Chen H, Zhou Z, Wang L, Wang H, Liu R, Zhang H, Song L. An invertebrate-specific miRNA targeted the ancient cholinergic neuroendocrine system of oyster. Open Biol 2017; 6:rsob.160059. [PMID: 27488375 PMCID: PMC5008008 DOI: 10.1098/rsob.160059] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 07/05/2016] [Indexed: 02/07/2023] Open
Abstract
Acetylcholine (ACh) is the main neurotransmitter in the cholinergic neuroendocrine system and plays an indispensable role in modulating diverse immune responses. As important transporters in choline uptake, choline transporter-like proteins (CTLs) can control ACh synthesis and release indirectly in multiple organisms. In this study, cgi-miR-2d, an invertebrate-specific miRNA in oyster Crassostrea gigas, is proved to repress the synthesis/release of ACh by targeting CgCTL1 and choline uptake in haemocytes during the early stage of pathogen infection. In short, an opposite expression pattern between CgCTL1 and cgi-miR-2d is observed during Vibrio splendidus infection, accompanied by changes in haemolymph ACh. In addition, the expression level of CgCTL1 is found to be significantly repressed after cgi-miR-2d overexpression in vivo, while both haemocyte choline and haemolymph ACh are also decreased simultaneously, similar to the finding in CgCTL1 knock-down assay. As a result, the expression of two tumour necrosis factor-like proteins and the bacteriostatic activity of oyster haemocytes are found to be altered significantly by either gain-of-function cgi-miR-2d or knock-down of CgCTL1. To our knowledge, this is the first miRNA identified in invertebrates that can target the ancient cholinergic system and augment immune response during infection.
Collapse
Affiliation(s)
- Hao Chen
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Zhi Zhou
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
| | - Lingling Wang
- Key Laboratory of Mariculture and Stock enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, People's Republic of China
| | - Hao Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
| | - Rui Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
| | - Huan Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
| | - Linsheng Song
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China Key Laboratory of Mariculture and Stock enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, People's Republic of China
| |
Collapse
|
32
|
Ylla G, Piulachs MD, Belles X. Comparative analysis of miRNA expression during the development of insects of different metamorphosis modes and germ-band types. BMC Genomics 2017; 18:774. [PMID: 29020923 PMCID: PMC5637074 DOI: 10.1186/s12864-017-4177-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/05/2017] [Indexed: 01/08/2023] Open
Abstract
Background Do miRNAs contribute to specify the germ-band type and the body structure in the insect embryo? Our goal was to address that issue by studying the changes in miRNA expression along the ontogeny of the German cockroach Blattella germanica, which is a short germ-band and hemimetabolan species. Results We sequenced small RNA libraries representing 11 developmental stages of B. germanica ontogeny (with especial emphasis on embryogenesis) and the changes in miRNA expression were examined. Data were compared with equivalent data for two long germ-band holometabolan species Drosophila melanogaster and Drosophila virilis, and the short germ-band holometabolan species Tribolium castaneum. The identification of B. germanica embryo small RNA sequences unveiled miRNAs not detected in previous studies, such as those of the MIR-309 family and 54 novel miRNAs. Four main waves of miRNA expression were recognized (with most miRNA changes occurring during the embryonic stages): the first from day 0 to day 1 of embryogenesis, the second during mid-embryogenesis (days 0–6), the third (with an acute expression peak) on day 2 of embryonic development, and the fourth during post-embryonic development. The second wave defined the boundaries of maternal-to-zygotic transition, with maternal mRNAs being cleared, presumably by Mir-309 and associated scavenger miRNAs. Conclusion miRNAs follow well-defined patterns of expression over hemimetabolan ontogeny, patterns that are more diverse during embryonic development than during the nymphal stages. The results suggest that miRNAs play important roles in the developmental transitions between the embryonic stages of development (starting with maternal loading), during which they might influence the germ-band type and metamorphosis mode. Electronic supplementary material The online version of this article (10.1186/s12864-017-4177-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Guillem Ylla
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Passeig Marítim 37, 08003, Barcelona, Spain
| | - Maria-Dolors Piulachs
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Passeig Marítim 37, 08003, Barcelona, Spain.
| | - Xavier Belles
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Passeig Marítim 37, 08003, Barcelona, Spain.
| |
Collapse
|
33
|
Fromm B, Ovchinnikov V, Høye E, Bernal D, Hackenberg M, Marcilla A. On the presence and immunoregulatory functions of extracellular microRNAs in the trematode Fasciola hepatica. Parasite Immunol 2017; 39. [PMID: 27809346 DOI: 10.1111/pim.12399] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/28/2016] [Indexed: 12/16/2022]
Abstract
Liver flukes represent a paraphyletic group of endoparasitic flatworms that significantly affect man either indirectly due to economic damage on livestock or directly as pathogens. A range of studies have focussed on how these macroscopic organisms can evade the immune system and live inside a hostile environment such as the mammalian liver and bile ducts. Recently, microRNAs, a class of short noncoding gene regulators, have been proposed as likely candidates to play roles in this scenario. MicroRNAs (miRNAs) are key players in development and pathogenicity and are highly conserved between metazoans: identical miRNAs can be found in flatworms and mammalians. Interestingly, miRNAs are enriched in extracellular vesicles (EVs) which are secreted by most cells. EVs constitute an important mode of parasite/host interaction, and recent data illustrate that miRNAs play a vital part. We have demonstrated the presence of miRNAs in the EVs of the trematode species Dicrocoelium dendriticum and Fasciola hepatica (Fhe) and identified potential immune-regulatory miRNAs with targets in the host. After our initial identification of miRNAs expressed by F. hepatica, an assembled genome and additional miRNA data became available. This has enabled us to update the known complement of miRNAs in EVs and speculate on potential immune-regulatory functions that we review here.
