Cyanobacteria are of special concern because they proliferate in eutrophic water bodies worldwide and affect water quality. As an ancient photosynthetic microorganism, cyanobacteria can survive in ecologically diverse habitats because of their capacity to rapidly respond to environmental changes through a web of complex signaling networks, including using second messengers to regulate physiology or metabolism. A ubiquitous second messenger, bis-(3′,5′)-cyclic-dimeric-guanosine monophosphate (c-di-GMP), has been found to regulate essential behaviors in a few cyanobacteria but not Microcystis, which are the most dominant species in cyanobacterial blooms. In this study, comparative genomics analysis was performed to explore the genomic basis of c-di-GMP signaling in Microcystis aeruginosa. Proteins involved in c-di-GMP metabolism and regulation, such as diguanylate cyclases, phosphodiesterases, and PilZ-containing proteins, were encoded in M. aeruginosa genomes. However, the number of identified protein domains involved in c-di-GMP signaling was not proportional to the size of M. aeruginosa genomes (4.97 Mb in average). Pan-genome analysis showed that genes involved in c-di-GMP metabolism and regulation are conservative in M. aeruginosa strains. Phylogenetic analysis showed good congruence between the two types of phylogenetic trees based on 31 highly conserved protein-coding genes and sensor domain-coding genes. Propensity for gene loss analysis revealed that most of genes involved in c-di-GMP signaling are stable in M. aeruginosa strains. Moreover, bioinformatics and structure analysis of c-di-GMP signal-related GGDEF and EAL domains revealed that they all possess essential conserved amino acid residues that bind the substrate. In addition, it was also found that all selected M. aeruginosa genomes encode PilZ domain containing proteins. Comparative genomics analysis of c-di-GMP metabolism and regulation in M. aeruginosa strains helped elucidating the genetic basis of c-di-GMP signaling pathways in M. aeruginosa. Knowledge of c-di-GMP metabolism and relevant signal regulatory processes in cyanobacteria can enhance our understanding of their adaptability to various environments and bloom-forming mechanism.

中文翻译：

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铜绿微囊藻c-di-GMP代谢与调控的比较基因组学分析


蓝藻受到特别关注，因为它们在全球富营养化水体中​​增殖并影响水质。作为一种古老的光合微生物，蓝藻能够在生态多样化的栖息地中生存，因为它们能够通过复杂的信号网络快速响应环境变化，包括使用第二信使来调节生理或新陈代谢。普遍存在的第二信使双-(3′,5′)-环状二聚鸟苷单磷酸 (c-di-GMP) 被发现可以调节少数蓝藻菌的基本行为，但不能调节最主要的微囊藻属物种在蓝藻水华中。在本研究中，进行比较基因组学分析，以探索铜绿微囊藻中 c-di-GMP 信号传导的基因组基础。参与 c-di-GMP 代谢和调节的蛋白质，如二鸟苷酸环化酶、磷酸二酯酶和含有 PilZ 的蛋白质，均在铜绿假单胞菌基因组中编码。然而，已鉴定的参与 c-di-GMP 信号传导的蛋白质结构域的数量与铜绿微囊菌基因组的大小（平均 4.97 Mb）不成正比。泛基因组分析表明，参与c-di-GMP代谢和调节的基因在铜绿假单胞菌菌株中是保守的。系统发育分析显示，基于 31 个高度保守的蛋白质编码基因和传感器域编码基因的两种类型的系统发育树之间具有良好的一致性。基因丢失分析的倾向表明，大多数参与 c-di-GMP 信号传导的基因在铜绿假单胞菌菌株中是稳定的。此外，c-di-GMP信号相关的GGDEF和EAL结构域的生物信息学和结构分析表明，它们都具有结合底物的必需保守氨基酸残基。 此外，还发现所有选定的铜绿假单胞菌基因组都编码含有PilZ结构域的蛋白质。铜绿假单胞菌菌株中 c-di-GMP 代谢和调控的比较基因组学分析有助于阐明铜绿假单胞菌中 c-di-GMP 信号通路的遗传基础。了解蓝藻中c-di-GMP代谢和相关信号调节过程可以增强我们对其对各种环境的适应性和水华形成机制的理解。