The replication initiator of the cholera pathogen's second chromosome shows structural similarity to plasmid initiators

Abstract

The conserved DnaA-oriC system is used to initiate replication of primary chromosomes throughout the bacterial kingdom; however, bacteria with multipartite genomes evolved distinct systems to initiate replication of secondary chromosomes. In the cholera pathogen, Vibrio cholerae, and in related species, secondary chromosome replication requires the RctB initiator protein. Here, we show that RctB consists of four domains. The structure of its central two domains resembles that of several plasmid replication initiators. RctB contains at least three DNA binding winged-helix-turn-helix motifs, and mutations within any of these severely compromise biological activity. In the structure, RctB adopts a head-to-head dimeric configuration that likely reflects the arrangement in solution. Therefore, major structural reorganization likely accompanies complex formation on the head-to-tail array of binding sites in oriCII. Our findings support the hypothesis that the second Vibrionaceae chromosome arose from an ancestral plasmid, and that RctB may have evolved additional regulatory features.

The Divided Bacterial Genome: Structure, Function, and Evolution

“…The term "chromid" itself is a combination of chromosome and plasmid (11) and underscores how chromid refers to a replicon that is an intermediate between a plasmid and a chromosome (11). The replication systems of chromids are similar to those of plasmids and megaplasmids (11) but may have additional regulatory controls that integrate their replication into the cell cycle (29,36,37). However, unlike plasmids and megaplasmids, chromids carry at least one gene that is essential for cell viability (i.e., a core gene whose loss would result in cell death) and generally have genomic signatures that better resemble those of the chromosome (11).…”

Vibrio cholerae chromosome 2 copy number is controlled by the methylation-independent binding of its monomeric initiator to the chromosome 1 crtS site

“…RctB is a 658 AA protein with four domains. Its central region (domains 2 and 3) is structurally homologous to iteron plasmid initiators while its outer domains (domains 1 and 4) are unique ( 25 ). RctB has three identified DNA binding surfaces in domains 1, 2 and 3 and the protein can adopt a monomeric or a dimeric form ( 25 ).…”

“…Its central region (domains 2 and 3) is structurally homologous to iteron plasmid initiators while its outer domains (domains 1 and 4) are unique ( 25 ). RctB has three identified DNA binding surfaces in domains 1, 2 and 3 and the protein can adopt a monomeric or a dimeric form ( 25 ). Its dimer interface is mediated by domain 2 and mutations impairing its dimerization such as RctB D314P , have been identified ( 25 ).…”

“…RctB has three identified DNA binding surfaces in domains 1, 2 and 3 and the protein can adopt a monomeric or a dimeric form ( 25 ). Its dimer interface is mediated by domain 2 and mutations impairing its dimerization such as RctB D314P , have been identified ( 25 ). Domain 4 could be involved in protein/protein interactions and promote RctB cooperative binding ( 17 , 25 ).…”

“…Its dimer interface is mediated by domain 2 and mutations impairing its dimerization such as RctB D314P , have been identified ( 25 ). Domain 4 could be involved in protein/protein interactions and promote RctB cooperative binding ( 17 , 25 ). RctB was reported to bind as a monomer or as a dimer onto iterons but only as a monomer on 39-mers ( 17 , 26 ).…”