Molecular Origins of Transcriptional Heterogeneity in Diazotrophic Klebsiella oxytoca

• Published in: mSystems Vol. 7; no. 5; p. e0059622
• Main Authors: Bashir, Tufail, Brackston, Rowan D, Waite, Christopher, Kotta-Loizou, Ioly, Carey, Matthew R, Engl, Christoph, Buck, Martin, Schumacher, Jörg
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 26.10.2022
• Subjects: Ammonia; Bacterial Proteins - genetics; Biotechnology; Fluorescence in situ hybridization; Gene expression; In Situ Hybridization, Fluorescence; Kinases; Klebsiella oxytoca; Klebsiella oxytoca - genetics; mathematical modeling; Molecular and Cellular Biology; Nitrogen; Nitrogen - metabolism; Nitrogen cycle; Nitrogen fixation; Nitrogen-fixing bacteria; Nitrogenase; Nitrogenase - genetics; Population; Propagation; Research Article; RNA polymerase; RNA probes; Stochasticity; Transcription; Transcription, Genetic; transcriptional regulation; mathematical modeling; nitrogen fixation; transcriptional regulation
• ISSN: 2379-5077; 2379-5077
• DOI: 10.1128/msystems.00596-22

Phenotypic heterogeneity in clonal bacterial batch cultures has been shown for a range of bacterial systems; however, the molecular origins of such heterogeneity and its magnitude are not well understood. Under conditions of extreme low-nitrogen stress in the model diazotroph Klebsiella oxytoca, we found remarkably high heterogeneity of gene expression, which codes for the structural genes of nitrogenase, one key enzyme of the global nitrogen cycle. This heterogeneity limited the bulk observed nitrogen-fixing capacity of the population. Using dual-probe, single-cell RNA fluorescent hybridization, we correlated expression with that of and - , which code for the main upstream regulatory components. Through stochastic transcription models and mutual information analysis, we revealed likely molecular origins for heterogeneity in nitrogenase expression. In the wild type and regulatory variants, we found that transcription was inherently bursty, but we established that noise propagation through signaling was also significant. The regulatory gene had the highest discernible effect on variance, while noise from factors outside the regulatory pathway were negligible. Understanding the basis of inherent heterogeneity of nitrogenase expression and its origins can inform biotechnology strategies seeking to enhance biological nitrogen fixation. Finally, we speculate on potential benefits of diazotrophic heterogeneity in natural soil environments. Nitrogen is an essential micronutrient for both plant and animal life and naturally exists in both reactive and inert chemical forms. Modern agriculture is heavily reliant on nitrogen that has been "fixed" into a reactive form via the energetically expensive Haber-Bosch process, with significant environmental consequences. Nitrogen-fixing bacteria provide an alternative source of fixed nitrogen for use in both biotechnological and agricultural settings, but this relies on a firm understanding of how the fixation process is regulated within individual bacterial cells. We examined the cell-to-cell variability in the nitrogen-fixing behavior of Klebsiella oxytoca, a free-living bacterium. The significance of our research is in identifying not only the presence of marked variability but also the specific mechanisms that give rise to it. This understanding gives insight into both the evolutionary advantages of variable behavior as well as strategies for biotechnological applications.