1
|
Wu Q, Xing L, Du M, Huang C, Liu B, Zhou H, Liu W, Wan F, Qian W. A Genome-Wide Analysis of Serine Protease Inhibitors in Cydia pomonella Provides Insights into Their Evolution and Expression Pattern. Int J Mol Sci 2023; 24:16349. [PMID: 38003538 PMCID: PMC10671500 DOI: 10.3390/ijms242216349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
Serine protease inhibitors (serpins) appear to be ubiquitous in almost all living organisms, with a conserved structure and varying functions. Serpins can modulate immune responses by negatively regulating serine protease activities strictly and precisely. The codling moth, Cydia pomonella (L.), a major invasive pest in China, can cause serious economic losses. However, knowledge of serpin genes in this insect remain largely unknown. In this study, we performed a systematic analysis of the serpin genes in C. pomonella, obtaining 26 serpins from the C. pomonella genome. Subsequently, their sequence features, evolutionary relationship, and expression pattern were characterized. Comparative analysis revealed the evolution of a number of serpin genes in Lepidoptera. Importantly, the evolutionary relationship and putative roles of serpin genes in C. pomonella were revealed. Additionally, selective pressure analysis found amino acid sites with strong evidence of positive selection. Interestingly, the serpin1 gene possessed at least six splicing isoforms with distinct reactive-center loops, and these isoforms were experimentally validated. Furthermore, we observed a subclade expansion of serpins, and these genes showed high expression in multiple tissues, suggesting their important roles in C. pomonella. Overall, this study will enrich our knowledge of the immunity of C. pomonella and help to elucidate the role of serpins in the immune response.
Collapse
Affiliation(s)
- Qiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Longsheng Xing
- College of Life Sciences, Hebei Basic Science Center for Biotic Interactions, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Min Du
- Shandong Province Key Laboratory for Integrated Control of Plant Diseases and Insect Pests, Sino-Australian Joint Research Institute of Agriculture and Environmental Health, College of Plant Health & Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Cong Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Bo Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hongxu Zhou
- Shandong Province Key Laboratory for Integrated Control of Plant Diseases and Insect Pests, Sino-Australian Joint Research Institute of Agriculture and Environmental Health, College of Plant Health & Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Wanxue Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fanghao Wan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wanqiang Qian
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| |
Collapse
|
2
|
Liu H, Xu J, Wang L, Guo P, Tang Z, Sun X, Tang X, Wang W, Wang L, Cao Y, Xia Q, Zhao P. Serpin-1a and serpin-6 regulate the Toll pathway immune homeostasis by synergistically inhibiting the Spätzle-processing enzyme CLIP2 in silkworm, Bombyx mori. PLoS Pathog 2023; 19:e1011740. [PMID: 37851691 PMCID: PMC10629668 DOI: 10.1371/journal.ppat.1011740] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 11/07/2023] [Accepted: 10/07/2023] [Indexed: 10/20/2023] Open
Abstract
The Toll receptor signaling pathway is an important innate immune response of insects to pathogen infection; its extracellular signal transduction involves serine protease cascade activation. However, excessive or constitutive activation of the Toll pathway can be detrimental. Hence, the balance between activation and inhibition of the extracellular protease cascade must be tightly regulated to achieve favorable outcomes. Previous studies have shown that serpins-serine protease inhibitors-negatively regulate insect innate immunity by inhibiting extracellular protease cascade signaling. Although the roles of serpins in insect innate immunity are well described, the physiological mechanisms underlying their synergistic effects remain poorly understand. Here, we characterize the molecular mechanism by which serpin-1a and serpin-6 synergistically maintain immune homeostasis of the silkworm Toll pathway under physiological and pathological conditions. Through in vitro biochemical assays and in vivo bioassays, we demonstrate that clip-domain serine protease 2 (CLIP2), as the Toll cascade-activating terminal protease, is responsible for processing proSpätzle1 to induce the expression of antimicrobial peptides. Further biochemical and genetic analyses indicate that constitutively expressed serpin-1a and inducible serpin-6 synergistically target CLIP2 to maintain homeostasis of the silkworm Toll pathway under physiological and pathological conditions. Taken together, this study provides new insights into the precise regulation of Toll cascade activation signals in insect innate immune responses and highlights the importance and complexity of insect immune homeostasis regulation.