Collapse
Affiliation(s)
- B Fromm
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Nydalen, Oslo, Norway
| | - V Ovchinnikov
- Department of Human and Animal Genetics, The Federal Research Center, Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - E Høye
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Nydalen, Oslo, Norway
| | - D Bernal
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, Valencia, Spain
| | - M Hackenberg
- Facultad de Ciencias, Departamento de Genética, Universidad de Granada, Granada, Spain.,Laboratorio de Bioinformática, Instituto de Biotecnología, Centro de Investigación Biomédica, Granada, Spain
| | - A Marcilla
- Área de Parasitología, Departamento de Farmacia y Tecnologia Farmacéutica y Parasitología, Universitat de València, Burjassot, Valencia, Spain.,Joint Research Unit on Endocrinology, Nutrition and Clinical Dietetics, Health Research Institute-La Fe, Universitat de Valencia, Valencia, Spain
| |
Collapse
|
34
|
O'Hern PJ, do Carmo G Gonçalves I, Brecht J, López Soto EJ, Simon J, Chapkis N, Lipscombe D, Kye MJ, Hart AC. Decreased microRNA levels lead to deleterious increases in neuronal M2 muscarinic receptors in Spinal Muscular Atrophy models. eLife 2017; 6. [PMID: 28463115 PMCID: PMC5413352 DOI: 10.7554/elife.20752] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 04/01/2017] [Indexed: 12/17/2022] Open
Abstract
Spinal Muscular Atrophy (SMA) is caused by diminished Survival of Motor Neuron (SMN) protein, leading to neuromuscular junction (NMJ) dysfunction and spinal motor neuron (MN) loss. Here, we report that reduced SMN function impacts the action of a pertinent microRNA and its mRNA target in MNs. Loss of the C. elegans SMN ortholog, SMN-1, causes NMJ defects. We found that increased levels of the C. elegans Gemin3 ortholog, MEL-46, ameliorates these defects. Increased MEL-46 levels also restored perturbed microRNA (miR-2) function in smn-1(lf) animals. We determined that miR-2 regulates expression of the C. elegans M2 muscarinic receptor (m2R) ortholog, GAR-2. GAR-2 loss ameliorated smn-1(lf) and mel-46(lf) synaptic defects. In an SMA mouse model, m2R levels were increased and pharmacological inhibition of m2R rescued MN process defects. Collectively, these results suggest decreased SMN leads to defective microRNA function via MEL-46 misregulation, followed by increased m2R expression, and neuronal dysfunction in SMA. DOI:http://dx.doi.org/10.7554/eLife.20752.001 Spinal muscular atrophy is a genetic disease that causes muscles to gradually weaken. In people with the disease, the nerve cells that control the movement of muscles – called motor neurons – deteriorate over time, hindering the person’s mobility and shortening their life expectancy. Spinal muscular atrophy is usually caused by genetic faults affecting a protein called SMN (which is short for “Survival of motor neuron”) and recent research suggested that disrupting this protein alters the function of short pieces of genetic material called microRNAs. However, the precise role that microRNAs play in the disease and their connection to the SMN protein was not clear. MicroRNAs interfere with the production of proteins by disrupting molecules called messenger RNAs, which are temporary strings of genetic code that carry the instructions for making protein. By disrupting messenger RNAs, microRNAs can delay or halt the production of specific proteins. This is an important part of the normal behavior of a cell, but disturbing the activity of microRNAs can lead to an unwanted rise or fall in crucial proteins. O’Hern et al. made use of engineered nematode worms and mice that share genetic features with spinal muscular atrophy patients, including disruption of the gene responsible for producing the SMN protein. These animal models of the disease were used to examine the relationship between decreased SMN levels and microRNAs in motor neurons. The experiments showed that reduced SMN activity affects a specific microRNA, which in turn causes motor neurons to produce more of a protein called m2R. This protein is a receptor for a molecule, called acetylcholine, which motor neurons use to send signals to muscle cells. Increased m2R may be detrimental to motor neurons. As such, O’Hern et al. decreased m2R protein activity to determine whether this could reverse the defects in motor neurons that arise in the animal models of the disease. Indeed, blocking this receptor rescued some of the defects seen in the animal models, supporting the link to spinal muscular atrophy. Several treatments that block m2R are already available to treat other conditions. As such, the next step is to determine whether these existing treatments are able to protect mice models of spinal muscular atrophy against muscle deterioration or increase their lifespan. If successful, this could open new avenues for the development of treatments in people. DOI:http://dx.doi.org/10.7554/eLife.20752.002
Collapse
Affiliation(s)
- Patrick J O'Hern
- Department of Neuroscience, Brown University, Providence, United States
| | | | - Johanna Brecht
- Institute of Human Genetics, University of Cologne, Cologne, Germany
| | | | - Jonah Simon
- Department of Neuroscience, Brown University, Providence, United States
| | - Natalie Chapkis
- Department of Neuroscience, Brown University, Providence, United States
| | - Diane Lipscombe
- Department of Neuroscience, Brown University, Providence, United States.,Brown Institute for Brain Science, Providence, United States
| | - Min Jeong Kye
- Institute of Human Genetics, University of Cologne, Cologne, Germany
| | - Anne C Hart
- Department of Neuroscience, Brown University, Providence, United States
| |
Collapse
|
35
|
Guo Q, Huang Y, Zou F, Liu B, Tian M, Ye W, Guo J, Sun X, Zhou D, Sun Y, Ma L, Shen B, Zhu C. The role of miR-2∼13∼71 cluster in resistance to deltamethrin in Culex pipiens pallens. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2017; 84:15-22. [PMID: 28342977 DOI: 10.1016/j.ibmb.2017.03.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 02/24/2017] [Accepted: 03/21/2017] [Indexed: 06/06/2023]
Abstract
Excessive and continuous application of deltamethrin has resulted in the development of deltamethrin resistance among mosquitoes, which becomes a major obstacle for mosquito control. In a previous study, differentially expressed miRNAs between deltamethrin-susceptible (DS) strain and deltamethrin-resistant (DR) strain using illumina sequencing in Culex pipiens pallens were identified. In this study, we applied RNAi and the Centers for Disease Control and Prevention (CDC) bottle bioassay to investigate the relationship between miR-2∼13∼71 cluster (miR-2, miR-13 and miR-71) and deltamethrin resistance. We used quantitative real-time PCR (qRT-PCR) to measure expression levels of miR-2∼13∼71 clusters. MiR-2∼13∼71 cluster was down regulated in adult female mosquitoes from the DR strain and played important roles in deltamethrin resistance through regulating target genes, CYP9J35 and CYP325BG3. Knocking down CYP9J35 and CYP325BG3 resulted in decreased mortality of DR mosquitoes. This study provides the first evidence that miRNA clusters are associated with deltamethrin resistance in mosquitoes. Moreover, we investigated the regulatory networks formed between miR-2∼13∼71 cluster and its target genes, which provide a better understanding of the mechanism involved in deltamethrin resistance.
