title: Aligning the proteome and genome of the silkworm, Bombyx mori.
abstract: A technology of mass spectrometry (MS) was used in this study for the large-scale proteomic identification and verification of protein-encoding genes present in the silkworm (Bombyx mori) genome. Peptide sequences identified by MS were compared with those from an open reading frame (ORF) library of the B. mori genome and a cDNA library, to validate the coding attributes of ORFs. Two databases were created. The first was based on a 9x draft sequence of the silkworm genome and contained 14,632 putative proteins. The second was based on a B. mori pupal cDNA library containing 3,187 putative proteins of at least 30 amino acid residues in length. A total of 81,000 peptide sequences with a threshold score of 60% were generated by the MS/MS analysis, and 55,400 of these were chosen for a sequence alignment. By searching these two databases, 6,649 and 250 proteins were matched, which accounted for approximately 45.4% and 7.8% of the peptide sequences and putative proteins, respectively. Further analyses carried out by several bioinformatic tools suggested that the matches included proteins with predicted transmembrane domains (1,393) and preproteins with a signal peptide (976). These results provide a fundamental understanding of the expression and function of silkworm proteins.
authors.affiliation: The Key Laboratory of Bioreactor and Biopharmacy of Zhejiang Province, Institute of Biochemistry, Zhejiang Sci-Tech University, Xiasha High-Tech Zone No 2 Road, Hangzhou, China. yaozhou@chinagene.com
authors.forename: Yaozhou
authors.initials: Y
authors.lastname: Zhang
authors.forename: Qingyou
authors.initials: Q
authors.lastname: Xia
authors.forename: Jie
authors.initials: J
authors.lastname: Xu
authors.forename: Jian
authors.initials: J
authors.lastname: Chen
authors.forename: Zuoming
authors.initials: Z
authors.lastname: Nie
authors.forename: Dan
authors.initials: D
authors.lastname: Wang
authors.forename: Wenping
authors.initials: W
authors.lastname: Zhang
authors.forename: Jianqing
authors.initials: J
authors.lastname: Chen
authors.forename: Qingliang
authors.initials: Q
authors.lastname: Zheng
authors.forename: Qing
authors.initials: Q
authors.lastname: Chen
authors.forename: Lingying
authors.initials: L
authors.lastname: Kong
authors.forename: Xiaoyuan
authors.initials: X
authors.lastname: Ren
authors.forename: Jiang
authors.initials: J
authors.lastname: Wang
authors.forename: Zhengbing
authors.initials: Z
authors.lastname: Lv
authors.forename: Wei
authors.initials: W
authors.lastname: Yu
authors.forename: Caiying
authors.initials: C
authors.lastname: Jiang
authors.forename: Lili
authors.initials: L
authors.lastname: Liu
authors.forename: Qing
authors.initials: Q
authors.lastname: Sheng
authors.forename: Yongfeng
authors.initials: Y
authors.lastname: Jin
authors.forename: Xiangfu
authors.initials: X
authors.lastname: Wu
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D012831:Bombyx / Q000737:chemistry / Q000235:genetics; D030541:Databases, Genetic; D016678:Genome; D019476:Insect Proteins / Q000032:analysis / Q000235:genetics; D013058:Mass Spectrometry / Q000379:methods; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D020543:Proteome
chemical_list: D019476:Insect Proteins; D020543:Proteome