Comparative genomics and transcriptomics insight into myxobacterial metabolism potentials and multiple predatory strategies

Chunling Wang; Yi Xiao; Yong Wang; Yumin Liu; Qing Yao; Honghui Zhu

doi:10.3389/fmicb.2023.1146523

Comparative genomics and transcriptomics insight into myxobacterial metabolism potentials and multiple predatory strategies

Front Microbiol. 2023 May 5:14:1146523. doi: 10.3389/fmicb.2023.1146523. eCollection 2023.

Authors

Chunling Wang^{1

2}, Yi Xiao², Yong Wang², Yumin Liu², Qing Yao³, Honghui Zhu²

Affiliations

¹ College of Life Science, Huizhou University, Huizhou, Guangdong, China.
² Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China.
³ College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangzhou, Guangdong, China.

Abstract

Myxobacteria are part of the phylum Myxococcota, encompassing four orders. Most of them display complex lifestyles and broad predation profiles. However, metabolic potential and predation mechanisms of different myxobacteria remains poorly understood. Herein, we used comparative genomics and transcriptomics to analyze metabolic potentials and differentially expressed gene (DEG) profiles of Myxococcus xanthus monoculture (Mx) compared to coculture with Escherichia coli (MxE) and Micrococcus luteus (MxM) prey. The results showed that myxobacteria had conspicuous metabolic deficiencies, various protein secretion systems (PSSs) and the common type II secretion system (T2SS). RNA-seq data demonstrated that M. xanthus overexpressed the potential predation DEGs, particularly those encoding T2SS, the tight adherence (Tad) pilus, different secondary metabolites (myxochelin A/B, myxoprincomide, myxovirescin A1, geosmin and myxalamide), glycosyl transferases and peptidase during predation. Furthermore, the myxalamide biosynthesis gene clusters, two hypothetical gene clusters and one arginine biosynthesis clusters were highly differential expressed in MxE versus MxM. Additionally, homologue proteins of the Tad (kil) system and five secondary metabolites were in different obligate or facultative predators. Finally, we provided a working model for exhibiting multiple predatory strategies when M. xanthus prey on M. luteus and E. coli. These results might spur application-oriented research on the development of novel antibacterial strategies.

Keywords: Tad pilus; genomics and transcriptomics; myxobacteria; predation; protein secretion systems; secondary metabolites.