Collapse
Affiliation(s)
- Qin Guo
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China
| | - Yun Huang
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China
| | - Feifei Zou
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China; Microbiology and Immunology Department, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, PR China
| | - Bingqian Liu
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China; Department of Clinical Laboratory, Subei People's Hospital of Jiangsu Province, Yangzhou, Jiangsu, 225001, PR China
| | - Mengmeng Tian
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China
| | - Wenyun Ye
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China
| | - Juxin Guo
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China
| | - Xueli Sun
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China
| | - Dan Zhou
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China
| | - Yan Sun
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China
| | - Lei Ma
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China
| | - Bo Shen
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China.
| | - Changliang Zhu
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, 211166, PR China.
| |
Collapse
|
36
|
Evolution of Fish Let-7 MicroRNAs and Their Expression Correlated to Growth Development in Blunt Snout Bream. Int J Mol Sci 2017; 18:ijms18030646. [PMID: 28300776 PMCID: PMC5372658 DOI: 10.3390/ijms18030646] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 03/12/2017] [Accepted: 03/13/2017] [Indexed: 12/12/2022] Open
Abstract
The lethal-7 (let-7) miRNA, known as one of the first founding miRNAs, is present in multiple copies in a genome and has diverse functions in animals. In this study, comparative genomic analysis of let-7 miRNAs members in fish species indicated that let-7 miRNA is a sequence conserved family in fish, while different species have the variable gene copy numbers. Among the ten members including let-7a/b/c/d/e/f/g/h/i/j, the let-7a precursor sequence was more similar to ancestral sequences, whereas other let-7 miRNA members were separate from the late differentiation of let-7a. The mostly predicted target genes of let-7 miRNAs are involved in biological process, especially developmental process and growth through Gene Ontology (GO) enrichment analysis. In order to identify the possible different functions of these ten miRNAs in fish growth development, their expression levels were quantified in adult males and females of Megalobrama amblycephala, as well as in 3-, 6-, and 12-months-old individuals with relatively slow- and fast-growth rates. These ten miRNAs had similar tissue expression patterns between males and females, with higher expression levels in the brain and pituitary than that in other tissues (p < 0.05). Among these miRNAs, the relative expression level of let-7a was the highest among almost all the tested tissues, followed by let-7b, let-7d and let-7c/e/f/g/h/i/j. As to the groups with different growth rates, the expression levels of let-7 miRNAs in pituitary and brain from the slow-growth group were always significantly higher than that in the fast-growth group (p < 0.05). These results suggest that let-7 miRNA members could play an important role in the regulation of growth development in M. amblycephala through negatively regulating expression of their target genes.
Collapse
|
37
|
Cock JM, Liu F, Duan D, Bourdareau S, Lipinska AP, Coelho SM, Tarver JE. Rapid Evolution of microRNA Loci in the Brown Algae. Genome Biol Evol 2017; 9:740-749. [PMID: 28338896 PMCID: PMC5381526 DOI: 10.1093/gbe/evx038] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2017] [Indexed: 02/06/2023] Open
Abstract
Stringent searches for microRNAs (miRNAs) have so far only identified these molecules in animals, land plants, chlorophyte green algae, slime molds and brown algae. The identification of miRNAs in brown algae was based on the analysis of a single species, the filamentous brown alga Ectocarpus sp. Here, we have used deep sequencing of small RNAs and a recently published genome sequence to identify miRNAs in a second brown alga, the kelp Saccharina japonica. S. japonica possesses a large number of miRNAs (117) and these miRNAs are highly diverse, falling into 98 different families. Surprisingly, none of the S. japonica miRNAs share significant sequence similarity with the Ectocarpus sp. miRNAs. However, the miRNA repertoires of the two species share a number of structural and genomic features indicating that they were generated by similar evolutionary processes and therefore probably evolved within the context of a common, ancestral miRNA system. This lack of sequence similarity suggests that miRNAs evolve rapidly in the brown algae (the two species are separated by ∼95 Myr of evolution). The sets of predicted targets of miRNAs in the two species were also very different suggesting that the divergence of the miRNAs may have had significant consequences for miRNA function.
Collapse
Affiliation(s)
- J. Mark Cock
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Fuli Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Delin Duan
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Qingdao National Laboratory for Marine Science and Technology, Lab for Marine Biology and Biotechnology, Qingdao, China
| | - Simon Bourdareau
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Agnieszka P. Lipinska
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Susana M. Coelho
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - James E. Tarver
- School of Earth Sciences, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
| |
Collapse
|
38
|
Li Y, Li S, Jin P, Chen L, Ma F. miR-11 regulates pupal size of Drosophila melanogaster via directly targeting Ras85D. Am J Physiol Cell Physiol 2017; 312:C71-C82. [DOI: 10.1152/ajpcell.00190.2016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/12/2016] [Indexed: 12/31/2022]
Abstract
MicroRNAs play diverse roles in various physiological processes during Drosophila development. In the present study, we reported that miR-11 regulates pupal size during Drosophila metamorphosis via targeting Ras85D with the following evidences: pupal size was increased in the miR-11 deletion mutant; restoration of miR-11 in the miR-11 deletion mutant rescued the increased pupal size phenotype observed in the miR-11 deletion mutant; ectopic expression of miR-11 in brain insulin-producing cells (IPCs) and whole body shows consistent alteration of pupal size; Dilps and Ras85D expressions were negatively regulated by miR-11 in vivo; miR-11 targets Ras85D through directly binding to Ras85D 3′-untranslated region in vitro; removal of one copy of Ras85D in the miR-11 deletion mutant rescued the increased pupal size phenotype observed in the miR-11 deletion mutant. Thus, our current work provides a novel mechanism of pupal size determination by microRNAs during Drosophila melanogaster metamorphosis.
