Methylation-related Epigenetic Signals in Bacterial DNA

Abstract

The term “epigenetic signals” may seem extraneous to the life-style of bacteria, because the classic concept of epigenetics has been applied to the changes in gene expression that govern differentiation and development (Waddington 1956). However, because differentiation is often associated with changes in DNA or chromatin structure (Holliday and Pugh 1975; Riggs 1975), DNA modification has provided an attractive model for the study of epigenetic regulation.

In prokaryotes, the most common DNA modification is methylation: For instance, DNAs from enteric bacteria contain minor amounts of 6-methyladenine and 5-methylcytosine (Marinus 1987). Base modifications are formed by two classes of methylases: (1) those associated with restriction/modification systems (Bickle and Krüger 1993) and (2) two methyltransferases that do not have a restriction enzyme counterpart: the Dam methylase (DNA adenine methyltransferase) and the Dcm methylase (DNA cytosine methyltransferase). Both enzymes transfer a methyl group from S-adenosylmethionine to a base located in specific, double-stranded DNA sequences (Noyer-Weidner and Trautner 1993). The target for Dam methylase is 5′-GATC-3′ (Lacks and Greenberg 1977; Hattman et al. 1978). The Dcm enzyme methylates the inner cytosine of the pentanucleotides 5′-CCAGG-3′ and 5′-CCTGG-3′ (May and Hattman 1975).

While the biological role of the Dcm enzyme remains largely unknown (Marinus 1987; Noyer-Weidner and Trautner 1993; Gläsner et al. 1995), Dam methyltransferase is known to participate in the control of many cellular processes: DNA replication, chromosome segregation, mismatch repair, and transcriptional regulation of certain genes (for reviews, see Marinus 1987; Messer and Noyer-Weidner 1988; Barras and Marinus 1989; Noyer-Weidner and Trautner 1993).