1
|
Guo R, Zhang K, Zang H, Guo S, Liu X, Jing X, Song Y, Li K, Wu Y, Jiang H, Fu Z, Chen D. Dynamics and regulatory role of circRNAs in Asian honey bee larvae following fungal infection. Appl Microbiol Biotechnol 2024; 108:261. [PMID: 38472661 DOI: 10.1007/s00253-024-13102-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/19/2024] [Accepted: 03/03/2024] [Indexed: 03/14/2024]
Abstract
Non-coding RNA (ncRNA) plays a vital part in the regulation of immune responses, growth, and development in plants and animals. Here, the identification, characteristic analysis, and molecular verification of circRNAs in Apis cerana cerana worker larval guts were conducted, followed by in-depth investigation of the expression pattern of larval circRNAs during Ascosphaera apis infection and exploration of the potential regulatory part of differentially expressed circRNAs (DEcircRNAs) in host immune responses. A total of 3178 circRNAs in the larval guts of A. c. cerana were identified, with a length distribution ranging from 15 to 96,007 nt. Additionally, 155, 95, and 86 DEcircRNAs were identified in the in the 4-, 5-, and 6-day-old larval guts following A. apis infection. These DEcircRNAs were predicted to target 29, 25, and 18 parental genes relevant to 12, 20, and 17 GO terms as well as 144, 114, and 61 KEGG pathways, including 5 cellular and 4 humoral immune pathways. Complex competing endogenous RNA (ceRNA) regulatory networks were detected as being formed among DEcircRNAs, DEmiRNAs, and DEmRNAs. The target DEmRNAs were engaged in 36, 47, and 47 GO terms as well as 331, 332, and 331 pathways, including 6 cellular and 6 humoral immune pathways. Further, 19 DEcircRNAs, 5 DEmiRNAs, and 3 mRNAs were included in the sub-networks relative to 3 antioxidant enzymes. Finally, back-splicing sites within 15 circRNAs and the difference in the 15 DEcircRNAs' expression between uninoculated and A. apis-inoculated larval guts were confirmed based on molecular methods. These findings not only enrich our understanding of bee host-fungal pathogen interactions but also lay a foundation for illuminating the mechanism underlying the DEcircRNA-mediated immune defense of A. c. cerana larvae against A. apis invasion. KEY POINTS: • The expression pattern of circRNAs was altered in the A. cerana worker larval guts following A. apis infection. • Back-splicing sites within 15 A. cerana circRNAs were verified using molecular approaches. DEcircRNAs potentially modulated immune responses and antioxidant enzymes in A. apis-challenged host guts.
Collapse
Affiliation(s)
- Rui Guo
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou, 350002, China.
- Apitherapy Research Institute of Fujian Province, Fuzhou, 350002, China.
| | - Kaiyao Zhang
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - He Zang
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Sijia Guo
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaoyu Liu
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xin Jing
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuxuan Song
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Kunze Li
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ying Wu
- Apiculture Science Institute of Jilin Province, Jilin, Jilin, 132000, China
| | - Haibing Jiang
- Apiculture Science Institute of Jilin Province, Jilin, Jilin, 132000, China
| | - Zhongmin Fu
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou, 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou, 350002, China
| | - Dafu Chen
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou, 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou, 350002, China
| |
Collapse
|
2
|
Massu A, Mahanil K, Limkul S, Phiwthong T, Boonanuntanasarn S, Teaumroong N, Somboonwiwat K, Boonchuen P. Identification of immune-responsive circular RNAs in shrimp (Litopenaeus vannamei) upon yellow head virus infection. Fish Shellfish Immunol 2024; 144:109246. [PMID: 38013134 DOI: 10.1016/j.fsi.2023.109246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 11/29/2023]
Abstract
Circular RNAs (circRNAs) are a subclass of non-coding RNAs (ncRNAs) formed through a process known as back-splicing. They play a crucial role in the genetic regulation of various biological processes. Currently, circRNAs have been identified as participants in the antiviral response within mammalian cells. However, circRNAs in shrimp infected with the yellow head virus (YHV) remain largely unexplored. Therefore, this study aims to identify circRNAs in the hemocytes of Litopenaeus vannamei during YHV infection. We discovered 358 differentially expressed circRNAs (DECs), with 177 of them being up-regulated and 181 down-regulated. Subsequently, eight DECs, including circ_alpha-1-inhibitor 3, circ_CDC42 small effector protein 2, circ_hemicentin 2, circ_integrin alpha V, circ_kazal-type proteinase inhibitor, circ_phenoloxidase 3, circ_related protein rab-8B, and circ_protein toll-like, were randomly selected for analysis of their expression patterns during YHV infection using qRT-PCR. Furthermore, the circRNAs' characteristics were confirmed through PCR, RNase R treatment, and Sanger sequencing, all of which were consistent with the features of circRNAs. These findings contribute to a better understanding of circRNAs' involvement in the antiviral response in shrimp.