Collapse
Affiliation(s)
- Yao Li
- Laboratory for Comparative Genomics and Bioinformatics and Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China; and
| | - Shengjie Li
- Laboratory for Comparative Genomics and Bioinformatics and Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China; and
| | - Ping Jin
- Laboratory for Comparative Genomics and Bioinformatics and Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China; and
| | - Liming Chen
- The Key Laboratory of Developmental Genes and Human Disease, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Fei Ma
- Laboratory for Comparative Genomics and Bioinformatics and Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China; and
| |
Collapse
|
39
|
Abstract
Is there a correlation between miRNA diversity and levels of organismic complexity? Exhibiting extraordinary levels of morphological and developmental complexity, insects are the most diverse animal class on earth. Their evolutionary success was in particular shaped by the innovation of holometabolan metamorphosis in endopterygotes. Previously, miRNA evolution had been linked to morphological complexity, but astonishing variation in the currently available miRNA complements of insects made this link unclear. To address this issue, we sequenced the miRNA complement of the hemimetabolan Blattella germanica and reannotated that of two other hemimetabolan species, Locusta migratoria and Acyrthosiphon pisum, and of four holometabolan species, Apis mellifera, Tribolium castaneum, Bombyx mori and Drosophila melanogaster. Our analyses show that the variation of insect miRNAs is an artefact mainly resulting from poor sampling and inaccurate miRNA annotation, and that insects share a conserved microRNA toolkit of 65 families exhibiting very low variation. For example, the evolutionary shift toward a complete metamorphosis was accompanied only by the acquisition of three and the loss of one miRNA families.
Collapse
|
40
|
Kao D, Lai AG, Stamataki E, Rosic S, Konstantinides N, Jarvis E, Di Donfrancesco A, Pouchkina-Stancheva N, Sémon M, Grillo M, Bruce H, Kumar S, Siwanowicz I, Le A, Lemire A, Eisen MB, Extavour C, Browne WE, Wolff C, Averof M, Patel NH, Sarkies P, Pavlopoulos A, Aboobaker A. The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion. eLife 2016; 5:20062. [PMID: 27849518 PMCID: PMC5111886 DOI: 10.7554/elife.20062] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/19/2016] [Indexed: 12/17/2022] Open
Abstract
The amphipod crustacean Parhyale hawaiensis is a blossoming model system for studies of developmental mechanisms and more recently regeneration. We have sequenced the genome allowing annotation of all key signaling pathways, transcription factors, and non-coding RNAs that will enhance ongoing functional studies. Parhyale is a member of the Malacostraca clade, which includes crustacean food crop species. We analysed the immunity related genes of Parhyale as an important comparative system for these species, where immunity related aquaculture problems have increased as farming has intensified. We also find that Parhyale and other species within Multicrustacea contain the enzyme sets necessary to perform lignocellulose digestion ('wood eating'), suggesting this ability may predate the diversification of this lineage. Our data provide an essential resource for further development of Parhyale as an experimental model. The first malacostracan genome will underpin ongoing comparative work in food crop species and research investigating lignocellulose as an energy source. DOI:http://dx.doi.org/10.7554/eLife.20062.001 The marine crustacean known as Parhyale hawaiensis is related to prawns, shrimps and crabs and is found at tropical coastlines around the world. This species has recently attracted scientific interest as a possible new model to study how animal embryos develop before birth and, because Parhyale can rapidly regrow lost limbs, how tissues and organs regenerate. Indeed, Parhyale has many characteristics that make it a good model organism, being small, fast-growing and easy to keep and care for in the laboratory. Several research tools have already been developed to make it easier to study Parhyale. This includes the creation of a system for using the popular gene editing technology, CRISPR, in this animal. However, one critical resource that is available for most model organisms was missing; the complete sequence of all the genetic information of this crustacean, also known as its genome, was not available. Kao, Lai, Stamataki et al. have now compiled the Parhyale genome – which is slightly larger than the human genome – and studied its genetics. Analysis revealed that Parhyale has genes that allow it to fully digest plant material. This is unusual because most animals that do this rely upon the help of bacteria. Kao, Lai, Stamataki et al. also identified genes that provide some of the first insights into the immune system of crustaceans, which protects these creatures from diseases. Kao, Lai, Stamataki et al. have provided a resource and findings that could help to establish Parhyale as a popular model organism for studying several ideas in biology, including organ regeneration and embryonic development. Understanding how Parhyale digests plant matter, for example, could progress the biofuel industry towards efficient production of greener energy. Insights from its immune system could also be adapted to make farmed shrimp and prawns more resistant to infections, boosting seafood production. DOI:http://dx.doi.org/10.7554/eLife.20062.002
Collapse
Affiliation(s)
- Damian Kao
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Alvina G Lai
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Evangelia Stamataki
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
| | - Silvana Rosic
- MRC Clinical Sciences Centre, Imperial College London, London, United Kingdom.,Clinical Sciences, Imperial College London, London, United Kingdom
| | - Nikolaos Konstantinides
- Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France
| | - Erin Jarvis
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | | | | | - Marie Sémon
- Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France
| | - Marco Grillo
- Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France
| | - Heather Bruce
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | - Suyash Kumar
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
| | - Igor Siwanowicz
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
| | - Andy Le
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
| | - Andrew Lemire
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
| | - Michael B Eisen
- Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Cassandra Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
| | - William E Browne
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, United States
| | - Carsten Wolff
- Vergleichende Zoologie, Institut fur Biologie,Humboldt-Universitat zu Berlin, Berlin, Germany
| | - Michalis Averof
- Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France
| | - Nipam H Patel
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | - Peter Sarkies
- MRC Clinical Sciences Centre, Imperial College London, London, United Kingdom.,Clinical Sciences, Imperial College London, London, United Kingdom
| | | | - Aziz Aboobaker
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
41
|
Allam M, Spillings BL, Abdalla H, Mapiye D, Koekemoer LL, Christoffels A. Identification and characterization of microRNAs expressed in the African malaria vector Anopheles funestus life stages using high throughput sequencing. Malar J 2016; 15:542. [PMID: 27825380 PMCID: PMC5101901 DOI: 10.1186/s12936-016-1591-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/28/2016] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Over the past several years, thousands of microRNAs (miRNAs) have been identified in the genomes of various insects through cloning and sequencing or even by computational prediction. However, the number of miRNAs identified in anopheline species is low and little is known about their role. The mosquito Anopheles funestus is one of the dominant malaria vectors in Africa, which infects and kills millions of people every year. Therefore, small RNA molecules isolated from the four life stages (eggs, larvae, pupae and unfed adult females) of An. funestus were sequenced using next generation sequencing technology. RESULTS High throughput sequencing of four replicates in combination with computational analysis identified 107 mature miRNA sequences expressed in the An. funestus mosquito. These include 20 novel miRNAs without sequence identity in any organism and eight miRNAs not previously reported in the Anopheles genus but are known in non-anopheles mosquitoes. Finally, the changes in the expression of miRNAs during the mosquito development were determined and the analysis showed that many miRNAs have stage-specific expression, and are co-transcribed and co-regulated during development. CONCLUSIONS This study presents the first direct experimental evidence of miRNAs in An. funestus and the first profiling study of miRNA associated with the maturation in this mosquito. Overall, the results indicate that miRNAs play important roles during the growth and development. Silencing such molecules in a specific life stage could decrease the vector population and therefore interrupt malaria transmission.
