Evolution and regulation of microbial secondary metabolism

Abstract

Many bacteria have an incredible ability to swarm cooperatively over surfaces. But swarming phenotypes can be quite different even between strains of the same species. What drives this diversity? We compared the metabolomes of 29 clinical Pseudomonas aeruginosa isolates with a range of swarming phenotypes. We identified that isolates incapable of secreting rhamnolipids—a surfactant needed for swarming—had perturbed tricarboxylic acid (TCA) cycle and amino acid pathways and grew exponentially slower in glycerol minimal medium. Analysis of the metabolome signatures and simulations using a genome-scale model led to a mechanism which joins these observations: Strains subject to higher oxidative stress levels grow slower and shut down rhamnolipids secretion, a carbon overflow mechanism possibly to direct carbon resources towards costly stress response pathways to maintain cell viability. In vitro experiments confirmed that rhamnolipid non-producers deal worse with oxidative stress, linking intracellular redox homeostasis—a individual-level trait—to swarming—a population-level behavior. This mechanism helps explain the metabolic constraints on bacteria when secreting byproducts to interact with others—competitively and cooperatively—in microbial communities.SignificanceSwarming motility has been associated with virulence of many human bacterial pathogens. The pathogen Pseudomonas aeruginosa swarms by cooperatively secreting surfactants called rhamnolipids to lubricate surfaces. To understand why some P. aeruginosa strains swarm and others do not, we combined metabolomics, computational modeling and in vitro experiments to study the different swarming behaviors of 29 isolates of Pseudomonas aeruginosa obtained from infected patients. We found that strains can only produce rhamnolipids if they can maintain redox homeostasis. We propose that single cells must have low internal redox stress levels before they can produce rhamnolipids, which work as an overflow of carbon metabolism into a cooperative secretion that brings a fitness benefit to the entire swarming population. This mechanism links single-cell physiology and a population-level cooperative behavior key to the fitness and virulence of P. aeruginosa, a major source of hospital acquired infections.SynopsisThis study combined metabolomics, computational modeling and experiments to explain the swarming diversity in Pseudomonas aeruginosa, yielding new insights on the genetic and metabolic controls of bacterial swarming behaviorRhamnolipid secretion is necessary, but insufficient, for swarmingP. aeruginosa strains unable to produce rhamnolipids in the glycerol minimal medium have perturbed metabolism, slow growth and elevated oxidative stressRhamnolipid producers cannot produce rhamnolipids in succinate as the sole carbon source which causes greater ROS (reactive oxygen species) productionThe requirement of redox homeostasis for rhamnolipid production ensures that the overflow of precious carbon for population-level benefit is prudently controlledThis study helps linking single cell physiology with collective behavior key to the fitness and virulence of a pathogenic bacterium.

The Impacts of Microgravity on Bacterial Metabolism

“…Secondary metabolites (also referred to as specialized metabolites), are bioactive compounds that can have potential advantageous properties including antioxidant, growth-promoting, anti-allergic, anti-inflammatory, anticancer, antihypertensive and antimicrobial properties, or can have potentially negative properties such as being carcinogenic or toxic/pathogenic [ 88 , 89 ] Secondary metabolites have also been reported to help maintain cellular homeostasis by regulating carbon and nitrogen flow in the cell [ 90 ], by re-generating intracellular NAD + concentrations [ 90 , 91 , 92 ] and by relieving cellular oxidative stress [ 93 ]. Most of these molecules are polyketides and non-ribosomal peptides and are produced by biochemical pathways that are encoded in discrete gene clusters.…”

Secondary metabolite profiling of Pseudomonas aeruginosa isolates reveals rare genomic traits

“…The remarkable phylogenetic and phenotypic diversity of P. aeruginosa, including varied virulence mechanisms, conversion to mucoid by overproduction of alginate, and altered quorum sensing (QS) pathways contribute to its survival in varied environments [1][2][3][4][5]. One mechanism P. aeruginosa uses to interact with its environment is through the production of secondary metabolites [6][7][8]. These compounds are known to mediate a variety of virulence mechanisms used by P. aeruginosa in the host environment, including swarming motility, QS, iron acquisition, and the production of reactive oxygen species [9][10][11].…”

In Silico Exploration of Mycobacterium tuberculosis Metabolic Networks Shows Host-Associated Convergent Fluxomic Phenotypes

“…GEMs have been used with success to predict phenotypes such as substrate utilization, gene essentiality, production of virulence factors or response to oxidative stress in different microorganisms [22][23][24]. In the context of M. tuberculosis, not only have they been used with similar aims [25,26], but also to determine the metabolic rewiring produced by subinhibitory concentrations of antibiotics, to assess the effect of SNPs in metabolic genes or to determine condition-specific biomass compositions, such as during infection [27][28][29].…”