Collapse
Affiliation(s)
- Huawei Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| | - Jiahui Xu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Luoling Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Pengchao Guo
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| | - Zhangchen Tang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Xiaotong Sun
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Xin Tang
- Chongqing Key Laboratory of Chinese Medicine & Health Science, Chongqing Academy of Chinese Materia Medica, Chongqing College of Traditional Chinese Medicine, Chongqing, China
| | - Wei Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| | - Lingyan Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| | - Yang Cao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| | - Qingyou Xia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| | - Ping Zhao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| |
Collapse
|
3
|
Suresh S, Crease TJ, Cristescu ME, Chain FJJ. Alternative splicing is highly variable among Daphnia pulex lineages in response to acute copper exposure. BMC Genomics 2020; 21:433. [PMID: 32586292 PMCID: PMC7318467 DOI: 10.1186/s12864-020-06831-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 06/15/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Despite being one of the primary mechanisms of gene expression regulation in eukaryotes, alternative splicing is often overlooked in ecotoxicogenomic studies. The process of alternative splicing facilitates the production of multiple mRNA isoforms from a single gene thereby greatly increasing the diversity of the transcriptome and proteome. This process can be important in enabling the organism to cope with stressful conditions. Accurate identification of splice sites using RNA sequencing requires alignment to independent exonic positions within the genome, presenting bioinformatic challenges, particularly when using short read data. Although technological advances allow for the detection of splicing patterns on a genome-wide scale, very little is known about the extent of intraspecies variation in splicing patterns, particularly in response to environmental stressors. In this study, we used RNA-sequencing to study the molecular responses to acute copper exposure in three lineages of Daphnia pulex by focusing on the contribution of alternative splicing in addition to gene expression responses. RESULTS By comparing the overall gene expression and splicing patterns among all 15 copper-exposed samples and 6 controls, we identified 588 differentially expressed (DE) genes and 16 differentially spliced (DS) genes. Most of the DS genes (13) were not found to be DE, suggesting unique transcriptional regulation in response to copper that went unnoticed with conventional DE analysis. To understand the influence of genetic background on gene expression and alternative splicing responses to Cu, each of the three lineages was analyzed separately. In contrast to the overall analysis, each lineage had a higher proportion of unique DS genes than DE genes suggesting that genetic background has a larger influence on DS than on DE. Gene Ontology analysis revealed that some pathways involved in stress response were jointly regulated by DS and DE genes while others were regulated by only transcription or only splicing. CONCLUSIONS Our findings suggest an important role for alternative splicing in shaping transcriptome diversity in response to metal exposure in Daphnia, highlighting the importance of integrating splicing analyses with gene expression surveys to characterize molecular pathways in evolutionary and environmental studies.
Collapse
Affiliation(s)
- Sneha Suresh
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, 01854, USA
- Present address: The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Pok Fu Lam, Hong Kong SAR
| | - Teresa J Crease
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Melania E Cristescu
- Department of Biology, McGill University, 1205 Docteur Penfield, Montreal, QC, H3A 1B1, Canada
| | - Frédéric J J Chain
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, 01854, USA.