Collapse
Affiliation(s)
- Mushal Allam
- SA Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Robert Sobukwe Road, Cape Town, 7535 South Africa
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, 1 Modderfontein Road, Johannesburg, 2131 South Africa
| | - Belinda L. Spillings
- Vector Control Reference Laboratory, Centre for Opportunistic, Tropical and Hospital Infections, National Institute for Communicable Diseases, National Health Laboratory Service, 1 Modderfontein Road, Johannesburg, 2131 South Africa
| | - Hiba Abdalla
- Vector Control Reference Laboratory, Centre for Opportunistic, Tropical and Hospital Infections, National Institute for Communicable Diseases, National Health Laboratory Service, 1 Modderfontein Road, Johannesburg, 2131 South Africa
- Faculty of Health Sciences, Wits Research Institute for Malaria, University of the Witwatersrand, 1 Jan Smuts Ave, Johannesburg, 2000 South Africa
- Vector Biology & Control Unit, Blue Nile National Institute for Communicable Disease, Wad Medani, Sudan
| | - Darlington Mapiye
- SA Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Robert Sobukwe Road, Cape Town, 7535 South Africa
| | - Lizette L. Koekemoer
- Vector Control Reference Laboratory, Centre for Opportunistic, Tropical and Hospital Infections, National Institute for Communicable Diseases, National Health Laboratory Service, 1 Modderfontein Road, Johannesburg, 2131 South Africa
- Faculty of Health Sciences, Wits Research Institute for Malaria, University of the Witwatersrand, 1 Jan Smuts Ave, Johannesburg, 2000 South Africa
| | - Alan Christoffels
- SA Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Robert Sobukwe Road, Cape Town, 7535 South Africa
| |
Collapse
|
42
|
Abstract
microRNAs are a subclass of small non-coding RNAs that fine-tune the regulation of gene expression at the post-transcriptional level. The miR-302/367 cluster, generally consisting of five members, miR-367, miR-302d, miR-302a, miR-302c and miR-302b, is ubiquitously distributed in vertebrates and occupies an intragenic cluster located in the gene La-related protein 7 (LARP7). The cluster was demonstrated to play an important role in diverse biological processes, such as the pluripotency of human embryonic stem cells (hESCs), self-renewal and reprogramming. This paper provides an overview of the mir-302/367 cluster, discusses our current understanding of the cluster's evolutionary history and transcriptional regulation and reviews the literature surrounding the cluster's roles in cell cycle regulation, epigenetic regulation and different cellular signalling pathways.
Collapse
Affiliation(s)
- Zeqian Gao
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 1 Xujiaping, Yanchangbu, Lanzhou, 730046 Gansu, China
| | - Xueliang Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 1 Xujiaping, Yanchangbu, Lanzhou, 730046 Gansu, China
| | - Yongxi Dou
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 1 Xujiaping, Yanchangbu, Lanzhou, 730046 Gansu, China
| |
Collapse
|
43
|
Leite DJ, Ninova M, Hilbrant M, Arif S, Griffiths-Jones S, Ronshaugen M, McGregor AP. Pervasive microRNA Duplication in Chelicerates: Insights from the Embryonic microRNA Repertoire of the Spider Parasteatoda tepidariorum. Genome Biol Evol 2016; 8:2133-44. [PMID: 27324919 PMCID: PMC4987109 DOI: 10.1093/gbe/evw143] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs are small (∼22 nt) noncoding RNAs that repress translation and therefore regulate the production of proteins from specific target mRNAs. microRNAs have been found to function in diverse aspects of gene regulation within animal development and many other processes. Among invertebrates, both conserved and novel, lineage specific, microRNAs have been extensively studied predominantly in holometabolous insects such as Drosophila melanogaster However little is known about microRNA repertoires in other arthropod lineages such as the chelicerates. To understand the evolution of microRNAs in this poorly sampled subphylum, we characterized the microRNA repertoire expressed during embryogenesis of the common house spider Parasteatoda tepidariorum We identified a total of 148 microRNAs in P. tepidariorum representing 66 families. Approximately half of these microRNA families are conserved in other metazoans, while the remainder are specific to this spider. Of the 35 conserved microRNAs families 15 had at least two copies in the P. tepidariorum genome. A BLAST-based approach revealed a similar pattern of duplication in other spiders and a scorpion, but not among other chelicerates and arthropods, with the exception of a horseshoe crab. Among the duplicated microRNAs we found examples of lineage-specific tandem duplications, and the duplication of entire microRNA clusters in three spiders, a scorpion, and in a horseshoe crab. Furthermore, we found that paralogs of many P. tepidariorum microRNA families exhibit arm switching, which suggests that duplication was often followed by sub- or neofunctionalization. Our work shows that understanding the evolution of microRNAs in the chelicerates has great potential to provide insights into the process of microRNA duplication and divergence and the evolution of animal development.