Collapse
Affiliation(s)
- Amarin Massu
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Kanjana Mahanil
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Sirawich Limkul
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Tannatorn Phiwthong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Surintorn Boonanuntanasarn
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Kunlaya Somboonwiwat
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Pakpoom Boonchuen
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand.
| |
Collapse
|
3
|
Limkul S, Phiwthong T, Massu A, Boonanuntanasarn S, Teaumroong N, Somboonwiwat K, Boonchuen P. Transcriptome-based insights into the regulatory role of immune-responsive circular RNAs in Litopanaeus vannamei upon WSSV infection. Fish Shellfish Immunol 2023; 132:108499. [PMID: 36549581 DOI: 10.1016/j.fsi.2022.108499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/14/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
Circular RNAs (circRNAs) are non-coding RNAs (ncRNAs) originating from a post-transcriptional modification process called back-splicing. Despite circRNAs being traditionally considered by-products rather than independently functional, circRNAs play many vital roles, such as in host immunity during viral infection. However, in shrimp, these remain largely unexplored. Therefore, this study aims to identify circRNAs in Litopenaeus vannamei in the context of WSSV infection, one of the most eradicative pathogens threatening shrimp populations worldwide. We identified 290 differentially expressed circRNAs (DECs) in L. vannamei upon WSSV infection. Eight DECs were expressed from their parental genes, including alpha-1-inhibitor-3, calpain-B, integrin-V, hemicentin-2, hemocytin, mucin-17, proPO2, and rab11-FIP4. These were examined quantitatively by qRT-PCR, which revealed the relevant expression profiles to those obtained from circRNA-Seq. Furthermore, the structural and chemical validation of the DECs conformed to the characteristics of circRNAs. One of the functional properties of circRNAs as a miRNA sponge was examined via the interaction network between DECs and WSSV-responsive miRNAs, which highlighted the targets of miRNA sponges. Our discovery could provide insight into the participation of these ncRNAs in shrimp antiviral responses.
Collapse
Affiliation(s)
- Sirawich Limkul
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Tannatorn Phiwthong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Amarin Massu
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Surintorn Boonanuntanasarn
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Kunlaya Somboonwiwat
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Pakpoom Boonchuen
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand.
| |
Collapse
|
4
|
Abstract
Non-coding RNAs (ncRNAs) comprise a set of abundant and functionally diverse RNA molecules. Since the discovery of the first ncRNA in the 1960s, ncRNAs have been shown to be involved in nearly all steps of the central dogma of molecular biology. In recent years, the pace of discovery of novel ncRNAs and their cellular roles has been greatly accelerated by high-throughput sequencing. Advances in sequencing technology, library preparation protocols as well as computational biology helped to greatly expand our knowledge of which ncRNAs exist throughout the kingdoms of life. Moreover, RNA sequencing revealed crucial roles of many ncRNAs in human health and disease. In this review, we discuss the most recent methodological advancements in the rapidly evolving field of high-throughput sequencing and how it has greatly expanded our understanding of ncRNA biology across a large number of different organisms.
Collapse
Affiliation(s)
| | | | - Damian Wollny
- RNA Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University, 07743 Jena, Germany; (J.M.); (A.S.)
| |
Collapse
|
5
|
Shao Q, Huang Y, Zhang C, Gao X, Gao S. Emerging landscape of circHIPK3 and its role in cancer and other diseases (Review). Mol Med Rep 2021; 23:409. [PMID: 33786629 PMCID: PMC8025471 DOI: 10.3892/mmr.2021.12048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 02/19/2021] [Indexed: 12/25/2022] Open
Abstract
Circular RNAs (circRNAs) are a special class of recently re‑discovered RNAs, which are covalently closed ring RNA molecules. circRNAs have been reported to possess multiple functions and are considered crucial regulators of several processes, and are therefore gaining increasing attention. In recent years, increasing evidence has shown that circRNAs are implicated in several crucial biological processes via regulation of gene expression, and their dysregulation is also associated with the development of numerous diseases, particularly acting as oncogenic or tumor‑suppressor molecules in cancer. Furthermore, circRNAs are involved in cell proliferation, differentiation, apoptosis, invasion and metastasis. In the present review, the biogenesis and functions of circRNAs are described, with a focus on the most recent research advances and the emerging roles of circular homeodomain‑interacting protein kinase 3 (circHIPK3) in human diseases. The present review may provide novel avenues for research on the roles of circHIPK3 as a clinical diagnostic and prognostic biomarker, as well as highlighting promising therapeutic targets for certain diseases and cancer.
Collapse
Affiliation(s)
- Qi Shao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, Henan 471023, P.R. China
| | - Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, Henan 471023, P.R. China
| | - Cai Zhang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, Henan 471023, P.R. China
| | - Xiaochan Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, Henan 471023, P.R. China
| | - Shiyang Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, Henan 471023, P.R. China
| |
Collapse
|