Evolution of sensory complexity recorded in a myxobacterial genome

Abstract

Myxobacteria are single-celled, but social, eubacterial predators. Upon starvation they build multicellular fruiting bodies using a developmental program that progressively changes the pattern of cell movement and the repertoire of genes expressed. Development terminates with spore differentiation and is coordinated by both diffusible and cell-bound signals. The growth and development of Myxococcus xanthus is regulated by the integration of multiple signals from outside the cells with physiological signals from within. A collection of M. xanthus cells behaves, in many respects, like a multicellular organism. For these reasons M. xanthus offers unparalleled access to a regulatory network that controls development and that organizes cell movement on surfaces. The genome of M. xanthus is large (9.14 Mb), considerably larger than the other sequenced delta-proteobacteria. We suggest that gene duplication and divergence were major contributors to genomic expansion from its progenitor. More than 1,500 duplications specific to the myxobacterial lineage were identified, representing >15% of the total genes. Genes were not duplicated at random; rather, genes for cell-cell signaling, small molecule sensing, and integrative transcription control were amplified selectively. Families of genes encoding the production of secondary metabolites are overrepresented in the genome but may have been received by horizontal gene transfer and are likely to be important for predation.

Fig. 1.

The lifecycle of M. xanthus. A swarm (a group of moving and interacting cells) can have either of two fates depending on their environment. The fruiting body (A) is a spherical structure of ≈1 × 10⁵ cells that have become stress-resistant spores (B). The fruiting body is small (0.10 mm high) and sticky, and its spores are tightly packed. When a fruiting body receives nutrients, the individual spores germinate (C) and thousands of M. xanthus cells emerge together as an “instant” swarm (D). When prey is available (micrococci in the figure), the swarm becomes a predatory collective that surrounds the prey. Swarm cells feed by contacting, lysing, and consuming the prey bacteria (E and F). Fruiting body development is advantageous given the collective hunting behavior. Nutrient-poor conditions elicit a unified starvation stress response. That response initiates a self-organized program that changes cell movement behavior, leading to aggregation. The movement behaviors include wave formation (G) and streaming into mounded aggregates (H), which become spherical (A). Spores differentiate within mounded and spherical aggregates. We use the term “swarming” in its general sense to denote a process “in which motile organisms actively spread on the surface of a suitably moist solid medium” (81).

Fig. 2.

Genome map: a single circle. The entire genome is summarized in five layers. The two outermost layers represent the genes expressed in the clockwise direction (layer 1) and the counterclockwise direction (layer 2). The role of genes such as fatty acid and phospholipids, metabolism, cell envelope, amino acid biosynthesis, DNA metabolism, protein synthesis, central intermediary metabolism, energy metabolism, and regulatory functions are color-coded. Layer 3 shows the lineage-specific duplications that are discussed in Results. The enzymes that catalyze production of secondary metabolites are in layer 4. Base pair 1 was assigned to the predicted origin of replication, located by GC nucleotide skew (82) among genes in the dnaA, dnaN, recF, and gyrA region. Layer 5 plots the GC skew.

Fig. 3.

The number of one-component, DNA-binding response regulators depends on genome size. The number of one-component, DNA-binding response regulators is plotted vs. genome size for 13 completely sequenced soil bacteria. The linear correlation between genome size and number of DNA-binding transcriptional regulators (excluding M. xanthus) is 97% over the range from 1.8 Mb for Thermatoga maritima to 9.0 Mb for St. avermitilis. St. coelicolor A3 (2) (8.6 Mb), Burkholderia pseudomallei K96243 (7.2 Mb), Pseudomonas putida KT 2440 (6.1 Mb), Bacillus cereus ATCC 14579 (5.5 Mb), Shewanella oneidensis MR-1 (5.1 Mb), Caulobacter crescentus CB 15 (4.0 Mb), G. sulfurreducens PCA (3.8 Mb), De. vulgaris Hildenborough (3.5 Mb), and Deinococcus radiodurans R1 (3.0 Mb) are also included.