Novel Transcriptome Patterns Accompany Evolutionary Restoration of Defective Social Development in the Bacterium Myxococcus xanthus

Abstract

Evolutionary trait losses can be restored by direct reversion or by compensatory pathways. Upon starvation, the bacterium Myxococcus xanthus develops into spore-bearing fruiting bodies, but this ability can be rapidly lost during evolution. Some developmentally defective strains of M. xanthus "cheat" on proficient strains during development by superior sporulation in mixed cultures. Here, we examine transcriptomic patterns accompanying the evolution of a cheater (obligate cheater [OC]) to a developmentally competent strain (PX) by a single mutation. Using quantitative real-time-polymerase chain reaction analysis of 5 genes essential for development, we initially show that restoration of development in strain PX was associated with increased expression of 4 of these genes, not only relative to OC but also relative to the developmentally proficient ancestor of both OC and PX (wild type [WT]). Global transcriptome analyses showed further that developmental expression of well more than 100 genes differ significantly between PX and the proficient WT ancestor. Moreover, the expression profile of PX was found to differ from that of WT more than does that of the defective intermediate strain OC. These results show that the restoration of a complex trait is accompanied by novel expression patterns across a large number and wide variety of genes, rather than by a large-scale return to ancestral expression patterns.

Global analysis of phase variation in Myxococcus xanthus

“…Published protocols that have been demonstrated to work with M. xanthus and related bacteria (Britton et al ., 2002; Call et al ., 2003; Jakobsen et al ., 2004; Pham et al ., 2006; Kadam et al ., 2008) were used to generate microarray data. Printed Corning slides were generated at the Research Technology Support facility at Michigan State University and contained single prints of 70‐mer single‐stranded DNA oligomers representing 7335 of the predicted annotated 7457 M. xanthus genes.…”

Next‐generation sequencing as a tool to study microbial evolution

“…While reconstructed strains carrying this mutation show expected benefits as well as large‐scale reorganization of the developmental transcriptional programme (Fiegna et al. 2006; Kadam et al. 2008), the precise cause of these changes remains obscure.…”

Spontaneous Reversions of an Evolutionary Trait Loss Reveal Regulators of a Small RNA That Controls Multicellular Development in Myxobacteria

“…Ambient nutrient levels determine whether or not a sufficiently dense population of M. xanthus will initiate development. The process involves a cascade of intra-and intercellular signaling and large changes in gene expression patterns (32). We hypothesized that Pxr serves as a gatekeeper for the transition from vegetative growth to development and that its function is modulated by ambient nutrient levels (22).…”

“…This mutation occurred in the intergenic region between MXAN_1078, the predicted 54 response regulator (RR) nla19 gene (31), and MXAN_1079, a predicted acetyltransferase gene (22), and it caused large-scale changes in gene expression patterns during starvation, both relative to the immediate parental strain OC and relative to the developmentally proficient ancestor of OC, GJV1 (32). This genetic region was demonstrated by Northern blotting to encode two small RNA elements, one long (Pxr-L) and one short (Pxr-S), apparently from a single gene (pxr) that is predicted to encode a small RNA with a triple-stem-loop structure similar to structures of several sRNAs found in other bacterial species (22).…”