Natural transformation is a key mechanism of bacterial adaptation in which exogenous DNA (eDNA) is taken up, processed into single-stranded DNA (ssDNA), and integrated into the genome. While earlier studies primarily focused on uptake mechanisms, transport proteins, and recombination processes, exonucleases were long regarded as merely nonspecific degradation enzymes in DNA uptake. However, recent studies show that nucleases, partly related to the SOS response, play a key role in processing uptake ssDNA. They affect the imported DNA, thereby promoting efficient recombination. This review highlights the interactions between nucleases and taken-up ssDNA, discusses the functional link between natural competence and the bacterial SOS damage response, and demonstrates that key components of these processes have been conserved in bacteria. This suggests a possible universal principle in which ssDNA-specific nucleases serve as switches between the DNA damage response, competence, and horizontal gene transfer.
Rebecca Hinrichs· Biochimica et biophysica act...· 0 citations
Diadenosine tetraphosphate (Ap4A) and related dinucleoside tetraphosphates (Ap4Ns) are important stress-signalling molecules that coordinate bacterial adaptation to changing environmental conditions. Although the enzymes for turnover of Ap4A are known in several bacteria, the structural basis for substrate recognition and the cellular consequences of impaired Ap4A turnover remain poorly understood. Here, we characterize the Histidine-Aspartate (HD)-domain hydrolase YqeK from Bacillus subtilis. Deletion of yqeK impaired growth in stationary-phase, sporulation, and biofilm formation demonstrating a general role upon nutrient limitation. YqeK forms a homodimer and functions as a manganese-dependent phosphohydrolase symmetrically cleaving Ap4A into two ADP molecules and removing Ap4A caps from RNA. The enzyme was active not only toward Ap4A but also toward the mixed dinucleotides Ap4G, Ap4C, and Ap4U in both in vitro and in vivo assays, hence acting as a broad-spectrum regulator of Ap4N homeostasis. To understand this promiscuity, we determined crystal structures of YqeK in its apo- and ADP-bound state and in complex with a non-hydrolysable Ap4A analogue. The structures revealed an asymmetric recognition mechanism in which one nucleoside moiety and the proximal phosphate groups are tightly coordinated, whereas the distal nucleoside is accommodated largely through nonspecific interactions, explaining the ability of YqeK to process diverse substrates. Together, our findings establish YqeK as a central regulator of dinucleotide homeostasis and RNA metabolism and provide the structural framework for Ap4N recognition by HD-domain phosphohydrolases.
Renuka Dharani Shivakumar, Natalie Happel, Fabiana Burchert et al.· Journal of Biological Chemis...· 0 citations
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