RESUMEN
The type VI secretion system (T6SS) of Gram-negative bacteria inhibits competitor cells through contact-dependent translocation of toxic effector proteins. In Proteobacteria, the T6SS is anchored to the cell envelope through a megadalton-sized membrane complex (MC). However, the genomes of Bacteroidota with T6SSs appear to lack genes encoding homologs of canonical MC components. Here, we identify five genes in Bacteroides fragilis (tssNQOPR) that are essential for T6SS function and encode a Bacteroidota-specific MC. We purify this complex, reveal its dimensions using electron microscopy, and identify a protein-protein interaction network underlying the assembly of the MC including the stoichiometry of the five TssNQOPR components. Protein TssN mediates the connection between the Bacteroidota MC and the conserved baseplate. Although MC gene content and organization varies across the phylum Bacteroidota, no MC homologs are detected outside of T6SS loci, suggesting ancient co-option and functional convergence with the non-homologous MC of Pseudomonadota.
Asunto(s)
Sistemas de Secreción Tipo VI , Sistemas de Secreción Tipo VI/genética , Membranas , Bacteroidetes , Membrana Celular , Pared CelularRESUMEN
Understanding the relationship between the composition of the human gut microbiota and the ecological forces shaping it is of great importance; however, knowledge of the biogeographical and ecological relationships between physically interacting taxa is limited. Interbacterial antagonism may play an important role in gut community dynamics, yet the conditions under which antagonistic behaviour is favoured or disfavoured by selection in the gut are not well understood. Here, using genomics, we show that a species-specific type VI secretion system (T6SS) repeatedly acquires inactivating mutations in Bacteroides fragilis in the human gut. This result implies a fitness cost to the T6SS, but we could not identify laboratory conditions under which such a cost manifests. Strikingly, experiments in mice illustrate that the T6SS can be favoured or disfavoured in the gut depending on the strains and species in the surrounding community and their susceptibility to T6SS antagonism. We use ecological modelling to explore the conditions that could underlie these results and find that community spatial structure modulates interaction patterns among bacteria, thereby modulating the costs and benefits of T6SS activity. Our findings point towards new integrative models for interrogating the evolutionary dynamics of type VI secretion and other modes of antagonistic interaction in microbiomes.
Asunto(s)
Microbioma Gastrointestinal , Microbiota , Humanos , Animales , Ratones , Proteínas Bacterianas/genética , Bacterias/genética , Microbioma Gastrointestinal/genética , Dinámica PoblacionalRESUMEN
Understanding the relationship between the composition of the human gut microbiota and the ecological forces shaping it is of high importance as progress towards therapeutic modulation of the microbiota advances. However, given the inaccessibility of the gastrointestinal tract, our knowledge of the biogeographical and ecological relationships between physically interacting taxa has been limited to date. It has been suggested that interbacterial antagonism plays an important role in gut community dynamics, but in practice the conditions under which antagonistic behavior is favored or disfavored by selection in the gut environment are not well known. Here, using phylogenomics of bacterial isolate genomes and analysis of infant and adult fecal metagenomes, we show that the contact-dependent type VI secretion system (T6SS) is repeatedly lost from the genomes of Bacteroides fragilis in adults compare to infants. Although this result implies a significant fitness cost to the T6SS, but we could not identify in vitro conditions under which such a cost manifests. Strikingly, however, experiments in mice illustrated that the B. fragilis T6SS can be favored or disfavored in the gut environment, depending on the strains and species in the surrounding community and their susceptibility to T6SS antagonism. We use a variety of ecological modeling techniques to explore the possible local community structuring conditions that could underlie the results of our larger scale phylogenomic and mouse gut experimental approaches. The models illustrate robustly that the pattern of local community structuring in space can modulate the extent of interactions between T6SS-producing, sensitive, and resistant bacteria, which in turn control the balance of fitness costs and benefits of performing contact-dependent antagonistic behavior. Taken together, our genomic analyses, in vivo studies, and ecological theory point toward new integrative models for interrogating the evolutionary dynamics of type VI secretion and other predominant modes of antagonistic interaction in diverse microbiomes.
RESUMEN
Bacteria have evolved systems dedicated to interbacterial competition. Here we highlight defenses utilized by Gram-negative cells against type VI secretion system (T6SS)-wielding competitors, including physical barriers, genetically encoded antidotes, and stress responses. Further investigation of specific and general defenses will reveal the interbacterial selective pressures impacting bacterial survival in nature.
Asunto(s)
Bacterias/metabolismo , Proteínas Bacterianas/metabolismo , Sistemas de Secreción Tipo VI/metabolismo , Bacterias/genética , Bacterias/crecimiento & desarrollo , Proteínas Bacterianas/genética , Regulación Bacteriana de la Expresión Génica , Sistemas de Secreción Tipo VI/genéticaRESUMEN
Pseudomonas aeruginosa exploits several types of motility behaviours to colonize diverse environments. One of these is swarming motility, a coordinated group movement on a semi-solid surface. This bacterium needs to express a functional flagellum and produce rhamnolipids to display this type of social motility. A ΔhptB mutant, a gene part of the Gac/Rsm signalling pathway, produces rhamnolipids and expresses a functional flagellum but has an important swarming defect. Experimental-directed evolution was performed on this mutant under swarming conditions to obtain compensatory mutations and thus identify genes responsible for its deficient swarming phenotype. Unexpectedly, a gain-of-function subpopulation emerged from this evolution with mutations in lasR, which codes for a key quorum-sensing transcriptional regulator. Furthermore, we found that lasR- mutants even emerge at high frequencies in the wild-type strain when using the same experimental evolution strategy. The resulting evolved population, largely composed of LasR-defective mutants, is fitter than the original strain in swarming motility. We also established that lasR- mutants have a growth advantage under swarming conditions when compared with wild-type. Our results demonstrate that a social phenotype, that is, swarming motility, favours the emergence of mutants deficient in a quorum-sensing regulatory pathway to the benefit of the whole population.