Xiongfeng Dai

Bacterial growth modulation is crucial in microbial synthetic biology. In this study, we found that glutamate is an extremely poor carbon source for Escherichia coli and Bacillus subtilis. The slow growth on glutamate can be effectively overcome by the heterologous expression of glutamate transporters from Vibrio natriegens. Our results revealed that cross-species substrate transporters could be employed to shift bacterial cellular resource allocation, offering a potential genetic strategy for modulating microbial biomass growth.

To thrive in nature, bacteria have to rapidly proliferate in favorable conditions while constantly adapt to the fluctuating nutrient environments. However, the molecular players that ensure rapid growth of bacteria in favorable conditions remain poorly understood. Here, we focus on the growth physiology of Bacillus subtilis and find that codY knockout strongly compromises cell growth in rich medium. Global proteome allocation analysis has shown that codY knockout causes a “waste” of cellular resources by stimulating unnecessary expression of many proteins, further reducing the cellular investment on translation machinery. Therefore, CodY‐dependent repression is crucial in ensuring rapid growth of B. subtilis in rich medium. On the other hand, the relief of CodY‐dependent repression could promote the bacterial adaption during transition from rich medium to minimal medium by shifting resource allocation from ribosome synthesis to amino acid biosynthesis. In addition, the relief of CodY‐dependent repression in minimal medium also stimulates pathways of alternative functions such as motility and biosynthesis of secondary metabolites. Our study has thus revealed the pivotal role of CodY in bacterial growth control via governing the condition‐dependent resource allocation of B. subtilis , further shedding light on the fundamental molecular strategy of bacteria to achieve fitness maximization.

Bacteria are known to allocate their proteomes according to how fast they grow, and the allocation strategies employed strongly affect bacterial adaptation to different environments. Much of what is currently known about proteome allocation is based on extensive studies of the model organism Escherichia coli . It is not clear how much of E. coli ’s proteome allocation strategy is applicable to other species, particularly since different species can grow at vastly different rates even in the same growth condition. In this study, we investigate differences in nutrient-dependent proteome allocation programs adopted by several distantly related bacterial species, including Vibrio natriegens , one of the fastest-growing bacteria known. Extensive quantitative proteome characterization across conditions reveals an invariant allocation program in response to changing nutrients despite systemic, species-specific differences in enzyme kinetics. This invariant program is not organized according to the growth rate but is based on a common internal metric of nutrient quality after scaling away species-specific differences in enzyme kinetics, with the faster species behaving as if it is growing under a higher temperature. The flexibility of enzyme kinetics and the rigidity of proteome allocation programs across species defy common notions of evolvability and resource optimization. Our results suggest the existence of a blueprint of proteome allocation shared by diverse bacterial species, with implications on common underlying regulatory strategies. Further knowledge on the existence and organization of such phylogeny-transcending relations also promises to simplify the bottom–up description and understanding of bacterial behaviors in ecological communities.

The trade-off between rapid growth and other important physiological traits (e.g., survival and adaptability) poses a fundamental challenge for microbes to achieve fitness maximization. Studies on Bacillus subtilis biology often use strains derived after a process of lab ‘domestication’ from an ancestral strain known as Marburg strain. The domestication process led to loss of a large plasmid (pBS32) encoding a phosphatase (RapP) that dephosphorylates the Spo0F protein and thus regulates biofilm formation and sporulation. Here, we show that plasmid pBS32, and more specifically rapP, enhance growth rates by preventing premature expression of the Spo0F-Spo0A-mediated adaptive response during exponential phase. This results in reallocation of proteome resources towards biosynthetic, growth-promoting pathways without compromising long-term fitness during stationary phase. Thus, RapP helps B. subtilis to constrain physiological trade-offs and economize cellular resources for fitness improvement.

Growth rate maximization is an important fitness strategy for microbes. However, the wide distribution of slow-growing oligotrophic microbes in ecosystems suggests that rapid growth is often not favored across ecological environments. In many circumstances, there exist trade-offs between growth and other important traits (e.g., adaptability and survival) due to physiological and proteome constraints. Investments on alternative traits could compromise growth rate and microbes need to adopt bet-hedging strategies to improve fitness in fluctuating environments. Here we review the mechanistic role of trade-offs in controlling bacterial growth and further highlight its ecological implications in driving the emergences of many important ecological phenomena such as co-existence, population heterogeneity and oligotrophic/copiotrophic lifestyles.

Growth and survival are key determinants of bacterial fitness. However, how resource allocation of bacteria could reconcile these two traits to maximize fitness remains poorly understood. Here, we find that the resource allocation strategy of Bacillus subtilis does not lead to growth maximization on various carbon sources. Survival-related pathways impose strong proteome constraints on B. subtilis . Knockout of a master regulator gene, spo0A , triggers a global resource reallocation from survival-related pathways to biosynthesis pathways, further strongly stimulating the growth of B. subtilis . However, the fitness of spo0A -null strain is severely compromised because of various disadvantageous phenotypes (e.g., abolished sporulation and enhanced cell lysis). In particular, it also exhibits a strong defect in peptide utilization, being unable to efficiently recycle nutrients from the lysed cell debris to maintain long-term viability. Our work uncovers a fitness trade-off between growth and survival that governed by Spo0A-mediated proteome allocation constraints in B. subtilis , further shedding light on the fundamental design principle of bacteria.