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A time-resolved multi-omics atlas of Acanthamoeba castellanii encystment

ABSTRACT: Encystment is a common stress response of most protists, including free-living amoebae. Cyst formation protects the amoebae from eradication and can increase virulence of the bacteria they harbor. Here, we mapped the global molecular changes that occur in the facultatively pathogenic amoeba Acanthamoeba castellanii during the early steps of the poorly understood process of encystment. By performing transcriptomic, proteomic, and phosphoproteomic experiments during encystment, we identified more than 150,000 previously undescribed transcripts and thousands of protein sequences absent from the reference genome. These results provide molecular details to the regulation of expected biological processes, such as cell proliferation shutdown, and reveal new insights such as a rapid phospho-regulation of sites involved in cytoskeleton remodeling and translation regulation. This work constitutes the first time-resolved molecular atlas of an encysting organism and a useful resource for further investigation of amoebae encystment to allow for a better control of pathogenic amoebae. Encystment is a process that allows free-living and parasitic amoebae to survive in unfavorable environments. Here, Bernard et al. provide detailed insights into the early stages of encystment of Acanthamoeba castellanii by integrating RNA-Seq, proteomics and phosphoproteomics data sets.

SUBMITTER: Bernard C

PROVIDER: S-EPMC9283445 | biostudies-literature |

REPOSITORIES: biostudies-literature

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A time-resolved multi-omics atlas of Acanthamoeba castellanii encystment

Project description:Encystment is a common response of most protists to stress. Although some signaling pathways regulating this process were reported, our knowledge remains limited. Here, we mapped the molecular changes occurring in the amoeba Acanthamoeba castellanii during the early steps of encystment. De novo analysis of the transcriptome identified more than 150,000 previously undescribed transcripts that were utilized for mass spectrometry-based proteomics analysis after triggering starvation. With this strategy, we identified thousands of protein sequences absent from the reference genome. These results revealed the regulation of expected biological processes, such as the shutdown of cell proliferation at transcript level followed by down-regulation of proteins. The phosphoproteome showed a quick regulation of phosphorylation sites involved in cytoskeleton remodeling and translation regulation, among other processes underlying A. castellanii encystment. To our knowledge, this work constitutes the first time-resolved molecular atlas of an encysting organism and a useful resource to further investigating amoebae encystment.

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