Table_7_Papain-Like Cysteine Protease Gene Family in Fig (Ficus carica L.): Genome-Wide Analysis and Expression Patterns.XLSX

The papain-like cysteine proteases (PLCPs) are the most abundant family of cysteine proteases in plants, with essential roles in biotic/abiotic stress responses, growth and senescence. Papain, bromelain and ficin are widely used in food, medicine and other industries. In this study, 31 PLCP genes (FcPCLPs) were identified in the fig (Ficus carica L.) genome by HMM search and manual screening, and assigned to one of nine subfamilies based on gene structure and conserved motifs. SAG12 and RD21 were the largest subfamilies with 10 and 7 members, respectively. The FcPCLPs ranged from 1,128 to 5,075 bp in length, containing 1–10 introns, and the coding sequence ranged from 624 to 1,518 bp, encoding 207–505 amino acids. Subcellular localization analysis indicated that 24, 2, and 5 PLCP proteins were targeted to the lysosome/vacuole, cytoplasm and extracellular matrix, respectively. Promoter (2,000 bp upstream) analysis of FcPLCPs revealed a high number of plant hormone and low temperature response elements. RNA-seq revealed differential expression of 17 FcPLCPs in the inflorescence and receptacle, and RD21 subfamily members were the major PLCPs expressed in the fruit; 16 and 5 FcPLCPs responded significantly to ethylene and light, respectively. Proteome analyses revealed 18 and 5 PLCPs in the fruit cell soluble proteome and fruit latex, respectively. Ficins were the major PLCP in fig fruit, with decreased abundance in inflorescences, but increased abundance in receptacles of commercial-ripe fruit. FcRD21B/C and FcALP1 were aligned as the genes encoding the main ficin isoforms. Our study provides valuable multi-omics information on the FcPLCP family and lays the foundation for further functional studies.

木瓜蛋白酶样半胱氨酸蛋白酶（papain-like cysteine proteases, PLCPs）是植物中分布最为广泛的半胱氨酸蛋白酶家族，在生物/非生物胁迫响应、生长发育及衰老过程中发挥关键作用。木瓜蛋白酶、菠萝蛋白酶和无花果蛋白酶已被广泛应用于食品、医药等多个行业。本研究通过隐马尔可夫模型（Hidden Markov Model, HMM）搜索结合人工筛选，在无花果（Ficus carica L.）基因组中鉴定出31个PLCP基因（命名为FcPCLPs），并根据基因结构与保守基序将其划分为9个亚家族。SAG12和RD21是成员数最多的两个亚家族，分别包含10和7个基因。FcPCLPs的基因长度介于1128 bp至5075 bp之间，包含1~10个内含子；其编码序列长度则为624 bp至1518 bp，编码207~505个氨基酸残基。亚细胞定位分析显示，分别有24、2和5个PLCP蛋白靶向定位于溶酶体/液泡、细胞质及细胞外基质。对FcPLCPs上游2000 bp的启动子区域进行分析，结果发现其富集大量植物激素响应元件与低温响应元件。转录组测序（RNA sequencing, RNA-seq）分析显示，17个FcPLCPs在无花果花序与花托中呈现差异表达，其中RD21亚家族成员是果实中表达量最高的PLCP类基因；分别有16和5个FcPLCPs对乙烯与光照处理存在显著响应。蛋白质组分析结果显示，在果实细胞可溶性蛋白质组与果实胶乳中分别鉴定到18和5个PLCP成员。无花果蛋白酶是无花果果实中的主要PLCP类蛋白，其在花序中的丰度呈下降趋势，但在商业成熟果实的花托中丰度显著升高。经序列比对发现，FcRD21B/C与FcALP1为编码主要无花果蛋白酶同工型的基因。本研究为无花果FcPLCP家族提供了极具价值的多组学数据资源，为后续功能研究奠定了坚实基础。