Collapse
Affiliation(s)
- Daniel J Leite
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, United Kingdom
| | - Maria Ninova
- Faculty of Life Sciences, University of Manchester, United Kingdom
| | - Maarten Hilbrant
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, United Kingdom
| | - Saad Arif
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, United Kingdom
| | | | | | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, United Kingdom
| |
Collapse
|
44
|
Chen H, Jiang S, Wang L, Wang L, Wang H, Qiu L, Song L. Cgi-miR-92d indirectly regulates TNF expression by targeting CDS region of lipopolysaccharide-induced TNF-α factor 3 (CgLITAF3) in oyster Crassostrea gigas. FISH & SHELLFISH IMMUNOLOGY 2016; 55:577-584. [PMID: 27346152 DOI: 10.1016/j.fsi.2016.06.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 06/13/2016] [Accepted: 06/22/2016] [Indexed: 06/06/2023]
Abstract
Tumor necrosis factor alpha (TNF-α) mediated inflammatory response plays indispensable roles in organisms defending against the invaded bacteria, during which microRNAs have been found crucial by controlling multiple TNF-α-related genes. In the present study, cgi-miR-92d was annotated as a member of miR-17-92 family and could target the CDS region of lipopolysaccharide (LPS)-induced TNF-α factor (CgLITAF3) in oyster Crassostrea gigas. It was observed that cgi-miR-92d could be vigorously modulated by Vibrio splendidus or LPS stimulation while CgLITAF3 altered oppositely. Two putative binding sites of cgi-miR-92d were then found at CDS region of CgLITAF3. The interaction between cgi-miR-92d and CgLITAF3 was subsequently verified both in vitro and in vivo. As a result, a significant decrease of cellular luminescence was observed in CgLITAF3 luciferase reporter assay when cgi-miR-92d was overexpressed. The luminescent decrease was then recuperated when cgi-miR-92d inhibitor was co-transfected with miRNA mimics. Besides, CgLITAF3 transcripts were significantly down-regulated when cgi-miR-92d was overexpressed in vivo during V. splendidus challenge. Gain-of-function assay of CgLITAF3 was then conducted in HEK293T cells to verify its function. Consequently, a significant increase of TNF-α was observed during the assay. At the meantime, CgTNF was also down-regulated in gain-of-function assay of cgi-miR-92 in vivo, which was a member of TNF superfamily in oysters which could be robustly induced after pathogen stimulation. Together, these results verify the interaction between CgLITAF3 and cgi-miR-92d, which might dedicate crucially in the repaid activation of CgTNF expression during inflammatory response of oysters.
Collapse
Affiliation(s)
- Hao Chen
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuai Jiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Lin Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lingling Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, China
| | - Hao Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Limei Qiu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Linsheng Song
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, China.
| |
Collapse
|
45
|
An invertebrate-specific and immune-responsive microRNA augments oyster haemocyte phagocytosis by targeting CgIκB2. Sci Rep 2016; 6:29591. [PMID: 27404434 PMCID: PMC4941716 DOI: 10.1038/srep29591] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 06/22/2016] [Indexed: 12/15/2022] Open
Abstract
Nuclear factor (NF)-κB pathway is an evolutionally conserved pathway in activating immune response, in which IκBs can repress the activation. In the present study, cgi-miR-2d, an invertebrate-specific microRNA, was proved to regulate CgIκB2 expression and haemocyte phagocytosis during bacterial infection in oyster Crassostrea gigas. The expression of cgi-miR-2d was significantly up-regulated after Vibrio splendidus challenge, while CgIκB2 transcripts decreased. Significant decreases in both luminescence and CgIκB2 3'UTR level was observed after transfection of cgi-miR-2d in CgIκB2 3'UTR luciferase reporter assay. CgIκB2 mRNA level decreased significantly (0.51-fold of control group, p < 0.05) in gain-of-function assay of cgi-miR-2d in vivo while it increased markedly (1.27-fold, p < 0.05) when cgi-miR-2d was repressed (0.10-fold, p < 0.01). A significant increase of haemocyte phagocytosis rate was observed in cgi-miR-2d overexpression group (p < 0.01), consistent with results in CgIκB2 knock-down group (p < 0.01). Moreover, the apoptosis rate of haemocytes was found significantly declined (28.57%, p < 0.01) in gain-of-function assay of cgi-miR-2d. Together, those results not only depicted the functional conservation of miR-2d family in anti-apoptosis of oysters but also highlighted its interaction with phagocytosis by modulating NF-κB pathway, which might dedicate critically to the well-balance of host immune response.
Collapse
|
46
|
Macedo LMF, Nunes FMF, Freitas FCP, Pires CV, Tanaka ED, Martins JR, Piulachs MD, Cristino AS, Pinheiro DG, Simões ZLP. MicroRNA signatures characterizing caste-independent ovarian activity in queen and worker honeybees (Apis mellifera L.). INSECT MOLECULAR BIOLOGY 2016; 25:216-26. [PMID: 26853694 DOI: 10.1111/imb.12214] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Queen and worker honeybees differ profoundly in reproductive capacity. The queen of this complex society, with 200 highly active ovarioles in each ovary, is the fertile caste, whereas the workers have approximately 20 ovarioles as a result of receiving a different diet during larval development. In a regular queenright colony, the workers have inactive ovaries and do not reproduce. However, if the queen is sensed to be absent, some of the workers activate their ovaries, producing viable haploid eggs that develop into males. Here, a deep-sequenced ovary transcriptome library of reproductive workers was used as supporting data to assess the dynamic expression of the regulatory molecules and microRNAs (miRNAs) of reproductive and nonreproductive honeybee females. In this library, most of the differentially expressed miRNAs are related to ovary physiology or oogenesis. When we quantified the dynamic expression of 19 miRNAs in the active and inactive worker ovaries and compared their expression in the ovaries of virgin and mated queens, we noted that some miRNAs (miR-1, miR-31a, miR-13b, miR-125, let-7 RNA, miR-100, miR-276, miR-12, miR-263a, miR-306, miR-317, miR-92a and miR-9a) could be used to identify reproductive and nonreproductive statuses independent of caste. Furthermore, integrative gene networks suggested that some candidate miRNAs function in the process of ovary activation in worker bees.
