Transcriptional patterns of the mutL-miaA superoperon of Escherichia coli K-12 suggest a model for posttranscriptional regulation

Abstract

The complex amiB-mutL-miaA-hfq-hflX-hflK-hflC superoperon of E coli contains important genes for several fundamental cellular processes, including cell-wall hydrolysis ( amiB), DNA repair ( mutL), tRNA modification ( miaA) and proteolysis ( hflX-hflK-hflC). We report here the transcriptional pattern and possible posttranscriptional regulation of mutL, miaA and hfq genes of this superoperon. RNase protection analysis of mRNA transcribed from the bacterial chromosome demonstrated that there is co-transcription of mutl and miaA. In addition, two internal promoters, P miaA and P1 hfq were identified and mapped to 201 and 837 nucleotides upstream from the respective translation start sites. P miaA contains poor matches to the −10 and −35 regions of the sigma-70 RNA polymerase concensus sequences, but it contains multiple potential Fis-binding sites and an upstream AT-rich region with poly(A) sequences. The basic arrangement of Fis-binding sites followed by an AT rich region is shared with promoters for rRNA operons and some of the tRNA and tRNA modification genes. As part of an initial study of mutL and miaA regulation, we measured transcript amounts in isogenic rne, rnc and rne rnc double mutants which are deficient in RNase E, RNase III or both. The amounts of steady state level mutL-miaA cotranscript, P miaA transcript and Pl hfq transcript increased eight-, nine- and three-fold respectively in an rne3071 mutant when compared to the rne + parent. In contrast, amounts of the three transcripts were the same in an rnc105 mutant and its rnc + parent. These results indicate that mutL, miaA, and hfq expression could be regulated by multiple mechanisms, including degree of cotranscription from upstream genes, modulation of internal promoter strength, and by RNase E activity. A model is presented for RNase E-mediated posttranscriptional regulation that may coordinated mutL expression with replication and miaA with tRNA amounts under different growth conditions, especially during nutrient upshifts.