| |
Collapse
|
4
|
Comparative Proteomic Analysis Reveals Immune Competence in Hemolymph of Bombyx mori Pupa Parasitized by Silkworm Maggot Exorista sorbillans. INSECTS 2019; 10:insects10110413. [PMID: 31752209 PMCID: PMC6920964 DOI: 10.3390/insects10110413] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/15/2019] [Accepted: 11/15/2019] [Indexed: 01/03/2023]
Abstract
The silkworm maggot, Exoristasorbillans, is a well-known larval endoparasitoid of the silkworm Bombyxmori that causes considerable damage to the silkworm cocoon crop. To gain insights into the response mechanism of the silkworm at the protein level, we applied a comparative proteomic approach to investigate proteomic differences in the hemolymph of the female silkworm pupae parasitized by E. sorbillans. In total, 50 differentially expressed proteins (DEPs) were successfully identified, of which 36 proteins were upregulated and 14 proteins were downregulated in response to parasitoid infection. These proteins are mainly involved in disease, energy metabolism, signaling pathways, and amino acid metabolism. Eight innate immune proteins were distinctly upregulated to resist maggot parasitism. Apoptosis-related proteins of cathepsin B and 14-3-3 zeta were significantly downregulated in E. sorbillans-parasitized silkworm pupae; their downregulation induces apoptosis. Quantitative PCR was used to further verify gene transcription of five DEPs, and the results are consistent at the transcriptional and proteomic levels. This was the first report on identification of possible proteins from the E. bombycis-parasitized silkworms at the late stage of parasitism, which contributes to furthering our understanding of the response mechanism of silkworms to parasitism and dipteran parasitoid biology.
Collapse
|
5
|
Li M, Christen JM, Dittmer NT, Cao X, Zhang X, Jiang H, Kanost MR. The Manduca sexta serpinome: Analysis of serpin genes and proteins in the tobacco hornworm. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 102:21-30. [PMID: 30237077 PMCID: PMC6249112 DOI: 10.1016/j.ibmb.2018.09.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/14/2018] [Accepted: 09/16/2018] [Indexed: 06/02/2023]
Abstract
Members of the serpin superfamily of proteins occur in animals, plants, bacteria, archaea and some viruses. They adopt a variety of physiological functions, including regulation of immune system, modulation of apoptosis, hormone transport and acting as storage proteins. Most members of the serpin family are inhibitors of serine proteinases. In this study, we searched the genome of Manduca sexta and identified 32 serpin genes. We analyzed the structure of these genes and the sequences of their encoded proteins. Three M. sexta genes (serpin-1, serpin-15, and serpin-28) have mutually exclusive alternatively spliced exons encoding the carboxyl-terminal reactive center loop of the protein, which is the site of interaction with target proteases. We discovered that MsSerpin-1 has 14 splicing isoforms, including two undiscovered in previous studies. Twenty-eight of the 32 M. sexta serpins include a putative secretion signal peptide and are predicted to be extracellular proteins. Phylogenetic analysis of serpins in M. sexta and Bombyx mori indicates that 17 are orthologous pairs, perhaps carrying out essential physiological functions. Analysis of the reactive center loop and hinge regions of the protein sequences indicates that 16 of the serpin genes encode proteins that may lack proteinase inhibitor activity. Our annotation and analysis of these serpin genes and their transcript profiles should lead to future advances in experimental study of their functions in insect biochemistry.
Collapse
Affiliation(s)
- Miao Li
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Jayne M Christen
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Neal T Dittmer
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Xiaolong Cao
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Xiufeng Zhang
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Haobo Jiang
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Michael R Kanost
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA.
| |
Collapse
|
6
|
Yang L, Mei Y, Fang Q, Wang J, Yan Z, Song Q, Lin Z, Ye G. Identification and characterization of serine protease inhibitors in a parasitic wasp, Pteromalus puparum. Sci Rep 2017; 7:15755. [PMID: 29147019 PMCID: PMC5691223 DOI: 10.1038/s41598-017-16000-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 11/03/2017] [Indexed: 11/08/2022] Open
Abstract
Serine protease inhibitors (SPIs) regulate protease-mediated activities by inactivating their cognate proteinases, and are involved in multiple physiological processes. SPIs have been extensively studied in vertebrates and invertebrates; however, little SPI information is available in parasitoids. Herein, we identified 57 SPI genes in total through the genome of a parasitoid wasp, Pteromalus puparum. Gene structure analyses revealed that these SPIs contain 7 SPI domains. Depending on their mode of action, these SPIs can be categorized into serpins, canonical inhibitors and alpha-2-macroglobulins (A2Ms). For serpins and canonical inhibitors, we predicted their putative inhibitory activities to trypsin/chymotrypsin/elastase-like enzymes based on the amino acids in cleaved reactive sites. Sequence alignment and phylogenetic tree indicated that some serpins similar to known functional inhibitory serpins may participate in immune responses. Transcriptome analysis also showed some canonical SPI genes displayed distinct expression patterns in the venom gland and this was confirmed by quantitative real-time PCR (qPCR) analysis, suggesting their specific physiological functions as venom proteins in suppressing host immune responses. The study provides valuable information to clarify the functions of SPIs in digestion, development, reproduction and innate immunity.