Collapse
Affiliation(s)
- L M F Macedo
- Departamento De Genética, Faculdade De Medicina De Ribeirão Preto, Universidade De São Paulo, Ribeirão Preto, Brazil
| | - F M F Nunes
- Departamento De Genética E Evolução, Centro De Ciências Biológicas E Da Saúde, Universidade Federal De São Carlos, São Carlos, Brazil
| | - F C P Freitas
- Departamento De Genética, Faculdade De Medicina De Ribeirão Preto, Universidade De São Paulo, Ribeirão Preto, Brazil
| | - C V Pires
- Departamento De Genética, Faculdade De Medicina De Ribeirão Preto, Universidade De São Paulo, Ribeirão Preto, Brazil
| | - E D Tanaka
- Departamento De Genética, Faculdade De Medicina De Ribeirão Preto, Universidade De São Paulo, Ribeirão Preto, Brazil
| | - J R Martins
- Departamento De Genética, Faculdade De Medicina De Ribeirão Preto, Universidade De São Paulo, Ribeirão Preto, Brazil
| | - M-D Piulachs
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - A S Cristino
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Australia
| | - D G Pinheiro
- Departamento De Tecnologia, Faculdade De Ciências Agrárias E Veterinárias, Universidade Estadual Paulista, Jaboticabal, Brazil
| | - Z L P Simões
- Departamento De Biologia, Faculdade De Filosofia, Ciências E Letras De Ribeirão Preto, Universidade De São Paulo, Ribeirão Preto, Brazil
| |
Collapse
|
47
|
Ling L, Ge X, Li Z, Zeng B, Xu J, Chen X, Shang P, James AA, Huang Y, Tan A. MiR-2 family targets awd and fng to regulate wing morphogenesis in Bombyx mori. RNA Biol 2016; 12:742-8. [PMID: 26037405 DOI: 10.1080/15476286.2015.1048957] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators that target specific mRNAs for repression and thus play key roles in many biological processes, including insect wing morphogenesis. miR-2 is an invertebrate-specific miRNA family that has been predicted in the fruit fly, Drosophila melanogaster, to be involved in regulating the Notch signaling pathway. We show here that miR-2 plays a critical role in wing morphogenesis in the silkworm, Bombyx mori, a lepidopteran model insect. Transgenic over-expression of a miR-2 cluster using a Gal4/UAS system results in deformed adult wings, supporting the conclusion that miR-2 regulates functions essential for normal wing morphogenesis. Two genes, abnormal wing disc (awd) and fringe (fng), which are positive regulators in Notch signaling, are identified as miR-2 targets and validated by a dual-luciferase reporter assay. The relative abundance of both awd and fng expression products was reduced significantly in transgenic animals, implicating them in the abnormal wing phenotype. Furthermore, somatic mutagenesis analysis of awd and fng using the CRISPR/Cas9 system and knock-out mutants also resulted in deformed wings similar to those observed in the miR-2 overexpression transgenic animals. The critical role of miR-2 in Bombyx wing morphogenesis may provide a potential target in future lepidopteran pest control.
Collapse
Affiliation(s)
- Lin Ling
- a Faculty of Life Sciences; Northwestern Polytechnical University ; Xi'an , China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Fontenla S, Dell'Oca N, Smircich P, Tort JF, Siles-Lucas M. The miRnome of Fasciola hepatica juveniles endorses the existence of a reduced set of highly divergent micro RNAs in parasitic flatworms. Int J Parasitol 2015; 45:901-13. [PMID: 26432296 DOI: 10.1016/j.ijpara.2015.06.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 06/27/2015] [Accepted: 06/30/2015] [Indexed: 12/20/2022]
Abstract
The liver fluke Fasciola hepatica is a foodborne zoonotic parasite affecting livestock worldwide, with increasing relevance in human health. The first developmental stage that the host meets after ingestion of the parasite is the newly excysted juvenile, that actively transverses the gut wall and migrates to its final location in the liver. The regulation of the early developmental events in newly excysted juveniles is still poorly understood and a relevant target for control strategies. Here we investigated the putative involvement of small regulatory RNAs in the invasion process. The small RNA population of the newly excysted juvenile fall into two classes, one represented by micro (mi)RNAs and a secondary group of larger (32-33 nucleotides) tRNA-derived sequences. We identified 40 different miRNAs, most of those belonging to ancient miRNAs conserved in protostomes and metazoans, notably with a highly predominant miR-125b variant. Remarkably, several protostomian and metazoan conserved families were not detected in consonance with previous reports of drastic miRnome reduction in parasitic flatworms. Additionally, a set of five novel miRNAs was identified, probably associated with specific gene regulation expression needs in F. hepatica. While sequence conservation in mature miRNA is high across the metazoan tree, we observed that flatworm miRNAs are more divergent, suggesting that mutation rates in parasitic flatworms could be high. Finally, the distinctive presence of tRNA-derived sequences, mostly 5' tRNA halves of selected tRNAs in the small RNA population of newly excysted juveniles, raises the possibility that both miRNA and tRNA fragments participate in the regulation of gene expression in this parasite.
