Bacteria may have multiple replication origins.

Abstract

Since the pioneer work of Woese and Fox (1977), it has been known that life on the Earth is generally classified into three main evolutionary lineages: Archaea, Bacteria, and Eukarya. In terms of DNA replication origin per chromosome, bacteria typically have a single replication origin (oriC), and eukaryotic organisms have multiple replication origins, whereas archaea are in between, see a recent review paper for the details (Leonard and Mechali, 2013). Among bacteria, one replication origin is the norm and there is currently no evidence that two functional origins are ever used on the same chromosome. However, it seems that there are always exceptions to the rules of biological systems. For example, Wang et al. have constructed Escherichia coli cells with two identical functional replication origins separated by 1 Mb in their 4.64-Mb chromosome artificially. Consequently, synchronous initiation at both spatially separate origins is followed by productive replication, and this is the first study in which cells with more than one WT origin on a bacterial chromosome have been extensively characterized (Wang et al., 2011). Recent developments in synthetic biology methodologies make the synthesis of synthetic chromosomes a feasible goal. Liang et al. fragmented the E. coli chromosome of 4.64 Mb into two linear autonomous replicating units with the E. coli oriC on the chromosome of 3.27 Mb and the replication origin of chromosome II in Vibrio cholerae on the chromosome of 1.37 Mb (Liang et al., 2013). Subsequently, Messerschmidt et al. also constructed the synthetic secondary E. coli chromosomes successfully based on the replication origin of chromosome II in V. cholerae (Messerschmidt et al., 2015). Recently, there are also a growing number of cases confirmed by experiments where the replication origin exists in a bipartite configuration in both Gram-positive and Gram-negative bacteria (Wolanski et al., 2015), such as Gram-positive Bacillus subtilis (Moriya et al., 1992) and Gram-negative Helicobacter pylori (Donczew et al., 2012). In addition, two autonomously replicating elements isolated from Pseudomonas aeruginosa have been characterized in vitro for pre-priming complex formation using combinations of replication proteins from P. aeruginosa and E. coli (Yee and Smith, 1990; Smith et al., 1991). Then, could multiple replication origins occur on a bacterial chromosome? This open question has even been raised by Prof. Pavel Pevzner in a popular online course “Bioinformatics Algorithms” on Coursera (http://coursera.org/course/bioinformatics) recently. Based on the summarization of the diverse patterns of strand asymmetry among different taxonomic groups, Xia suggested that the single-origin replication may not be universal among some bacterial species that exhibit strand asymmetry patterns consistent with the multiple origins of replication (Xia, 2012). However, the strand asymmetry patterns were caused not only by replication-associated mutational pressure, and many phenomena, such as genome rearrangements, could influence the strand asymmetry patterns. Consequently, the local minima in the skew diagram do not always correspond to the positions of functional replication origins (Mackiewicz et al., 2004). Therefore, more evidences are needed to support multiple replication origins on a bacterial chromosome.