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Shen Y, Zeng X, Chen G, Wu X. Comparative transcriptome analysis reveals regional specialization of gene expression in larval silkworm (Bombyx mori) midgut. INSECT SCIENCE 2022; 29:1329-1345. [PMID: 34997945 DOI: 10.1111/1744-7917.13001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/14/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
Insect midgut plays a central role in food digestion and nutrition absorption. Larval silkworm midgut could be divided into 3 distinct regions based on their morphological colors. However, it remains rudimentary of regional gene expression and physiological function in larval silkworm midgut. Through transcriptome sequencing of 3 midgut compartments, a comprehensive analysis of gene expression atlas along the anterior-posterior axis was conducted. Posterior midgut was found transcriptionally divergent from anterior and middle midgut. Differentially expressed gene analysis revealed the regional specialization of digestive enzyme production, transmembrane transport, chitin metabolism, and hormone regulation in different midgut regions. In addition, gene subsets of pan-midgut and region-specific transcription factors (TFs) along the length of midgut were also identified. The results suggested that homeobox TFs might play an essential role in transcriptional variations across the midgut. Altogether, our study provided the first fundamental resource to investigate physiological function and regulation mechanism in larval midgut compartmentalization.
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Affiliation(s)
- Yunwang Shen
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou, China
| | - Xiaoqun Zeng
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou, China
| | - Guanping Chen
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou, China
| | - Xiaofeng Wu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou, China
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Ioannidis P, Buer B, Ilias A, Kaforou S, Aivaliotis M, Orfanoudaki G, Douris V, Geibel S, Vontas J, Denecke S. A spatiotemporal atlas of the lepidopteran pest Helicoverpa armigera midgut provides insights into nutrient processing and pH regulation. BMC Genomics 2022; 23:75. [PMID: 35073840 PMCID: PMC8785469 DOI: 10.1186/s12864-021-08274-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 10/20/2021] [Indexed: 12/13/2022] Open
Abstract
Background Caterpillars from the insect order Lepidoptera are some of the most widespread and destructive agricultural pests. Most of their impact is at the larval stage, where the midgut epithelium mediates the digestion and absorption of an astonishing amount of food. Although this tissue has been the subject of frequent investigation in Lepidoptera, a comprehensive expression atlas has yet to be generated. Results Here, we perform RNA-sequencing and proteomics on the gut of the polyphagous pest Helicoverpa armigera across, life stages, diet types, and compartments of the anterior-posterior axis. A striking relationship between the structural homology and expression pattern of a group of sugar transporters was observed in the early larval stages. Further comparisons were made among the spatial compartments of the midgut, which suggested a putative role for vATPases and SLC9 transporters in the generation of alkaline conditions in the H. armigera midgut. Conclusions This comprehensive resource will aid the scientific community in understanding lepidopteran gut physiology in unprecedented resolution. It is hoped that this study advances the understanding of the lepidopteran midgut and also facilitates functional work in this field. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08274-x.
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Shen Y, Chen G, Zhao S, Wu X. Genome-wide identification of lipases in silkworm (Bombyx mori) and their spatio-temporal expression in larval midgut. Gene 2021; 813:146121. [PMID: 34915049 DOI: 10.1016/j.gene.2021.146121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/20/2021] [Accepted: 12/06/2021] [Indexed: 01/15/2023]
Abstract
Lipases play crucial roles in food digestion by degrading dietary lipids into free fatty acids and glycerols. The domesticated silkworm (Bombyx mori) has been widely used as an important Lepidopteran model for decades. However, little is known about the lipase gene family in the silkworm, especially their hydrolytic activities as digestive enzymes. In this study, a total of 38 lipase genes were identified in the silkworm genome. Phylogenetic analysis indicated that they were divided into three major groups. Twelve lipases were confirmed to be expressed in the midgut at both transcriptional and translational levels. They were grouped into the same gene cluster, suggesting that they could have similar physiological functions. Quantitative real-time PCR (qRT-PCR) analyses indicated that lipases were mainly expressed in anterior and middle midgut regions, and their expression levels varied greatly along the length of midgut. A majority of lipases were down-regulated in the midgut when larvae stopped feeding. However, a unique lipase gene (Bmlip10583) showed low expression level during feeding stage, but it was significantly up-regulated during the larvae-pupae transition. These results demonstrated that expression of silkworm lipases was spatially and temporally regulated in the midgut during larval development. Taken together, our results provide a fundamental research of the lipase gene family in the silkworm.
