Bioinformatics Prediction and Evolution Analysis of Arabinogalactan Proteins in the Plant Kingdom

Abstract

Arabinogalactan proteins (AGPs) are a family of extracellular glycoproteins implicated in plant growth and development. With a rapid growth in the number of genomes sequenced in many plant species, the family members of AGPs can now be predicted to facilitate functional investigation. Building upon previous advances in identifying Arabidopsis AGPs, an integrated strategy of systematical AGP screening for “classical” and “chimeric” family members is proposed in this study. A Python script named Finding-AGP is compiled to find AGP-like sequences and filter AGP candidates under the given thresholds. The primary screening of classical AGPs, Lys-rich classical AGPs, AGP-extensin hybrids, and non-classical AGPs was performed using the existence of signal peptides as a necessary requirement, and BLAST searches were conducted mainly for fasciclin-like, phytocyanin-like and xylogen-like AGPs. Then glycomodule index and partial PAST (Pro, Ala, Ser, and Thr) percentage are adopted to identify AGP candidates. The integrated strategy successfully discovered AGP gene families in 47 plant species and the main results are summarized as follows: (i) AGPs are abundant in angiosperms and many “ancient” AGPs with Ser-Pro repeats are found in Chlamydomonas reinhardtii; (ii) Classical AGPs, AG-peptides, and Lys-rich classical AGPs first emerged in Physcomitrella patens, Selaginella moellendorffii, and Picea abies, respectively; (iii) Nine subfamilies of chimeric AGPs are introduced as newly identified chimeric subfamilies similar to fasciclin-like, phytocyanin-like, and xylogen-like AGPs; (iv) The length and amino acid composition of Lys-rich domains are largely variable, indicating an insertion/deletion model during evolution. Our findings provide not only a powerful means to identify AGP gene families but also probable explanations of AGPs in maintaining the plant cell wall and transducing extracellular signals into the cytoplasm.

Pollen tube growth and guidance: Occam's razor sharpened on a molecular arabinogalactan glycoprotein Rosetta Stone

“…Finally, the reason for the wide range in classical AGP structure includes the complex glycosylation of its protein core. Clearly the tiny minority of AGPs characterized biochemically only hints at their true diversity and versatility emphasized by recent bioinformatics that show higher plants have heavily invested in AGPs (Ma et al ., ). Thus, diverse stimuli might generate specific Ca 2+ signatures (Rudd & Franklin‐Tong, ) based on the distribution, size and composition of AGP glycomodules.…”

Plant glycosylphosphatidylinositol anchored proteins at the plasma membrane‐cell wall nexus

“…A study of the hydroxyproline‐rich glycoproteins (HRGP) superfamily in the 1,000 plant transcriptomics data (1KP) showed that GPI anchored AGPs (GPI‐AGPs) can be identified early in land plant lineages, being present in Glaucophyta, Chromista and green algae (Johnson et al ) and were found throughout land plant evolution in all 1KP groups. Evolutionary studies of chimeric AGPs, many of which are predicted to be GPI‐anchored, could also be identified in the genomes of 47 plant species (Ma et al ). In addition, studies of GPI‐LTPs, proposed to function in the synthesis and/or deposition of cutin and cuticular waxes, in the moss Physcomitrella suggest they share similar features and function to GPI‐LTPs found in flowering plants (Edstam and Edqvist ; Edstam et al ).…”

The Role of the Primary Cell Wall in Plant Morphogenesis

“…On the other hand, cytosolic Ca 2+ gradients originate from Ca 2+ stored in a cell surface AGP-Ca 2+ capacitor [ 12 ]. AGPs are essential components of the Hechtian growth oscillator that amplifies the magnitude and direction of stress vectors regulating plant growth [ 6 ]; that explains why plants have heavily invested in AGPs [ 13 ] and why this investment is so highly diversified [ 14 ]. Many AGPs are developmentally regulated and tissue-specific [ 15 , 16 , 17 , 18 ].…”