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For: Li JY, Ye LP, Che JQ, Song J, You ZY, Wang SH, Zhong BX. Proteome identification of the silkworm middle silk gland. Data Brief 2016;6:903-7. [PMID: 26937469 PMCID: PMC4753389 DOI: 10.1016/j.dib.2016.01.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 12/21/2015] [Accepted: 01/25/2016] [Indexed: 12/01/2022] Open

For:	Li JY, Ye LP, Che JQ, Song J, You ZY, Wang SH, Zhong BX. Proteome identification of the silkworm middle silk gland. Data Brief 2016;6:903-7. [PMID: 26937469 PMCID: PMC4753389 DOI: 10.1016/j.dib.2016.01.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 12/21/2015] [Accepted: 01/25/2016] [Indexed: 12/01/2022] Open

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Cited by Other Article(s)

Li T, Xu C, Xu J, Luo J, Yu B, Meng X, Li C, Pan G, Zhou Z. Proteomic Identification of Bombyx mori Organelles Using the Engineered Ascorbate Peroxidase APEX and Development of Silkworm Organelle Proteome Database (SilkOrganPDB). Int J Mol Sci 2021;22:ijms22095051. [PMID: 34068790 PMCID: PMC8126250 DOI: 10.3390/ijms22095051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 11/16/2022] Open

Abstract

Silkworm Bombyx mori is an economically important insect and a lepidopteran model. Organelle proteome is vital to understanding gene functions; however, it remains to be identified in silkworm. Here, using the engineered ascorbate peroxidase APEX, we constructed transgenic B. mori embryo cells (BmE) expressing APEX-NLS, COX4-APEX, APEX-Rev, and APEX-KDEL in nucleus, mitochondrial matrix (MM), cytosol, and endoplasmic reticulum (ER), and isolated the biotin-labeled proteins using streptavidin-affinity purification, respectively. The isolated proteins were determined using LC-MS/MS and annotated by searching B. mori genomes downloaded from GenBank, SilkBase, SilkDB 2.0, and SilkDB 3.0, resulting in 842, 495, 311, and 445 organelle proteins identified, respectively. We mapped the 296 MM proteins annotated in the GenBank data to mitochondrial protein databases of the fly, human, and mouse, and found that 140 (47%) proteins are homologous to 80 fly proteins, and 65 (22%) proteins match to 31 and 29 human and mouse proteins, respectively. Protein orthology was predicted in multiple insects using OrthoMCL, producing 460 families containing 839 proteins we identified. Out of 460 families, 363 were highly conserved and found in all insects, leaving only three proteins without orthology in other insects, indicating that the identified proteins are highly conserved and probably play important roles in insects. A gene ontology enrichment analysis by clusterProfiler revealed that the nucleus proteins significantly enriched in cellular component terms of nucleus and nucleolus, the MM proteins markedly enriched in molecular function terms of nucleotide binding, and the cytosol proteins mainly enriched in biological process terms of small molecule metabolism. To facilitate the usage and analysis of our data, we developed an open-access database, Silkworm Organelle Proteome Database (SilkOrganPDB), which provides multiple modules for searching, browsing, downloading, and analyzing these proteins, including BLAST, HMMER, Organelle Proteins, Protein Locations, Sequences, Gene Ontology, Homologs, and Phylogeny. In summary, our work revealed the protein composition of silkworm BmE organelles and provided a database resource helpful for understanding the functions and evolution of these proteins.

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Affiliation(s)

Tian Li State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.) Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China Correspondence: (T.L.); (Z.Z.)
Chen Xu State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.) Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
Jinzhi Xu State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.) Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
Jian Luo State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.) Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
Bin Yu State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.) Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
Xianzhi Meng State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.) Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
Chunfeng Li State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.) Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
Guoqing Pan State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.) Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
Zeyang Zhou State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (C.X.); (J.X.); (J.L.); (B.Y.); (X.M.); (C.L.); (G.P.) Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China College of Life Science, Chongqing Normal University, Chongqing 400047, China Correspondence: (T.L.); (Z.Z.)

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Sun F, Ye CJ, Li B, Wang T, Fan T. Application of mass spectrometry in silkworm research-Review. Biomed Chromatogr 2019;33:e4476. [PMID: 30578558 DOI: 10.1002/bmc.4476] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 12/12/2018] [Accepted: 12/17/2018] [Indexed: 12/13/2022]

Bovilla VR, Padwal MK, Siripurapu P, Basu B, Mamillapalli A. Developmental proteome dynamics of silk glands in the 5th instar larval stage of Bombyx mori L (CSR2×CSR4). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016;1864:860-8. [PMID: 27032299 DOI: 10.1016/j.bbapap.2016.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/23/2016] [Accepted: 03/15/2016] [Indexed: 10/22/2022]

Abstract

UNLABELLED

Bivoltine breed of Bombyx mori (B. mori), CSR2×CSR4 is an Indian high yielding silkworm strain. Silk gland proteome of this strain was not studied till now. Methods of improving silk production by chemical approaches have reached saturation and transgenic methods are needed in further to boost silk production. An understanding of proteomic changes during silk gland development helps in designing experiments to enhance silk production by transgenic approaches. The present study reports comprehensive developmental proteomic analysis of CSR2×CSR4, 5th instar whole silk glands. Eighty six unique protein IDs were obtained from the analysis of one hundred and twenty protein spots. Among the identified proteins, majority of the proteins were involved in metabolism (41%) followed by proteins involved in protein homeostasis (30%). Sixty percent of the identified proteins showed dynamic nature by expression analysis from day 1, day 3, day 5 and day 7 gels. In comparison to the published data till now on silk gland proteomics this study reports identification of 20 new proteins from the silk glands for the first time.

SIGNIFICANCE

The paper reports for the first time proteomic analysis of high yielding silkworm strain of India. The study analyzes whole silk glands to understand the tissue in total during 5th instar development. Lowering fibroin content made us to identify a large number of new proteins which were not reported till now in the silk gland proteome. Proteins which are involved in silk synthesis and release were found to be developmentally regulated. The study identified alanine, serine and glycine tRNA ligases for the first time and also showed their up-regulation on day 7 of 5th instar larval stage. The amino acid repeat of fibroin protein is enriched with the three amino acids, glycine, serine and alanine. The identified proteins could be studied further to understand their functional role in-depth.

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