Summary:
YefM is a transcriptional DNA-binding autorepressor for the yefM-yoeB operon. In addition, YefM also functions as an antitoxin to form a complex with YoeB, which is a toxin that is counteracted by YefM antitoxin [1] YefM can bind alone with low affinity to the yefM-yoeB operator, but together with YoeB it has an enhanced DNA-binding affinity compared to free YefM [1] YoeB enhances the interaction with YefM by affecting the YefM conformation to one that is more favorable for DNA binding and/or by stabilizing the nucleoprotein complex at the operator site and reducing basal expression of the yefM-yoeB operon [1, 3]
The yefM gene is upregulated during growth in biofilms [4]and yefM-yoeB is upregulated in persister cells [5] it is probable that derepression of yefM-yoeB autoregulation occurs in these circumstances in response to an as-yet-unknown environmental or cell cycle signal(s) that interferes with the YefM-YoeB-operator interaction [3]
The operator site 5' of yefM-yoeB comprises adjacent long (L) and short (S) palindromes with core 5'-TGTACA-3' motifs with a center-to-center distance of 12 bp [1] which was suggested to be crucial for the correct stable positioning of YefM-YoeB at the two repeats [3] The palindrome L covers the whole -10 box and the S palindrome surrounds the transcription start site; because of these placements, the YoeB-YefM complex specifically represses the transcription of the system by blocking RNA polymerase binding [2].This sequence organization is common in yefM-yoeB regulatory regions in diverse genomes, suggesting that interaction of YefM-YoeB with these motifs is a conserved mechanism of operon autoregulation [1]
The -35 region of the yefM-yoeB promoter does not have the conserved motif of σ70 promoters, and this results in a low transcriptional activity relative to that of other toxin-antitoxin operons with the cognate motif (i.e., axe-txe) [2].
The sequences of the core repressor binding sites of homologous toxin-antitoxin systems can be nearly identical; however, they can be differently positioned in relation to the main promoter elements, resulting in important differences in the level of transcription repression [2].
YefM originally was described as a native unstructured protein [6] later it was reevaluated as experimental, and modeling data have demonstrated that the protein is at least partially folded [1, 7]and dimeric [1]
The YefM antitoxin forms a heterotrimeric complex with the YoeB toxin (YefM2-YoeB) [8, 9] The tertiary structure of the YoeB toxin and the YefM2-YoeB complex has been described [9] In the complex, one C terminus in the YefM homodimer is unfolded and the other one shows an α-helical conformation and conceals the endoribonuclease fold of YoeB.
Two N-terminal segments of YefM form a symmetrical dimer within the YefM
2-YoeB heterotrimeric complex and do not contact YoeB directly
[3]
YefM does not possess a canonical DNA-binding motif, but instead a pair of basic residues, R10 and R31, conserved in many YefM homologs are absolutely necessary for DNA binding by the YefM-YoeB complex
[3, 9, 10]
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis