Abstract
Myxobacteria are fascinating and complex microbes. They prey upon other members of the soil microbiome by secreting antimicrobial proteins and metabolites, and will undergo multicellular development if starved. The genome sequence of the model myxobacterium Myxococcus xanthus DK1622 was published in 2006 and 15 years later, 163 myxobacterial genome sequences have now been made public. This explosion in genomic data has enabled comparative genomics analyses to be performed across the taxon, providing important insights into myxobacterial gene conservation and evolution. The availability of myxobacterial genome sequences has allowed system-wide functional genomic investigations into entire classes of genes. It has also enabled post-genomic technologies to be applied to myxobacteria, including transcriptome analyses (microarrays and RNA-seq), proteome studies (gel-based and gel-free), investigations into protein–DNA interactions (ChIP-seq) and metabolism. Here, we review myxobacterial genome sequencing, and summarise the insights into myxobacterial biology that have emerged as a result. We also outline the application of functional genomics and post-genomic approaches in myxobacterial research, highlighting important findings to emerge from seminal studies. The review also provides a comprehensive guide to the genomic datasets available in mid-2021 for myxobacteria (including 24 genomes that we have sequenced and which are described here for the first time).
Highlights
As of 2021, commercial services are typically offering 30x coverage of a bacterial genome for less than $70 USD, making genome sequencing an affordable activity even for undergraduate projects and laboratories without large grant incomes. This has resulted in a dramatic exponential increase in the number of available myxobacterial genome sequences (Figure 1)
Despite their traditional description as soil bacteria, it remains surprising that approximately two-thirds of myxobacterial MAGs originated from aquatic samples—both saline and freshwater (Figure 3), while less than 20% originated from soil samples, this may reflect bias in selection of sample sources for metagenomic studies rather than having any ecological significance
Other examples of myxobacterial genes gained by horizontal gene transfer (HGT) include those encoding sterol biosynthesis, an unusual phenomenon in bacteria, which myxobacteria likely acquired from eukaryotes [87]
Summary
Myxobacteria are ubiquitous soil-dwelling bacteria which have attracted considerable research interest due to their complex behaviours, ecological importance and production of potentially useful bio-active compounds [1,2]. Investigated the possibility that the large size of fruiting myxobacterial genomes was due to whole genome duplication, but found no evidence for that scenario, instead reinforcing the importance of gene duplications. Such duplications seemed to have disproportionately affected genes encoding signalling proteins (Ser/Thr protein kinases, two-component signal transduction systems), transcriptional regulators, chemosensory and motility proteins. The genome sequence of M. xanthus DK1622 revealed the presence of large gene clusters for the synthesis of secondary metabolites (biosynthetic gene clusters—BGCs), which together comprise 8.6% of the genome This percentage is approximately twice that of Streptomyces spp. genomes (which are a similar size to large myxobacterial genomes), suggesting that DK1622 has acquired additional BGCs by HGT [18]
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