Global gene expression analysis of the Myxococcus xanthus developmental time course

Sharma, Gaurav; Yao, Andrew I.; Smaldone, Gregory T.; Liang, Jennifer O.; Long, Matt; Facciotti, Marc T.; Singer, Mitchell

doi:10.1016/j.ygeno.2020.11.030

Cited by 18 publications

(35 citation statements)

References 74 publications

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“…As a quality control of the RNAseq data, we observed that the expression patterns of four developmentally regulated genes matched those from previous reports, with spiA , fruA , and devT showing substantial early upregulation, and fmgE demonstrating transcription later during development (Fig. 2 a-d) [ 26 , 34 , 35 , 54 ]. We also looked more generally at expression in 95 previously identified genes specifically important for fruiting body formation and sporulation [ 32 ].…”

Section: Resultssupporting

confidence: 83%

“…In contrast, the methods used in this work to induce fruiting body formation and to generate the transcriptomes are similar to those used by Sharma at al, so we were able to compare our results to theirs [ 35 ]. We carried out pairwise comparisons of data from all timepoints in both studies for both WT and ΔfruA strains, and looked at Pearson correlations, Spearman correlations, and scatter plots comparing expression for each gene (Additional file 9 ).…”

Section: Discussionmentioning

confidence: 99%

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Transcriptomic analysis of the Myxococcus xanthus FruA regulon, and comparative developmental transcriptomic analysis of two fruiting body forming species, Myxococcus xanthus and Myxococcus stipitatus

et al. 2021

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Background The Myxococcales are well known for their predatory and developmental social processes, and for the molecular complexity of regulation of these processes. Many species within this order have unusually large genomes compared to other bacteria, and their genomes have many genes that are unique to one specific sequenced species or strain. Here, we describe RNAseq based transcriptome analysis of the FruA regulon of Myxococcus xanthus and a comparative RNAseq analysis of two Myxococcus species, M. xanthus and Myxococcus stipitatus, as they respond to starvation and begin forming fruiting bodies. Results We show that both species have large numbers of genes that are developmentally regulated, with over half the genome showing statistically significant changes in expression during development in each species. We also included a non-fruiting mutant of M. xanthus that is missing the transcriptional regulator FruA to identify the direct and indirect FruA regulon and to identify transcriptional changes that are specific to fruiting and not just the starvation response. We then identified Interpro gene ontologies and COG annotations that are significantly up- or down-regulated during development in each species. Our analyses support previous data for M. xanthus showing developmental upregulation of signal transduction genes, and downregulation of genes related to cell-cycle, translation, metabolism, and in some cases, DNA replication. Gene expression in M. stipitatus follows similar trends. Although not all specific genes show similar regulation patterns in both species, many critical developmental genes in M. xanthus have conserved expression patterns in M. stipitatus, and some groups of otherwise unstudied orthologous genes share expression patterns. Conclusions By identifying the FruA regulon and identifying genes that are similarly and uniquely regulated in two different species, this work provides a more complete picture of transcription during Myxococcus development. We also provide an R script to allow other scientists to mine our data for genes whose expression patterns match a user-selected gene of interest.

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Section: Resultssupporting

confidence: 83%

Section: Discussionmentioning

confidence: 99%

Transcriptomic analysis of the Myxococcus xanthus FruA regulon, and comparative developmental transcriptomic analysis of two fruiting body forming species, Myxococcus xanthus and Myxococcus stipitatus

et al. 2021

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“…Subsequent analysis of the RNA-seq data was also able to identify tens of non-coding RNAs in the M. xanthus transcriptome, many of which were differentially regulated by nutrient availability [ 69 ]. Subsequently, RNA-seq studies have investigated the regulation of fruiting body formation—variously identifying eight or ten distinct sets of expression profiles [ 122 , 123 ], differentiation of peripheral rods—specialised developmental cell types [ 124 ], and genes whose expression was induced by UV light—which included BGCs as well as genes of the LexA/SOS response [ 125 ].…”

Section: Myxobacterial Post-genomicsmentioning

confidence: 99%

Myxobacterial Genomics and Post-Genomics: A Review of Genome Biology, Genome Sequences and Related ‘Omics Studies

2021

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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).

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“…Withstanding regular confinement endeavors, myxospores sprout with the onset of favorable conditions into full-fledged structures, with the exception of depicted facultative anaerobic species, Anaeromyxobacter dehalogenans [ 7 ]. Recently, a large number of studies have been performed to gain a detailed account of the Myxobacterial properties along with types, dynamics and biogenesis of Myxobacteria-derived secondary metabolites [ 8 , 9 , 10 , 11 , 12 ].…”

Section: Introductionmentioning

confidence: 99%

Myxobacteria as a Source of New Bioactive Compounds: A Perspective Study

et al. 2021

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Myxobacteria are unicellular, Gram-negative, soil-dwelling, gliding bacteria that belong to class δ-proteobacteria and order Myxococcales. They grow and proliferate by transverse fission under normal conditions, but form fruiting bodies which contain myxospores during unfavorable conditions. In view of the escalating problem of antibiotic resistance among disease-causing pathogens, it becomes mandatory to search for new antibiotics effective against such pathogens from natural sources. Among the different approaches, Myxobacteria, having a rich armor of secondary metabolites, preferably derivatives of polyketide synthases (PKSs) along with non-ribosomal peptide synthases (NRPSs) and their hybrids, are currently being explored as producers of new antibiotics. The Myxobacterial species are functionally characterized to assess their ability to produce antibacterial, antifungal, anticancer, antimalarial, immunosuppressive, cytotoxic and antioxidative bioactive compounds. In our study, we have found their compounds to be effective against a wide range of pathogens associated with the concurrence of different infectious diseases.

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Global gene expression analysis of the Myxococcus xanthus developmental time course

Cited by 18 publications

References 74 publications

Transcriptomic analysis of the Myxococcus xanthus FruA regulon, and comparative developmental transcriptomic analysis of two fruiting body forming species, Myxococcus xanthus and Myxococcus stipitatus

Transcriptomic analysis of the Myxococcus xanthus FruA regulon, and comparative developmental transcriptomic analysis of two fruiting body forming species, Myxococcus xanthus and Myxococcus stipitatus

Myxobacterial Genomics and Post-Genomics: A Review of Genome Biology, Genome Sequences and Related ‘Omics Studies

Myxobacteria as a Source of New Bioactive Compounds: A Perspective Study

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