Caro, E. A. | Search bioRxiv

bioRxiv2023

Stochastic bounds of aggregation dynamics distinguish near-wild-type from wild-type strains in social bacteria

The genotype-to-phenotype problem (G2P) for multicellular development asks how genetic inputs control collective phenotypic outputs. It is a difficult problem even to observe. On the genotype side, the phenotypic impact of mutation is often subtle due at least partly to gene redundancy and myriad other factors. On the phenotype side, biological and even technical developmental replicates can display significant phenotypic variation due at least in part to stochasticity, again with other factors. We attempt to partially resolve the G2P inputs and outputs from the obfuscating effects of factors like redundancy and stochasticity. As a model organism, we selected the biofilm-forming species Myxococcus xanthus, a motile self-organizing bacterium that forms three-dimensional cell aggregates that grow and mature into spore-filled fruiting bodies when under starvation stress. We developed data acquisition tools and analysis and visualization methods that can produce a topological map of M. xanthus development. We demonstrate that even subtle effects on developmental dynamics caused by mutation can be identified, discriminated, characterized, and given statistical significance.

biophysics↗

bioRxiv2021

Unraveling a Bacterial Starvation Response Through the Direct Targets of a Starvation-Induced Transcriptional Activator

Organisms frequently encounter environments with nutrient shortages and their survival depends on changes in physiology and the ability to conserve resources. In bacteria, many physiological changes associated with starvation have been identified, but the underlying genetic components and regulatory networks that direct these physiological changes are often poorly defined. Here, we aimed to better define the gene regulatory networks that mediate the starvation response in Myxococcus xanthus, a bacterium that copes with starvation by producing fruiting bodies filled with dormant and stress-resistant spores. We focused on the direct promoter/gene targets of Nla28, a transcriptional activator/enhancer binding protein (EBP) that is important for early rounds of gene expression following starvation. Using expression profiling to identify genes that are downregulated in nla28 mutant cells and bioinformatics to identify the putative promoters of these genes, 12 potential promoter targets (37 genes) of Nla28 were identified. The results of in vitro promoter binding assays, coupled with in vitro and in vivo mutational analyses, suggested that the 12 promoters are in vivo targets of Nla28 and that Nla28 dimers use tandem, imperfect repeats of an 8-bp sequence for binding. Interestingly, nine of the Nla28 target promoters are intragenic, located in the protein coding sequence of an upstream gene or in the protein coding sequence of one gene within an operon (internal promoters). Based on mutational analyses, we concluded that the 12 Nla28 target loci contain at least one gene important for production of stress-resistant spores following starvation. Most of these loci contain genes predicted to be involved in regulatory or defense-related functions. Using the consensus Nla28 binding sequence, followed by bioinformatics and expression profiling, 58 additional promoters and 102 genes were tagged as potential Nla28 targets. Among these putative Nla28 targets, functions such as regulatory, metabolic and cell envelope biogenesis were commonly assigned to genes.

microbiology↗