Fig 1.
Strategy for integration of transcriptome and proteome sequencing.
(a) The foot area, byssal threads and byssal plaques (rectangles from bottom to top) were dissected for sequencing. (b) Transcriptome sequencing of the foot area was performed for subsequent de novo assembly and annotation. (c) Thread and plaque proteins were separated by SDS-PAGE before LC-MS/MS analysis. (d) The generated transcriptome data were integrated with the proteome sequencing data to identify interesting transcripts and deduce their corresponding protein sequences. Further protein structural analysis, recombinant protein engineering, and biomimetic material processing are examples of potential applications.
Table 1.
Design of the enrichment experiment.
Fig 2.
Validation of byssal proteins by RT-PCR with further confirmation by Sanger sequencing.
Fig 3.
Content and distribution of histidine (H) and cysteine (C) residues in the byssal protein sequences of P. viridis. The x-axis represents the content of histidine (red) and cysteine (blue) in each protein. The y-axis represents the number of proteins.
Table 2.
Identified byssal proteins from the Chinese green mussel.
Fig 4.
Comparison of partial preCol-P sequences between P. viridis and Mytilus species.
Red underlined sequences are XGXPG repeats.
Table 3.
Byssal proteins identified and annotated from the transcriptome and proteome of P. viridis.
Fig 5.
Accumulation of Cd2+ by the recombinant Pvpf-5-1 protein.
Blue bars represent initial Cd2+ concentration, and red or green bars indicate the Cd2+ concentrations after addition of the empty pET-32a vector or Pvfp-5-1, respectively. See more details about the groups in Table 1.
Fig 6.
Sequence comparisons of several important byssal proteins.
(a) antistasin-like protein (ALP). (b) SPI-like protein, which contains 6 repeated regions. (c) Oikosin-like protein; (d) Pernin precursor protein, which contains 3 repeated regions (Cu-Zn SODs in the red boxes). Note that the underlined regions are signal sequences. The cysteine (Cys, C) and Histidine (His, H) residues are highlighted in red and blue, respectively. Yellow areas are the identified peptides by LC-MS/MS.