Temporal evolution of master regulator Crp identifies pyrimidines as catabolite modulator factors

Abstract

The evolution of microorganisms often involves changes of unclear relevance, such as transient phenotypes and sequential development of multiple adaptive mutations in hotspot genes. Previously, we showed that ageing colonies of an E. coli mutant unable to produce cAMP when grown on maltose, accumulated mutations in the crp gene (encoding a global transcription factor) and in genes involved in pyrimidine metabolism such as cmk; combined mutations in both crp and cmk enabled fermentation of maltose (which usually requires cAMP-mediated Crp activation for catabolic pathway expression). Here, we study the sequential generation of hotspot mutations in those genes, and uncover a regulatory role of pyrimidine nucleosides in carbon catabolism. Cytidine binds to the cytidine regulator CytR, modifies the expression of sigma factor 32 (RpoH), and thereby impacts global gene expression. In addition, cytidine binds and activates a Crp mutant directly, thus modulating catabolic pathway expression, and could be the catabolite modulating factor whose existence was suggested by Jacques Monod and colleagues in 1976. Therefore, transcription factor Crp appears to work in concert with CytR and RpoH, serving a dual role in sensing both carbon availability and metabolic flux towards DNA and RNA. Our findings show how certain alterations in metabolite concentrations (associated with colony ageing and/or due to mutations in metabolic or regulatory genes) can drive the evolution in non-growing cells.

Unified Access to Pyrimidines and Quinazolines Enabled by N–N Cleaving Carbon Atom Insertion

“…Heterocycles are highly valuable scaffolds for medicinal chemistry, as evidenced by their presence in a majority of biologically active compounds. , More specifically, pyrimidines and quinazolines are frequently featured substructures in drug discovery campaigns and remain popular, appearing, for example, in the recently approved kinase inhibitor Belumosudil and the classic HMG-CoA reductase inhibitor Rosuvastatin (Figure A). − …”

“… 1 , 2 More specifically, pyrimidines and quinazolines are frequently featured substructures in drug discovery campaigns and remain popular, appearing, for example, in the recently approved kinase inhibitor Belumosudil and the classic HMG-CoA reductase inhibitor Rosuvastatin ( Figure 1 A). 3 − 10 …”

Inactivation of the Pyrimidine Biosynthesis pyrD Gene Negatively Affects Biofilm Formation and Virulence Determinants in the Crohn’s Disease-Associated Adherent Invasive Escherichia coli LF82 Strain

“…While the role of curli fibers in AIEC infection has not yet been fully characterised, type 1 fimbriae are considered bona fide AIEC virulence factors that are able to promote bacterial adhesion to epithelial cells [ 18 ]. Interestingly, the expression of both curli fibers- and type 1 pili-encoding genes are negatively regulated in the presence of glucose in LF82, suggesting positive control by the CAP master regulator [ 25 ], whose activity appears to respond also to pyrimidine intracellular concentrations, as recently proposed [ 51 ]. At any rate, the inhibition of pyrimidine biosynthesis appears to have a very extensive impact on AIEC adhesion factors, reiterating its potential as a target for antimicrobial drugs.…”

Missing Links Between Gene Function and Physiology in Genomics

“…Yet, years later it was shown that virtually identical CRP orthologs found in other bacterial species [e.g., Pseudomonas ( Milanesio et al, 2011 )] have nothing whatsoever to do with metabolism but play a role in membrane-related functions. Finally, recent data suggest that in reality CRP in E. coli is not only a promoter-specific regulator but also an authentic genome-scaffolding protein ( Heyde et al, 2021 ) which responds not just to cAMP but to other physiological effectors like cytidine ( Lauritsen et al, 2021 ) and thus has an additional global role. This highlights the importance of maintaining ontologies and the databases relying on them up to date to represent as closely as possible the current state of knowledge.…”