Of the two V. cholerae chromosomes, the larger one (chr1) carries most of the housekeeping genes and is considered the primary chromosome. The smaller (secondary) chromosome (chr2) seems to have evolved from a plasmid. Plasmids, although prevalent in bacteria, rarely serve as the source of replicons that drive chromosomal replication. One reason could be that the firing of plasmid origins is generally not restricted to a specific time of the cell cycle, whereas timely firing is common among chromosomal origins. Comparison of plasmid and chr2 systems could thus be valuable for understanding how the timing of a biological process is regulated in the cell cycle. Chr2 replication seems also to depend on chrI replication. How the two chromosomes communicate to coordinate replication is largely unknown and this knowledge is basic to our understanding of how multipartite genomes are maintained in bacteria. In eukaryotes, in addition to incomplete and over-replication, uncoordinated replication causes developmental abnormalities and cancer. Finally, chr2 replication is controlled by a segregation protein. The discovery of the influence of segregation on replication is a recent development in the field of chromosome dynamics in bacteria, and cross-talk between replication and segregation has been demonstrated recently in human cells. Our progress in understanding these processes is reported below. Transition from random to cell-cycle regulated timing of replication initiation: The initial characterization of chr2 replication suggested that its control would be more complex than that of its presumed progenitor plasmid. Our past studies identified three new features of the chr2 origin: 1) Requirement for methylation of initiator binding sites in the origin for initiator-origin interactions. Several bacterial origins have methylation sites and timely firing of origins depends on methylation;2) Presence of a new kind of initiator binding site (39-mers) in the origin exclusively for inhibiting replication;3) Presence of an extra regulatory feedback loop to more tightly control initiator synthesis. In the past year, we discovered three additional regulators in the control of chr2 replication. Thus, cell-cycle regulation of replication initiation appears to be considerably more involved than the mechanisms that regulate plasmid replication in a cell cycle independent manner. The mechanisms of action of the new regulators are discussed below. Participation of initiator monomers and dimers in the control of chr2 replication: The chr2 initiator does not have any enzymatic activity but uses dimerization for this purpose. Only monomer binding to the replication origin leads to initiation and the dimers compete with monomers for binding to the origin. The dimerization also precludes initiator binding to replication inhibitory 39-mer, and helps in initiation. Controlling the association state of the initiator is thus critical for controlling chr2 replication. One of determinants of the association state of the initiator was found to be the DnaK (Hsp70) chaperone system. Control of chr2 replication by a site in chrI: We hypothesize that the timely replication and segregation of the two chromosomes of V. cholerae require communication between them, so that both can complete the processes prior to cell division. Preliminary evidence for inter-chromosomal communication has been obtained. We identified a locus on chr1 that can significantly stimulate chr2 replication, likely by remodeling the chrII initiator. The DNA site also made the normally chaperone (DnaK)-dependent replication of chr2 chaperone-independent. For many DNA binding proteins, specific binding is known to remodel the protein. The novelty of the chrI site is that its sequence has no similarity to the known specific binding sites of the initiator. Characterization of this atypical DNA-protein interaction is our goal for the immediate future. In any event, the finding suggests a mechanism that may coordinate replication of the two chromosomes. Control of chr2 replication by a segregation protein: The fact that segregation can influence replication was not known until recently. Our knowledge of chromosome segregation in bacteria comes primarily from studies of plasmids, where genes dedicated to plasmid segregation (par genes) were first found. Homologues of plasmid par genes have now been identified near the origin of replication in most bacteria, including V. cholerae. Both of the Vibrio chromosomes have their own par genes. We showed earlier that one of the par genes (parA1) of chr1 specifically promoted chr1 replication. A similar finding was also made in B. subtilis. In both B. subtilis and V. cholerae, the universal bacterial initiator, DnaA, was found to be the direct target of Par proteins. We now find that ParB2 of chr2 can also specifically stimulate replication of chr2 but through different mechanisms. ParB2 can spread beyond the centromere where they normally bind and cover one of the replication inhibitory 39-mer site. This likely interferes with the 39-mer interaction with the initiator, which is required for its replication inhibitory function. Unexpectedly, ParB2 could also promote replication without requiring the centromere by directly binding to a different 39-mer. ParB2 thus appears to promote replication by competing with the initiator for binding to two strong replication inhibitory sites, by spreading into one and binding specifically to the other. Spreading represents a novel replication control mechanism that acts from a distance, whereas non-centromeric binding is a novel mechanism for control by a segregation protein. These studies establish several ways by which segregation proteins could influence replication. We suggest that involving a segregation protein directly in replication control is a feature of the putative adaptation of an acquired plasmid to permanent residency as a secondary chromosome in V. cholerae. Generation of Vibrio specific antimicrobial agents: Given the increasing prevalence of multi-drug resistance in pathogenic vibrios, there is a need for new targets and drugs to combat these pathogens. The chr2 initiator, RctB, is conserved only in the family Vibrionaceae and appears ideally suited for developing potential anti-vibrio specific drugs. 3-D structural information of target proteins greatly facilitates drug design. Towards this goal we have started a systematic domain analysis of RctB. Replication initiators in general have proven refractory to structural studies most likely because they have unstructured regions and require remodeling by chaperone proteins and/or binding to specific DNA for activity. Initial attempts to form crystals of RctB have failed. We are attempting deletion analysis to isolate functional domains. These smaller derivatives might be more amenable to structural studies.

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Ramachandran, Revathy; Ciaccia, Peter N; Filsuf, Tara A et al. (2018) Chromosome 1 licenses chromosome 2 replication in Vibrio cholerae by doubling the crtS gene dosage. PLoS Genet 14:e1007426
Jha, Jyoti K; Chattoraj, Dhruba K (2016) Inactivation of Individual SeqA Binding Sites of the E. coli Origin Reveals Robustness of Replication Initiation Synchrony. PLoS One 11:e0166722
Jha, Jyoti K; Ramachandran, Revathy; Chattoraj, Dhruba K (2016) Opening the Strands of Replication Origins-Still an Open Question. Front Mol Biosci 3:62
Baek, Jong Hwan; Chattoraj, Dhruba K (2014) Chromosome I controls chromosome II replication in Vibrio cholerae. PLoS Genet 10:e1004184
Baek, Jong Hwan; Rajagopala, Seesandra V; Chattoraj, Dhruba K (2014) Chromosome segregation proteins of Vibrio cholerae as transcription regulators. MBio 5:e01061-14
Ramachandran, Revathy; Jha, Jyoti; Chattoraj, Dhruba K (2014) Chromosome segregation in Vibrio cholerae. J Mol Microbiol Biotechnol 24:360-70
Venkova-Canova, Tatiana; Baek, Jong Hwan; Fitzgerald, Peter C et al. (2013) Evidence for two different regulatory mechanisms linking replication and segregation of vibrio cholerae chromosome II. PLoS Genet 9:e1003579
Kadoya, Ryosuke; Chattoraj, Dhruba K (2012) Insensitivity of chromosome I and the cell cycle to blockage of replication and segregation of Vibrio cholerae chromosome II. MBio 3:
Jha, Jyoti K; Baek, Jong Hwan; Venkova-Canova, Tatiana et al. (2012) Chromosome dynamics in multichromosome bacteria. Biochim Biophys Acta 1819:826-9
Venkova-Canova, Tatiana; Saha, Anik; Chattoraj, Dhruba K (2012) A 29-mer site regulates transcription of the initiator gene as well as function of the replication origin of Vibrio cholerae chromosome II. Plasmid 67:102-10

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