Development versus predation: Transcriptomic changes during the lifecycle of Myxococcus xanthus

Abstract

Myxococcus xanthus is a multicellular bacterium with a complex lifecycle. It is a soil-dwelling predator that preys on a wide variety of microorganisms by using a group and collaborative epibiotic strategy. In the absence of nutrients this myxobacterium enters in a unique developmental program by using sophisticated and complex regulatory systems where more than 1,400 genes are transcriptional regulated to guide the community to aggregate into macroscopic fruiting bodies filled of environmentally resistant myxospores. Herein, we analyze the predatosome of M. xanthus, that is, the transcriptomic changes that the predator undergoes when encounters a prey. This study has been carried out using as a prey Sinorhizobium meliloti, a nitrogen fixing bacteria very important for the fertility of soils. The transcriptional changes include upregulation of genes that help the cells to detect, kill, lyse, and consume the prey, but also downregulation of genes not required for the predatory process. Our results have shown that, as expected, many genes encoding hydrolytic enzymes and enzymes involved in biosynthesis of secondary metabolites increase their expression levels. Moreover, it has been found that the predator modifies its lipid composition and overproduces siderophores to take up iron. Comparison with developmental transcriptome reveals that M. xanthus downregulates the expression of a significant number of genes coding for regulatory elements, many of which have been demonstrated to be key elements during development. This study shows for the first time a global view of the M. xanthus lifecycle from a transcriptome perspective.

Keywords: Myxococcus xanthus; Sinorhizobacterium meliloti; bacterial predation; development; predatosome; transcriptome.

Figure 1

Differential expression response of M. xanthus during predation. Screening of differentially upregulated (A) and downregulated (B) genes by volcano at t2 and t6 in predatory conditions. Volcano plots show the estimated fold changes (x-axis) versus the minus log10 of the adjusted p-values (y-axis) from DEseq analysis. Significant genes with absolute values of |Log2 Fold Change|>0 and padj<0.05 are shown in red (upregulated) or in blue (downregulated). Black vertical dotted line indicates zero-fold change. Green dots indicate non-regulated genes.

Figure 2

Heatmap with upregulated genes during predation at t2 and/or t6. (A) Hydrolytic enzymes. (B) LysM proteins. (C) S-motility. (D) Secondary metabolites. Red edges indicate genes with Log2 Fold Change > 1.

Figure 3

Differential expression during predation at t2 and t6 of genes involved in lipid biosynthesis and degradation, and their possible implication in lipid external use, and secondary metabolites biosynthesis. Red text indicates genes upregulated during predation. Blue text indicates downregulated genes. In bold, |Log2 Fold Change|> 1.

Figure 4

Iron uptake mechanisms are induced in co-culture. (A) Genes predicted to be involved in iron uptake and that are upregulated in co-culture at t2 and/or t6. The numbers of the genes depicted in the figure are the corresponding MXAN_ identifiers. (B) Graphical representation of the cluster of genes involved in myxochelin biosynthesis. The seven upregulated transcripts are indicated by their corresponding gene name. (C) Fur box (FB) predicted by using the Virtual Footprint database. Red balls: Fe³⁺; blue balls: Fe²⁺. OM, outer membrane; IM, inner membrane. For more details please see the text and Supplementary Table S2A.

Figure 5

Comparison of the predatosomes of M. xanthus on S. meliloti and S. coelicolor. (A) Venn diagram of upregulated genes with Log2 Fold Change>0 and padj<0.05. (B) Proportion of different pathways and protein functions of the 76 common genes.

Figure 6

Differentially expressed genes (DEGs) during predation clustered in developmental groups (DGs) of M. xanthus. (A) DGs described by Muñoz-Dorado et al. (2019). (B) Venn diagram of up and down-DEGs during predation, and DEGs during development (not shown to scale). (C) Number of DEGs during predation included in each DG. As indicated in the text, DG1 and DG2 are downregulated genes during development, while DG3-10 are genes upregulated during development.