Adaptation to Overflow Metabolism by Mutations That Impair tRNA Modification in Experimentally Evolved Bacteria

Distal Domains of the Bacterial-Exclusive Wobble-Modifying Enzyme TilS Contribute to Catalysis

tRNAIle2 lysidine synthetase (TilS) is a bacterial-specific wobble-modifying enzyme that acts on the isoleucine-accepting tRNAIle2 CAU. TilS installs a lysine at the C34 position of the anticodon, generating the lysidine modification. The resulting LAU anticodon enables exclusive decoding of infrequently used AUA isoleucine codons, rejecting AUG methionine codons. Compared to other wobble-modifying enzymes that contact only the anticodon arm of their cognate tRNAs, TilS is distinct in containing additional domains outside of the N-terminal active site. For type I TilS enzymes such as the B. cenocepacia TilS (BcTilS) investigated here, appended domains contact the tRNAIle2 substrate along the body and through the acceptor stem, up to 60 Å away from the target C34. Among bacterial tRNAs, only unmodified tRNAIle2 and tRNAMet share an anticodon, suggesting that the appended domains of TilS provide substrate recognition strategies that other wobble-modifying enzymes do not need. Here, we investigate both protein and tRNA elements to understand the strategy by which TilS accepts its cognate tRNAIle2 substrate and rejects the near-cognate tRNAMet.

History shapes regulatory and evolutionary responses to tigecycline in strains of Acinetobacter baumannii from the pre- and post-antibiotic eras

Evolutionary history encompasses genetic and phenotypic bacterial differences, but the extent to which history influences drug response and antimicrobial resistance (AMR) adaptation is unclear. Historical contingencies arise when elements from an organism's past leave lasting effects on the genome, altering the paths available for adaptation. We utilize strains isolated before and after widespread antibiotic use to study the impact of deep historical differences shaped by decades of evolution in varying antibiotic and host pressures. We evaluated these effects by comparing immediate and adaptive responses of two strains of Acinetobacter baumannii to the last-resort antibiotic, tigecycline (TGC). When grown in subinhibitory TGC, the two strains demonstrated divergent transcriptional responses suggesting that baseline transcript levels may dictate global responses to drug and their subsequent evolutionary trajectories. Experimental evolution in TGC revealed clear differences in population-genetic dynamics - with hard sweeps in populations founded by one strain and no mutations reaching fixation in the other strain. Transcriptomes of evolved populations no longer showed signatures of drug response, as was seen in the ancestors, suggesting that genetic adaptation may outweigh preexisting differences in transcriptional networks. Genetically, AMR was acquired through predictable mechanisms of increased efflux and drug target modification; however, the two strains adapted by mutations in different efflux regulators. Fitness tradeoffs of AMR were only observed in lineages evolved from the pre-antibiotic era strain, suggesting that decades of adaptation to antibiotics resulted in preexisting compensatory mechanisms in the more contemporary isolate, an important example of a beneficial effect of historical contingencies.

Comparative whole genome analysis of face-derived Streptococcus infantis CX-4 unravels the functions related to skin barrier

BACKGROUND

The skin microbiome is essential in guarding against harmful pathogens and responding to environmental changes by generating substances useful in the cosmetic and pharmaceutical industries. Among these microorganisms, Streptococcus is a bacterial species identified in various isolation sources. In 2021, a strain of Streptococcus infantis, CX-4, was identified from facial skin and found to be linked to skin structure and elasticity. As the skin-derived strain differs from other S. infantis strains, which are usually of oral origin, it emphasizes the significance of bacterial variation by the environment.

OBJECTIVE

This study aims to explore the unique characteristics of the CX-4 compared to seven oral-derived Streptococcus strains based on the Whole-Genome Sequencing data, focusing on its potential role in skin health and its possible application in cosmetic strategies.

METHODS

The genome of the CX-4 strain was constructed using PacBio Sequencing, with the assembly performed using the SMRT protocol. Comparative whole-genome analysis was then performed with seven closely related strains, utilizing web-based tools like PATRIC, OrthoVenn3, and EggNOG-mapper, for various analyses, including protein association analysis using STRING.

RESULTS

Our analysis unveiled a substantial number of Clusters of Orthologous Groups in diverse functional categories in CX-4, among which sphingosine kinase (SphK) emerged as a unique product, exclusively present in the CX-4 strain. SphK is a critical enzyme in the sphingolipid metabolic pathway, generating sphingosine-1-phosphate. The study also brought potential associations with isoprene formation and retinoic acid synthesis, the latter being a metabolite of vitamin A, renowned for its crucial function in promoting skin cell growth, differentiation, and maintaining of skin barrier integrity. These findings collectively suggest the potential of the CX-4 strain in enhancing of skin barrier functionality.

CONCLUSION

Our research underscores the potential of the skin-derived S. infantis CX-4 strain by revealing unique bacterial compounds and their potential roles on human skin.

Dynamically Regulating Glucose Uptake to Reduce Overflow Metabolism with a Quorum-Sensing Circuit for the Efficient Synthesis of d-Pantothenic Acid in Bacillus subtilis

In response to a high concentration of glucose, Bacillus subtilis, a microbial chassis for producing many industrial metabolites, rapidly takes up glucose using the phosphotransferase system (PTS), leading to overflow metabolism, a common phenomenon observed in many bacteria. Although overflow metabolism affects cell growth and reduces the production of many metabolites, effective strategies that reduce overflow metabolism while maintaining normal cell growth remain to be developed. Here, we used a quorum sensing (QS)-mediated circuit to tune the glucose uptake rate and thereby relieve overflow metabolism in an engineered B. subtilis for producing d-pantothenic acid (DPA). A low-efficiency non-PTS system was used for glucose uptake at the early growth stages to avoid a rapid glycolytic flux, while an efficient PTS system, which was activated by a QS circuit, was automatically activated at the late growth stages after surpassing a threshold cell density. This strategy was successfully applied as a modular metabolic engineering process for the high production of DPA. By enhancing the translation levels of key enzymes (3-methyl-2-oxobutanoate hydroxymethytransferase, pantothenate synthetase, aspartate 1-decarboxylase proenzyme, 2-dehydropantoate 2-reductase, dihydroxy-acid dehydratase, and acetolactate synthase) with engineered 5'-untranslated regions (UTRs) of mRNAs, the metabolic flux was promoted in the direction of DPA production, elevating the yield of DPA to 5.11 g/L in shake flasks. Finally, the engineered B. subtilis produced 21.52 g/L of DPA in fed-batch fermentations. Our work not only revealed a new strategy for reducing overflow metabolism by adjusting the glucose uptake rate in combination with promoting the translation of key metabolic enzymes through engineering the 5'-UTR of mRNAs but also showed its power in promoting the bioproduction of DPA in B. subtilis, exhibiting promising application prospects.