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Affiliation(s)
- Yunwang Shen
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou 310058, China
| | - Guanping Chen
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou 310058, China
| | - Shudi Zhao
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou 310058, China
| | - Xiaofeng Wu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou 310058, China.
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Denecke S, Rankić I, Driva O, Kalsi M, Luong NBH, Buer B, Nauen R, Geibel S, Vontas J. Comparative and functional genomics of the ABC transporter superfamily across arthropods. BMC Genomics 2021; 22:553. [PMID: 34281528 PMCID: PMC8290562 DOI: 10.1186/s12864-021-07861-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/23/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The ATP-binding cassette (ABC) transporter superfamily is comprised predominantly of proteins which directly utilize energy from ATP to move molecules across the plasma membrane. Although they have been the subject of frequent investigation across many taxa, arthropod ABCs have been less well studied. While the manual annotation of ABC transporters has been performed in many arthropods, there has so far been no systematic comparison of the superfamily within this order using the increasing number of sequenced genomes. Furthermore, functional work on these genes is limited. RESULTS Here, we developed a standardized pipeline to annotate ABCs from predicted proteomes and used it to perform comparative genomics on ABC families across arthropod lineages. Using Kruskal-Wallis tests and the Computational Analysis of gene Family Evolution (CAFE), we were able to observe significant expansions of the ABC-B full transporters (P-glycoproteins) in Lepidoptera and the ABC-H transporters in Hemiptera. RNA-sequencing of epithelia tissues in the Lepidoptera Helicoverpa armigera showed that the 7 P-glycoprotein paralogues differ substantially in their tissue distribution, suggesting a spatial division of labor. It also seems that functional redundancy is a feature of these transporters as RNAi knockdown showed that most transporters are dispensable with the exception of the highly conserved gene Snu, which is probably due to its role in cuticular formation. CONCLUSIONS We have performed an annotation of the ABC superfamily across > 150 arthropod species for which good quality protein annotations exist. Our findings highlight specific expansions of ABC transporter families which suggest evolutionary adaptation. Future work will be able to use this analysis as a resource to provide a better understanding of the ABC superfamily in arthropods.
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Affiliation(s)
- Shane Denecke
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, 700 13, Heraklion Crete, Greece.
| | - Ivan Rankić
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czechia
| | - Olympia Driva
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, 700 13, Heraklion Crete, Greece
| | - Megha Kalsi
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, 700 13, Heraklion Crete, Greece
| | - Ngoc Bao Hang Luong
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, 700 13, Heraklion Crete, Greece
| | - Benjamin Buer
- CropScience Division, Bayer AG, R&D Pest Control, D-40789, Monheim, Germany
| | - Ralf Nauen
- CropScience Division, Bayer AG, R&D Pest Control, D-40789, Monheim, Germany
| | - Sven Geibel
- CropScience Division, Bayer AG, R&D Pest Control, D-40789, Monheim, Germany
| | - John Vontas
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, 700 13, Heraklion Crete, Greece.,Laboratory of Pesticide Science, Department of Crop Science, Agricultural University of Athens, Athens, Greece
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Yue L, Guan Z, Zhong M, Zhao L, Pang R, Liu K. Genome-Wide Identification and Characterization of Amino Acid Polyamine Organocation Transporter Family Genes Reveal Their Role in Fecundity Regulation in a Brown Planthopper Species ( Nilaparvata lugens). Front Physiol 2021; 12:708639. [PMID: 34335311 PMCID: PMC8316623 DOI: 10.3389/fphys.2021.708639] [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: 05/12/2021] [Accepted: 06/21/2021] [Indexed: 11/13/2022] Open
Abstract
