Zhang Yuxin, Zhang Yirong, Yu Ze, Wang Hanyu, Ping Boya, Liu Yunxiao, Liang Jiakai, Ma Fengwang, Zou Yangjun, Zhao Tao
State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China.
Genes Genomics. 2024 Oct;46(10):1209-1223. doi: 10.1007/s13258-024-01551-5. Epub 2024 Aug 14.
ACO (1-aminocyclopropane-1-carboxylic acid) serves as a pivotal enzyme within the plant ethylene synthesis pathway, exerting influence over critical facets of plant biology such as flowering, fruit ripening, and seed development.
This study aims to identify ACO genes from representative Rosaceae genomes, reconstruct their phylogenetic relationships by integrating synteny information, and investigate their expression patterns and networks during fruit development.
we utilize a specialized Hidden Markov Model (HMM), crafted on the sequence attributes of ACO gene-encoded proteins, to systematically identify and analyze ACO gene family members across 12 representative species within the Rosaceae botanical family. Through transcriptome analysis, we delineate the expression patterns of ACO genes in six distinct Rosaceae fruits.
Our investigation reveals the presence of 62 ACO genes distributed among the surveyed Rosaceae species, characterized by hydrophilic proteins predominantly expressed within the cytoplasm. Phylogenetic analysis categorizes these ACO genes into three discernible classes, namely Class I, Class II, and Class III. Further scrutiny via collinearity assessment indicates a lack of collinearity relationships among these classes, highlighting variations in conserved motifs and promoter types within each class. Transcriptome analysis unveils significant disparities in both expression levels and trends of ACO genes in fruits exhibiting respiratory bursts compared to those that do not. Employing Weighted Gene Co-Expression Network Analysis (WGCNA), we discern that the co-expression correlation of ACO genes within loquat fruit notably differs from that observed in apples. Our findings, derived from Gene Ontology (GO) enrichment results, signify the involvement of ACO genes and their co-expressed counterparts in biological processes linked to terpenoid metabolism and carbohydrate synthesis in loquat. Moreover, our exploration of gene regulatory networks (GRN) highlights the potential pivotal role of the GNAT transcription factor (Ejapchr1G00010380) in governing the overexpression of the ACO gene (Ejapchr10G00001110) within loquat fruits.
The constructed HMM of ACO proteins offers a precise and systematic method for identifying plant ACO proteins, facilitating phylogenetic reconstruction. ACO genes from representative Rosaceae fruits exhibit diverse expression and regulative patterns, warranting further function characterizations.
1-氨基环丙烷-1-羧酸氧化酶（ACO）是植物乙烯合成途径中的关键酶，对植物生物学的关键方面如开花、果实成熟和种子发育产生影响。
本研究旨在从代表性蔷薇科基因组中鉴定ACO基因，通过整合共线性信息重建它们的系统发育关系，并研究它们在果实发育过程中的表达模式和网络。
我们利用基于ACO基因编码蛋白序列特征构建的专门隐马尔可夫模型（HMM），系统地鉴定和分析蔷薇科12个代表性物种中的ACO基因家族成员。通过转录组分析，我们描绘了ACO基因在六种不同蔷薇科果实中的表达模式。
我们的研究揭示了在所调查的蔷薇科物种中存在62个ACO基因，其特征是主要在细胞质中表达的亲水性蛋白。系统发育分析将这些ACO基因分为三个可识别的类别，即I类、II类和III类。通过共线性评估的进一步审查表明这些类别之间缺乏共线性关系，突出了每个类别中保守基序和启动子类型的差异。转录组分析揭示了与无呼吸跃变的果实相比，有呼吸跃变的果实中ACO基因在表达水平和趋势上的显著差异。采用加权基因共表达网络分析（WGCNA），我们发现枇杷果实中ACO基因的共表达相关性与苹果中观察到的明显不同。我们从基因本体论（GO）富集结果中得出的发现表明，ACO基因及其共表达的对应基因参与了与枇杷萜类代谢和碳水化合物合成相关的生物学过程。此外，我们对基因调控网络（GRN）的探索突出了GNAT转录因子（Ejapchr1G00010380）在调控枇杷果实中ACO基因（Ejapchr10G00001110）过表达方面的潜在关键作用。
构建的ACO蛋白HMM为鉴定植物ACO蛋白提供了一种精确而系统的方法，有助于系统发育重建。代表性蔷薇科果实中的ACO基因表现出多样的表达和调控模式，有待进一步进行功能表征。
