Biology subjects

Junkins, E. N.

Publications and source records attributed to Junkins, E. N..

2 recordsLinked to original sources

bioRxiv2023

Targeted hypermutation of putative antigen sensors in multicellular bacteria

Diversity-generating retroelements (DGRs) are used by bacteria, archaea and viruses as a targeted mutagenesis tool. Through error-prone reverse transcription, DGRs introduce random mutations at specific genomic loci, enabling rapid evolution of these targeted genes. However, the function and benefits of DGR-diversified proteins in cellular hosts remains elusive. We find that 85% of DGRs from one of the major monophyletic lineages of DGR reverse transcriptases are encoded by multicellular bacteria, which often have two or more DGR loci in their genomes. Using the multicellular purple sulfur bacterium Thiohalocapsa sp. PB-PSB1 as an example, we characterized nine distinct DGR loci that cumulatively lead to more than 10294 possible different combinations of target polypeptides. With environmental metagenomes from individual Thiohalocapsa aggregates, we show that most of PB-PSB1s DGR targets are diversified across its biogeographic range, with spatial heterogeneity in the diversity of each locus. In PSB1 and other members of this lineage of cellular DGRs, diversified target genes are associated with NACHT-domain anti-phage defenses and putative ternary conflict systems previously shown to be enriched in multicellular bacteria. We propose that these DGR-diversified target genes act as antigen sensors that confer a form of adaptive immunity to their multicellular consortia. These findings have implications for the emergence of multicellularity, as the NACHT-domain anti-phage systems and ternary systems share both domain homology and conceptual similarities with the innate immune and programmed cell death pathways of plants and metazoans. SignificanceTo defend themselves against predators, bacteria employ a wide range of conflict systems, some of which are enriched in multicellular bacteria. Here, we show that numerous multicellular bacteria use related diversity-generating retroelements (DGRs) to diversify such conflict systems. Error-prone reverse transcription in DGRs introduces random, targeted mutations and rapid diversification. We used Thiohalocapsa PB-PSB1, a member of multicellular bacterial consortia, as a model to study this association between conflict systems and DGRs. We characterized the natural diversity of PB-PSB1 DGRs and propose they function as hypervariable antigen sensors. The accumulation of such DGR-diversified defense systems in multicellular bacteria emphasizes the fitness advantage of a rapidly diversifying immune system for the evolution of multicellularity.

microbiology↗

bioRxiv2020

High-Throughput Sequencing can be used to Measure and Maximize Cultivated Diversity

Molecular techniques continue to reveal a growing disparity between the immense diversity of microbial life and the small proportion that is in pure culture. The disparity, originally dubbed "the great plate count anomaly" by Staley and Konopka, has become even more vexing given our increased understanding of the importance of microbiomes to a host and the role of microorganisms in the vital biogeochemical functions of our biosphere. Searching for novel antimicrobial drug targets often focuses on screening a broad diversity of microorganisms. If diverse microorganisms are to be screened, they need to be cultivated. Recent innovative research has used molecular techniques to assess the efficacy of cultivation efforts, providing invaluable feedback to cultivation strategies for isolating targeted and/or novel microorganisms. Here, we aimed to determine the efficiency of cultivating representative microorganisms from a non-human, mammalian microbiome, identify those microorganisms, and determine the bioactivity of isolates. Molecular methods indicated that around 57% of the ASVs detected in the original inoculum were cultivated in our experiments, but nearly 53% of the total ASVs that were present in our cultivation experiments were not detected in the original inoculum. In light of our controls, our data suggests that when molecular tools were used to characterize our cultivation efforts, they provided a more complete, albeit more complex, understanding of which organisms were present compared to what was eventually cultivated. Lastly, about 3% of the isolates collected from our cultivation experiments showed inhibitory bioactivity against a multidrug-resistant pathogen panel, further highlighting the importance of informing and directing future cultivation efforts with molecular tools. ImportanceCultivation is the definitive tool to understand a microorganisms physiology, metabolism, and ecological role(s). Despite continuous efforts to hone this skill, researchers are still observing yet-to-be cultivated organisms through high-throughput sequencing studies. Here, we use the very same tool that highlights biodiversity to assess cultivation efficiency. When applied to drug discovery, where screening a vast number of isolates for bioactive metabolites is common, cultivating redundant organisms is a hindrance. However, we observed that cultivating in combination with molecular tools can expand the observed diversity of an environment and its community, potentially increasing the number of microorganisms to be screened for natural products.

microbiology↗