The brown planthopper (BPH), Nilaparvata lugens Stål (Hemiptera:Delphacidae), is one of the most destructive pests of rice worldwide. As a sap-feeding insect, the BPH is incapable of synthesizing several amino acids which are essential for normal growth and development. Therefore, the insects have to acquire these amino acids from dietary sources or their endosymbionts, in which amino acid transporters (AATs) play a crucial role by enabling the movement of amino acids into and out of insect cells. In this study, a common amino acid transporter gene family of amino acid/polyamine/organocation (APC) was identified in BPHs and analyzed. Based on a homology search and conserved functional domain recognition, 20 putative APC transporters were identified in the BPH genome. Molecular trait analysis showed that the verified BPH APC family members were highly variable in protein features, conserved motif distribution patterns, and exon/intron organization. Phylogenetic analysis of five hemipteran species revealed an evolutionary pattern of interfamily conservation and lineage-specific expansion of this gene family. Moreover, stage- and tissue-specific expression analysis revealed diverse expression patterns in the 20 BPH APC transporter genes. Lastly, a potential BPH fecundity regulatory gene of NlAPC09 was identified and shown to participate in the fecundity regulation through the use of quantitative polymerase chain reaction (qPCR) and RNA inference experiments. Our results provide a basis for further functional investigations of APC transporters in BPH.
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Affiliation(s)
- Lei Yue
- Innovative Institute for Plant Health, College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Ziying Guan
- Innovative Institute for Plant Health, College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Mingzhao Zhong
- Innovative Institute for Plant Health, College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Luyao Zhao
- Innovative Institute for Plant Health, College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Rui Pang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Kai Liu
- Innovative Institute for Plant Health, College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
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Denecke SM, Driva O, Luong HNB, Ioannidis P, Linka M, Nauen R, Geibel S, Vontas J. The Identification and Evolutionary Trends of the Solute Carrier Superfamily in Arthropods. Genome Biol Evol 2020; 12:1429-1439. [PMID: 32681801 PMCID: PMC7487162 DOI: 10.1093/gbe/evaa153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2020] [Indexed: 12/12/2022] Open
Abstract
The solute carrier (SLC) transporter superfamily comprises an ancient and ubiquitous group of proteins capable of translocating a range of nutrients, endogenous molecules, and xenobiotics. Although the group has been the subject of intense investigation in both bacteria and mammals, its systematic identification in arthropods has not yet been undertaken. Here, we present a genome-wide identification of all 66 human SLC families in 174 arthropod species. A pipeline (SLC_id) was constructed to identify and group SLCs using a combination of hidden Markov model and BLAST searches followed by filtering based on polypeptide length and the number of transmembrane domains. Comparative analysis of the number of transporters in each family across diverse arthropod lineages was accomplished using one-way analysis of variance (ANOVA) and the Computational Analysis of gene Family Evolution (CAFE). These results suggested that many SLC families have undergone expansions or contractions in particular evolutionary lineages. Notably, the sugar transporting SLC2 family was significantly larger in insects compared with arachnids. This difference may have been complemented by a rapid expansion of the SLC60 family in arachnids which also acts on dietary sugars. Furthermore, the SLC33 family underwent a recent and drastic expansion in aphids, although the biological relevance of this expansion was not possible to infer. Information on specific SLC transporter families across arthropod species can be accessed through an R shiny web application at http://chrysalida.imbb.forth.gr : 3838/Arthropod_SLC_Database/. The present study greatly facilitates further investigation of the diverse group of SLC transporters in arthropods.
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Affiliation(s)
- Shane M Denecke
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Olympia Driva
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Hang Ngoc Bao Luong
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Panagiotis Ioannidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Marc Linka
- R&D Pest Control, Bayer AG, Crop Science Division, Monheim, Germany
| | - Ralf Nauen
- R&D Pest Control, Bayer AG, Crop Science Division, Monheim, Germany
| | - Sven Geibel
- R&D Pest Control, Bayer AG, Crop Science Division, Monheim, Germany
| | - John Vontas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
- Pesticide Science Lab, Department of Crop Science, Agricultural University of Athens, Greece
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