Collapse
Affiliation(s)
- Santiago Fontenla
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Nicolás Dell'Oca
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Pablo Smircich
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UdelaR), Montevideo, Uruguay; Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - José F Tort
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UdelaR), Montevideo, Uruguay.
| | - Mar Siles-Lucas
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA), Consejo Superior de Investigaciones Científicas (CSIC), Salamanca, Spain
| |
Collapse
|
49
|
Tarver JE, Cormier A, Pinzón N, Taylor RS, Carré W, Strittmatter M, Seitz H, Coelho SM, Cock JM. microRNAs and the evolution of complex multicellularity: identification of a large, diverse complement of microRNAs in the brown alga Ectocarpus. Nucleic Acids Res 2015; 43:6384-98. [PMID: 26101255 PMCID: PMC4513859 DOI: 10.1093/nar/gkv578] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 04/19/2015] [Accepted: 05/21/2015] [Indexed: 01/02/2023] Open
Abstract
There is currently convincing evidence that microRNAs have evolved independently in at least six different eukaryotic lineages: animals, land plants, chlorophyte green algae, demosponges, slime molds and brown algae. MicroRNAs from different lineages are not homologous but some structural features are strongly conserved across the eukaryotic tree allowing the application of stringent criteria to identify novel microRNA loci. A large set of 63 microRNA families was identified in the brown alga Ectocarpus based on mapping of RNA-seq data and nine microRNAs were confirmed by northern blotting. The Ectocarpus microRNAs are highly diverse at the sequence level with few multi-gene families, and do not tend to occur in clusters but exhibit some highly conserved structural features such as the presence of a uracil at the first residue. No homologues of Ectocarpus microRNAs were found in other stramenopile genomes indicating that they emerged late in stramenopile evolution and are perhaps specific to the brown algae. The large number of microRNA loci in Ectocarpus is consistent with the developmental complexity of many brown algal species and supports a proposed link between the emergence and expansion of microRNA regulatory systems and the evolution of complex multicellularity.
Collapse
Affiliation(s)
- James E Tarver
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK Genome Evolution Laboratory, Department of Biology, The National University of Ireland, Maynooth, Kildare, Ireland
| | - Alexandre Cormier
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Natalia Pinzón
- Institute of Human Genetics, UPR 1142, CNRS, 34396 Montpellier Cedex 5, France
| | - Richard S Taylor
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Wilfrid Carré
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Martina Strittmatter
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Hervé Seitz
- Institute of Human Genetics, UPR 1142, CNRS, 34396 Montpellier Cedex 5, France
| | - Susana M Coelho
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - J Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| |
Collapse
|
50
|
Ovchinnikov VY, Afonnikov DA, Vasiliev GV, Kashina EV, Sripa B, Mordvinov VA, Katokhin AV. Identification of microRNA genes in three opisthorchiids. PLoS Negl Trop Dis 2015; 9:e0003680. [PMID: 25898350 PMCID: PMC4405270 DOI: 10.1371/journal.pntd.0003680] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 03/05/2015] [Indexed: 12/21/2022] Open
Abstract
Background Opisthorchis felineus, O. viverrini, and Clonorchis sinensis (family Opisthorchiidae) are parasitic flatworms that pose a serious threat to humans in some countries and cause opisthorchiasis/clonorchiasis. Chronic disease may lead to a risk of carcinogenesis in the biliary ducts. MicroRNAs (miRNAs) are small noncoding RNAs that control gene expression at post-transcriptional level and are implicated in the regulation of various cellular processes during the parasite- host interplay. However, to date, the miRNAs of opisthorchiid flukes, in particular those essential for maintaining their complex biology and parasitic mode of existence, have not been satisfactorily described. Methodology/Principal Findings Using a SOLiD deep sequencing-bioinformatic approach, we identified 43 novel and 18 conserved miRNAs for O. felineus (miracidia, metacercariae and adult worms), 20 novel and 16 conserved miRNAs for O. viverrini (adult worms), and 33 novel and 18 conserved miRNAs for C. sinensis (adult worms). The analysis of the data revealed differences in the expression level of conserved miRNAs among the three species and among three the developmental stages of O. felineus. Analysis of miRNA genes revealed two gene clusters, one cluster-like region and one intronic miRNA in the genome. The presence and structure of the two gene clusters were validated using a PCR-based approach in the three flukes. Conclusions This study represents a comprehensive description of miRNAs in three members of the family Opistorchiidae, significantly expands our knowledge of miRNAs in multicellular parasites and provides a basis for understanding the structural and functional evolution of miRNAs in these metazoan parasites. Results of this study also provides novel resources for deeper understanding the complex parasite biology, for further research on the pathogenesis and molecular events of disease induced by the liver flukes. The present data may also facilitate the development of novel approaches for the prevention and treatment of opisthorchiasis/clonorchiasis. Liver flukes of the family Opisthorchiidae cause diseases of the hepatobiliary system, known as opisthorchiasis/clonorchiasis. The chronic forms of these diseases greatly increase the risk of cancer developing in the biliary ducts. Much has been elucidated regarding the developmental biology of opisthorchiid flukes and the molecular pathological effects on the definitive host; however, the role of microRNAs (short non-coding RNAs) capable of influencing the pathogenic process and host-parasite interactions have not yet been comprehensively studied. The aim of the present work was to identify the miRNA genes of the liver flukes and provide a basis for further investigating the roles of these miRNAs in the complex opisthorchiidae life cycle and the pathogenesis of disease.
Collapse
Affiliation(s)
- Vladimir Y Ovchinnikov
- Department of Human and Animal Genetics, Institute of Cytology and Genetics, Novosibirsk, Russian Federation
| | - Dmitry A Afonnikov
- Department of System Biology, Institute of Cytology and Genetics, Novosibirsk, Russian Federation; Department of Natural Science, Novosibirsk State University, Novosibirsk, Russian Federation
| | - Gennady V Vasiliev
- Sector of Genomic Investigation, Institute of Cytology and Genetics, Novosibirsk, Russian Federation
| | - Elena V Kashina
- Department of Human and Animal Genetics, Institute of Cytology and Genetics, Novosibirsk, Russian Federation
| | - Banchob Sripa
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Muang District, Khon Kaen, Thailand
| | - Viacheslav A Mordvinov
- Department of Human and Animal Genetics, Institute of Cytology and Genetics, Novosibirsk, Russian Federation
| | - Alexey V Katokhin
- Department of Human and Animal Genetics, Institute of Cytology and Genetics, Novosibirsk, Russian Federation; Department of Natural Science, Novosibirsk State University, Novosibirsk, Russian Federation
| |
Collapse
|