Collapse
Affiliation(s)
- Lei Yang
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yaotian Mei
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qi Fang
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jiale Wang
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhichao Yan
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qisheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, Missouri, USA
| | - Zhe Lin
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Gongyin Ye
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China.
| |
Collapse
|
7
|
Serpins in arthropod biology. Semin Cell Dev Biol 2016; 62:105-119. [PMID: 27603121 DOI: 10.1016/j.semcdb.2016.09.001] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 08/31/2016] [Accepted: 09/02/2016] [Indexed: 12/21/2022]
Abstract
Serpins are the largest known family of serine proteinase inhibitors and perform a variety of physiological functions in arthropods. Herein, we review the field of serpins in arthropod biology, providing an overview of current knowledge and topics of interest. Serpins regulate insect innate immunity via inhibition of serine proteinase cascades that initiate immune responses such as melanization and antimicrobial peptide production. In addition, several serpins with anti-pathogen activity are expressed as acute-phase serpins in insects upon infection. Parasitoid wasps can downregulate host serpin expression to modulate the host immune system. In addition, examples of serpin activity in development and reproduction in Drosophila have also been discovered. Serpins also function in host-pathogen interactions beyond immunity as constituents of venom in parasitoid wasps and saliva of blood-feeding ticks and mosquitoes. These serpins have distinct effects on immunosuppression and anticoagulation and are of interest for vaccine development. Lastly, the known structures of arthropod serpins are discussed, which represent the serpin inhibitory mechanism and provide a detailed overview of the process.
Collapse
|
8
|
Barribeau SM, Sadd BM, du Plessis L, Brown MJF, Buechel SD, Cappelle K, Carolan JC, Christiaens O, Colgan TJ, Erler S, Evans J, Helbing S, Karaus E, Lattorff HMG, Marxer M, Meeus I, Näpflin K, Niu J, Schmid-Hempel R, Smagghe G, Waterhouse RM, Yu N, Zdobnov EM, Schmid-Hempel P. A depauperate immune repertoire precedes evolution of sociality in bees. Genome Biol 2015; 16:83. [PMID: 25908406 PMCID: PMC4408586 DOI: 10.1186/s13059-015-0628-y] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 03/11/2015] [Indexed: 11/10/2022] Open
Abstract
Background Sociality has many rewards, but can also be dangerous, as high population density and low genetic diversity, common in social insects, is ideal for parasite transmission. Despite this risk, honeybees and other sequenced social insects have far fewer canonical immune genes relative to solitary insects. Social protection from infection, including behavioral responses, may explain this depauperate immune repertoire. Here, based on full genome sequences, we describe the immune repertoire of two ecologically and commercially important bumblebee species that diverged approximately 18 million years ago, the North American Bombus impatiens and European Bombus terrestris. Results We find that the immune systems of these bumblebees, two species of honeybee, and a solitary leafcutting bee, are strikingly similar. Transcriptional assays confirm the expression of many of these genes in an immunological context and more strongly in young queens than males, affirming Bateman’s principle of greater investment in female immunity. We find evidence of positive selection in genes encoding antiviral responses, components of the Toll and JAK/STAT pathways, and serine protease inhibitors in both social and solitary bees. Finally, we detect many genes across pathways that differ in selection between bumblebees and honeybees, or between the social and solitary clades. Conclusions The similarity in immune complement across a gradient of sociality suggests that a reduced immune repertoire predates the evolution of sociality in bees. The differences in selection on immune genes likely reflect divergent pressures exerted by parasites across social contexts. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0628-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Seth M Barribeau
- Experimental Ecology, Institute of Integrative Biology, ETH Zürich, CH-8092, Zürich, Switzerland. .,Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
| | - Ben M Sadd
- Experimental Ecology, Institute of Integrative Biology, ETH Zürich, CH-8092, Zürich, Switzerland. .,School of Biological Sciences, Illinois State University, Normal, IL, 61790, USA.
