Multiple-sequence alignment and phylogenetic tree structure The ProtParam ( ) of ExPASy (Expert protein analysis system, ) tool was used to compute the physicochemical characteristics of AGPase proteins in the three species, including the number of amino acids, molecular weight, theoretical isoelectric point (pI), instability (II) and aliphatic index (AI), and grand average of hydropathy (GRAVY) ( Gasteiger et al. The amino acid sequence of the AGPase protein IbAGPa1 (BAF47744.2) was used as the driver sequence for BLAST-search. Sweetpotato Genomics Resource ( ) and NCBI databases ( ) were used to identify the AGPase domain-containing proteins in the three species. Identification of AGPase amino acid sequences The differences in these domains can be used to confirm the molecular functions of the AGPase proteins in sweetpotato and its two relatives. In this study, we aimed to screen the AGPase genes from sweetpotato and its two related species to investigate the conserved domains of the coding proteins. (2n = 2x = 30), have been reported to be the putative progenitors of sweetpotato, which are commonly considered to be model species for sweetpotato research ( Roullier et al. Two non-tuberization diploid Ipomoea species, I. Sweetpotato ( Ipomoea batatas (L.) Lam.) is a hexaploid (2n = 6x = 90) perennial tuberization crop belonging to the family Convolvulaceae ( Welbaum 2015). Conserved domains are defined by a conserved domain database (CDD) as repeating units in molecular evolution, the extent of which can be determined by sequence and structural analysis ( Marchler-Bauer et al. 2012), and protein engineering ( Guerois and Serrano 2001). In molecular evolution, these domains may have been reorganized in different arrangements in protein function annotation ( Ingolfsson and Yona 2008), protein structure determination ( Marchler-Bauer et al. The protein domains can be considered distinct functions and structural units of proteins that are usually identified as repeating (sequence or structural) units ( Ingolfsson and Yona 2008 Li et al. Many AGPase genes have been cloned and studied in sweetpotatoes ( Lee et al. In sweetpotato, AGPase is a key enzyme controlling starch synthesis and is considered an important determinant of the sink activity of the roots ( Tsubone et al. These subunits are necessary for the optimal activity of the native enzyme in plants a lack of one of the subunits will reduce the activity of the AGPase and influence the synthesis of starch ( Li and Preiss 1992). The small subunit is responsible for the catalytic activity, whereas the large subunit plays regulatory roles ( Ballicora et al. In higher plants, it is a heterotetramer composed of two different but closely related subunits (α2β2): “small” (α subunit, 50-54 kDa) and “large” subunits (β subunit, 51-60 kDa) based on the size difference ( Ballicora et al. Keywords ADP-glucose pyrophosphorylase, conserved domain, AGPase small subunit, AGPase large subunit, tuberization, sweetpotatoĪDP-glucose pyrophosphorylase (AGPase EC: 2.7.7.27) is a regulatory enzyme that catalyzes the biosynthesis of alpha 1,4-glucans (glycogen or starch) in photosynthetic bacteria and plants ( Smith-White and Preiss 1992). The study may enable research on the AGPase-related specific characteristics of sweetpotatoes that do not exist in the other two species, such as starch metabolism and tuberization mechanism. These findings suggested that these conserved domains were species-specific and related to the subunit types of AGPase proteins. triloba) were found to only contain the NTP_transferase domain in the N-terminal region. Conversely, most of its two relatives ( I. The AGPase proteins from sweetpotato were found to contain an LbH_G1P_AT_C domain in the C-terminal region and various domains (NTP_transferase, ADP_Glucose_PP, or Glyco_tranf_GTA) in the N-terminal region. The aliphatic index values of sweetpotato AGPase proteins were higher in the small subunit than in the large subunit. The molecular weight, isoelectric point, instability index, and grand average of hyropathy markedly differed among the three species. Herein, the ADP-glucose pyrophosphorylase (AGPase) amino acid sequences of three species of the Ipomoea genus were identified to investigate their physicochemical and biochemical characteristics. Conserved domains are defined as recurring units in molecular evolution and are commonly used to interpret the molecular function and biochemical structure of proteins.
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