Abstract
Arabinogalactan proteins (AGPs) belong to a class of Pro/Hyp-rich glycoproteins and are some of the most complex types of macromolecules found in plants. In the economically important plant species, Brassica rapa, only chimeric AGPs have been identified to date. This has significantly limited our understanding of the functional roles of AGPs in this plant. In this study, 64 AGPs were identified in the genome of B. rapa, including 33 classical AGPs, 28 AG peptides and three lys-rich AGPs. Syntenic gene analysis between B. rapa and A. thaliana suggested that the whole genome triplication event dominated the expansion of the AGP gene family in B. rapa. This resulted in a high retained proportion of the AGP family in the B. rapa genome, especially in the least fractionated subgenome. Phylogenetic and motif analysis classified the classical AGPs into six clades and three orphan genes, and the AG peptides into three clades and five orphan genes. Classical AGPs has a faster rate of molecular evolution than AG peptides revealed by estimation of molecular evolution rates. However, no significant differences were observed between classical AGPs and lys-rich AGPs. Under control conditions and in response to phytohormones treatment, a complete expression profiling experiment has identified five anther-specific AGPs and quite a number of AGPs responding to abscisic acid, methyl jasmonate and/or gibberellin. In this study, we presented a bioinformatics approach to identify important types of AGPs. Moreover, the association between their function and their protein structure, as well as the evolution and the expression of AGP genes were investigated, which might provide fundamental information for revealing the roles of AGPs in B. rapa.
Highlights
Arabinogalactan proteins (AGPs), together with proline-rich proteins (PRPs) and extensins (EXTs), constitute the superfamily of proline/hydroxyproline-rich glycoproteins (P/HRGPs), which are abundant in the extracellular matrix throughout the plant kingdom (Gaspar et al, 2001; Showalter, 2001)
Orthologous genes of all the annotated classical AGPs, AG peptides and lys-rich AGPs in A. thaliana were screened in the proteome of B. rapa
For the first time, 33 classical AGPs, 28 AG peptides, and three lys-rich AGPs in the genome of B. rapa
Summary
Arabinogalactan proteins (AGPs), together with proline-rich proteins (PRPs) and extensins (EXTs), constitute the superfamily of proline/hydroxyproline-rich glycoproteins (P/HRGPs), which are abundant in the extracellular matrix throughout the plant kingdom (Gaspar et al, 2001; Showalter, 2001). Most AGPs are characterized by the entire protein containing only P/HRGP modules, while chimeric AGPs are consisted of one or two known P/HRGP motifs and Abbreviations: AGPs, Arabinogalactan proteins; ABA, abscisic acid; AK, ancestral karyotype; AtAGPs, A. thaliana AGPs; BLAST, the basic local alignment search tool; BRAD, Brassica database; BrAGPs, B. rapa AGPs; ENODL, eNodlike AGPs; EXTs, extensions; FLAs, fasciclin-like AGPs; GA, gibberellin; GPI, glycosylphosphatidylinositol; HAP, hour after pollination; HAT, hours after treatment; HMM, hidden Markov model; Ka, nonsynonymous substitution rate; Ks, synonymous substitution rate; MeJA, methyl jasmonate; MEME, Multiple Em for Motif Elicitation; ML, maximum likelihood; NJ, neighbor-joining; P/HRGPs, proline/hydroxyproline-rich glycoproteins; PAST, Pro, Ala, Ser, Thr; Pro/Hyp, proline or hydroxyproline; PRPs, proline-rich proteins; qRT-PCR, quantitative real-time PCR; RT-PCR, reverse transcription polymerase chain reaction; TAIR, The Arabidopsis Information Resource; WGT, whole genome triplication
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