| | - Louis du Plessis
- Theoretical Biology, Institute of Integrative Biology, ETH Zürich, CH-8092, Zürich, Switzerland. .,Computational Evolution, Department of Biosystems Science and Evolution, ETH Zürich, 4058, Basel, Switzerland. .,Swiss Institute of Bioinformatics, 1211, Lausanne, Switzerland.
| | - Mark J F Brown
- School of Biological Sciences, Royal Holloway University of London, London, TW20 0EX, UK.
| | - Severine D Buechel
- Experimental Ecology, Institute of Integrative Biology, ETH Zürich, CH-8092, Zürich, Switzerland.
| | - Kaat Cappelle
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium.
| | - James C Carolan
- Maynooth University Department of Biology, Maynooth University, Maynooth, Kildare, Ireland.
| | - Olivier Christiaens
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium.
| | - Thomas J Colgan
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin, 2, Ireland. .,School of Biological and Chemical Sciences, Queen Mary University of London, E1 41NS, London, UK.
| | - Silvio Erler
- Department of Apiculture and Sericulture, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Cluj-Napoca, 400372, Romania. .,Institut für Biologie, Molekulare Ökologie, Martin-Luther-Universität Halle-Wittenberg, Wittenberg, 06120, Germany.
| | - Jay Evans
- USDA-ARS Bee Research Laboratory, Beltsville, MD, 20705, USA.
| | - Sophie Helbing
- Institut für Biologie, Molekulare Ökologie, Martin-Luther-Universität Halle-Wittenberg, Wittenberg, 06120, Germany.
| | - Elke Karaus
- Experimental Ecology, Institute of Integrative Biology, ETH Zürich, CH-8092, Zürich, Switzerland.
| | - H Michael G Lattorff
- Institut für Biologie, Molekulare Ökologie, Martin-Luther-Universität Halle-Wittenberg, Wittenberg, 06120, Germany. .,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany. .,Institut für Biologie, Tierphysiologie, Martin-Luther-Universität Halle-Wittenberg, Wittenberg, 06099, Germany.
| | - Monika Marxer
- Experimental Ecology, Institute of Integrative Biology, ETH Zürich, CH-8092, Zürich, Switzerland.
| | - Ivan Meeus
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium.
| | - Kathrin Näpflin
- Experimental Ecology, Institute of Integrative Biology, ETH Zürich, CH-8092, Zürich, Switzerland.
| | - Jinzhi Niu
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium. .,College of Plant Protection, Southwest University, Chongqing, 400716, PR China.
| | - Regula Schmid-Hempel
- Experimental Ecology, Institute of Integrative Biology, ETH Zürich, CH-8092, Zürich, Switzerland.
| | - Guy Smagghe
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium. .,College of Plant Protection, Southwest University, Chongqing, 400716, PR China.
| | - Robert M Waterhouse
- Swiss Institute of Bioinformatics, 1211, Lausanne, Switzerland. .,Department of Genetic Medicine and Development, University of Geneva Medical School, 1211, Geneva, Switzerland. .,Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - Na Yu
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium.
| | - Evgeny M Zdobnov
- Swiss Institute of Bioinformatics, 1211, Lausanne, Switzerland. .,Department of Genetic Medicine and Development, University of Geneva Medical School, 1211, Geneva, Switzerland.
| | - Paul Schmid-Hempel
- Experimental Ecology, Institute of Integrative Biology, ETH Zürich, CH-8092, Zürich, Switzerland.
| |
Collapse
|
9
|
Liu C, Han Y, Chen X, Zhang W. Structure-function relationship of SW-AT-1, a serpin-type protease inhibitor in silkworm. PLoS One 2014; 9:e99013. [PMID: 24901510 PMCID: PMC4047069 DOI: 10.1371/journal.pone.0099013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 05/07/2014] [Indexed: 01/29/2023] Open
Abstract
Although SW-AT-1, a serpin-type trypsin inhibitor from silkworm (Bombyx mori), was identified in previous study, its structure-function relationship has not been studied. In this study, SW-AT-1 was cloned from the body wall of silkworm and expressed in E. coli. rSW-AT-1 inhibited both trypsin and chymotrypsin in a concentration-dependent manner. The association rate constant for rSW-AT-1 and trypsin is 1.31×10-5 M-1s-1, for rSW-AT-1 and chymotrpsin is 2.85×10-6 M-1s-1. Circular dichroism (CD) assay showed 33% α-helices, 16% β-sheets, 17% turns, and 31% random coils in the secondary structure of the protein. Enzymatic and CD analysis indicated that rSW-AT-1 was stable at wide pH range between 4-10, and exhibited the highest activity at weakly acidic or alkaline condition. The predicted three-dimensional structure of SW-AT-1 by PyMOL (v1.4) revealed a deductive reactive centre loop (RCL) near the C-terminus, which was extended from the body of the molecule. In addition to trypsin cleavage site in RCL, matrix-assisted laser desorption ionization time of flight mass spectrometry indicated that the chymotrypsin cleavage site of SW-AT-1 was between F336 and T337 in RCL. Directed mutagenesis indicated that both the N- and C-terminal sides of RCL have effects on the activity, and G327 and E329 played an important role in the proper folding of RCL. The physiological role of SW-AT-1 in the defense responses of silkworm were also discussed.
Collapse
Affiliation(s)
- Cheng Liu
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yue Han
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Xi Chen
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Wei Zhang
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu, China
- * E-mail:
| |
Collapse
|
10
|
Li Y, Wang G, Tian J, Liu H, Yang H, Yi Y, Wang J, Shi X, Jiang F, Yao B, Zhang Z. Transcriptome analysis of the silkworm (Bombyx mori) by high-throughput RNA sequencing. PLoS One 2012; 7:e43713. [PMID: 22928022 PMCID: PMC3426547 DOI: 10.1371/journal.pone.0043713] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Accepted: 07/24/2012] [Indexed: 11/23/2022] Open
Abstract
The domestic silkworm, Bombyx mori, is a model insect with important economic value for silk production that also acts as a bioreactor for biomaterial production. The functional complexity of the silkworm transcriptome has not yet been fully elucidated, although genomic sequencing and other tools have been widely used in its study. We explored the transcriptome of silkworm at different developmental stages using high-throughput paired-end RNA sequencing. A total of about 3.3 gigabases (Gb) of sequence was obtained, representing about a 7-fold coverage of the B. mori genome. From the reads that were mapped to the genome sequence; 23,461 transcripts were obtained, 5,428 of them were novel. Of the 14,623 predicted protein-coding genes in the silkworm genome database, 11,884 of them were found to be expressed in the silkworm transcriptome, giving a coverage of 81.3%. A total of 13,195 new exons were detected, of which, 5,911 were found in the annotated genes in the Silkworm Genome Database (SilkDB). An analysis of alternative splicing in the transcriptome revealed that 3,247 genes had undergone alternative splicing. To help with the data analysis, a transcriptome database that integrates our transcriptome data with the silkworm genome data was constructed and is publicly available at http://124.17.27.136/gbrowse2/. To our knowledge, this is the first study to elucidate the silkworm transcriptome using high-throughput RNA sequencing technology. Our data indicate that the transcriptome of silkworm is much more complex than previously anticipated. This work provides tools and resources for the identification of new functional elements and paves the way for future functional genomics studies.
Collapse
Affiliation(s)
- Yinü Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guozeng Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huifen Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huipeng Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongzhu Yi
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinhui Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaofeng Shi
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Feng Jiang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bin Yao
- Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (ZZ); (BY)
| | - Zhifang Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (ZZ); (BY)
| |
Collapse
|