Dhruba K. Chattoraj, Ph.D.
Dhruba K. Chattoraj, Ph.D.
Senior Investigator
Head, Control of DNA Replication Section

Center for Cancer Research
National Cancer Institute

Building 37, Room 6044C
Bethesda, MD 20892-4260
301-496-9194

Dr. Chattoraj investigates the molecular mechanisms that control chromosome replication and segregation in the model organisms Escherichia coli and Vibrio cholerae. He elucidated the mechanism of plasmid copy number control using simple repeat sequences in E. coli and how such a mechanism might have evolved to control chromosomal replication to once-per-cell-cycle in V. cholerae. His lab also discovered mechanisms by which chromosomes might communicate in bacteria with multipartite genome and by which the processes of replication and segregation influence each other. Other notable contributions have included the understanding of the role of molecular chaperones, DNA methylation, and activation and inactivation of regulatory suites by the act of transcription.

Areas of Expertise
1) DNA-protein interactions 2) chromosome replication 3) chromosome segregation 4) bacterial cell-cycle 5) plasmid maintenance 6) protein structure-function

Chromosome Maintenance in Bacteria

The faithful replication of chromosomes and their segregation to incipient daughter cells before cell division are required for the stable transmission of the genome. A host of intricate control mechanisms allow chromosome duplication once and only once per cell cycle, and ensure that a full complement of chromosomes is passed into each daughter cell. Defects in any aspect of chromosome replication or segregation pose significant threats to genome stability, and underlie the development of many human diseases, foremost among them being cancer.

While most bacterial genomes consist of a single circular chromosome, it is becoming clear from genome sequencing projects that about 10% of bacterial genomes are divided into multiple chromosomes, as in eukaryotes. These bacteria provide a unique opportunity to probe the mechanisms involved in the maintenance of multiple chromosomes. We study how replication and segregation are controlled and coordinated in a model organism with a divided genome, Vibrio cholerae. It has two chromosomes (chrI and chrII) but otherwise it is closely related to the paradigmatic model organism Escherichia coli. V. cholerae is also a potent human pathogen. A better understanding of the mechanisms operating in bacterial models will enhance our general understanding of chromosome replication and segregation, and can guide the rational development of therapeutics for many human diseases.

Cell cycle control of V. cholerae replication. The chrI of V. cholerae, like the E. coli chromosome are controlled by the highly conserved initiator protein DnaA. The initiator is also homologous to one of the ORC proteins that initiate replication in eukaryotes. ChrII is controlled differently, but retains the salient features of bona fide chromosomal replication: initiation of replication once per cell cycle replication and at a particular time of the cell cycle. Understanding replication control of chrII thus is likely to provide a fresh perspective on the basic regulatory principles that govern chromosomal replication. We are determining the genetic basis of the regulation and, where identified, the mechanisms behind the functioning of the regulators.

The chrII initiator protein, RctB, as a therapeutic target. An added value of studying chrII replication is that the knowledge gained has the potential to contribute to anti-Vibrio therapy. V. cholerae causes significant human suffering world-wide, as recently evidenced in Haiti. The initiator protein specific to chrII, RctB, is essential for Vibrio survival and is unique to the Vibrio family, offering a specific target for chemotherapy. The protein has several distinct essential functions, offering the opportunities to develop drug inhibitors specific to the different functions. These considerations have prompted us to embark on a systematic structure-function analysis of the protein.

Inter-chromosome communication in V. cholerae. One of the advantages afforded in studying a bacterium with a divided genome is to be able to ask: Do the chromosomes communicate to improve stability of their maintenance? We are approaching this question by developing systems in which replication or segregation is specifically blocked one chromosome at a time. When chrI replication is selectively blocked, both chrII replication and cell division are inhibited. However, when chrII replication is blocked, replication and segregation of chrI and cell division remain unaffected. Apparently, there is no checkpoint to ensure completion of replication and segregation of both chromosomes before cell division. It also appears that there has been a one-way adaptation of chrII to the maintenance of the main chromosome (chrI), and not the reverse. An understanding of chromosome coordination is expected to bear on the evolutionary process of chromosome acquisition and cooption.

Communication between replication and segregation in V. cholerae. The processes that contribute to chromosome segregation in bacteria are still poorly understood. In addition to the range of mechanisms proposed, which includes chromosome replication, there are clearly additional mechanisms that anchor the centromere analog to the cell pole in some bacteria, including V. cholerae. We are specifically interested in studying the role of chromosome replication in the segregation process and how the centromeres are retained at the pole after they have segregated.

Most sequenced bacterial genomes have orthologs of genes that help in segregation/partition of plasmids (par genes). Studies in several bacteria indicate that par genes, in addition to their role in chromosome segregation, contribute to other cellular processes such as chromosome replication and cell division. We have found that one of the proteins encoded by the par locus of chrI both promotes chrI segregation and regulates chrI replication. The results are strikingly similar to those found in Bacillus subtilis. It is remarkable that the replication phenotype of par has been retained or has independently evolved in a convergent fashion in the two bacteria that are believed to have diverged more than a billion years ago. We are interested in determining whether par genes in general modulate chromosomal replication.

Scientific Focus Areas:
Chromosome Biology, Genetics and Genomics, Microbiology and Infectious Diseases, Molecular Biology and Biochemistry
Selected Key Publications
  1. Chattoraj DK, Gosule LC, Schellman A.
    J. Mol. Biol. 121: 327-37, 1978. [ Journal Article ]
  2. Chattoraj DK.
    Cell. 19: 143-9, 1980. [ Journal Article ]
  3. Chattoraj DK, Mason RJ, Wickner SH.
    Cell. 52: 551-7, 1988. [ Journal Article ]
  4. Park K, Han E, Paulsson J, Chattoraj DK.
    EMBO J. 20: 7323-32, 2001. [ Journal Article ]
  5. Baek JH, Chattoraj DK.
    PLoS Genet. 10: e1004184, 2014. [ Journal Article ]

Dr Chattoraj received his Ph.D. in Biophysics in 1970 from the University of Calcutta, India, where he studied chromatin structure. As a postdoctoral associate, he studied nucleic acid-protein interactions involved in phage DNA replication and recombination at the University of Wisconsin with Dr. Ross Inman and at the University of Oregon with Dr. Frank Stahl. His current research interest is on replication and segregation of chromosomes in the bacterial cell cycle. He is an editor of Plasmid and an editorial board member of the Journal of Bacteriology, and a Fellow of the American Academy of Microbiology.

Name Position
Abhishek Goel Summer Student
Jyoti Jha Ph.D. Postdoctoral Fellow (Visiting)
Revathy Ramachandran Postdoctoral Fellow (Visiting)
Shanmuga Sozhamannan Ph.D. Special Volunteer

Summary

Dr. Chattoraj investigates the molecular mechanisms that control chromosome replication and segregation in the model organisms Escherichia coli and Vibrio cholerae. He elucidated the mechanism of plasmid copy number control using simple repeat sequences in E. coli and how such a mechanism might have evolved to control chromosomal replication to once-per-cell-cycle in V. cholerae. His lab also discovered mechanisms by which chromosomes might communicate in bacteria with multipartite genome and by which the processes of replication and segregation influence each other. Other notable contributions have included the understanding of the role of molecular chaperones, DNA methylation, and activation and inactivation of regulatory suites by the act of transcription.

Areas of Expertise
1) DNA-protein interactions 2) chromosome replication 3) chromosome segregation 4) bacterial cell-cycle 5) plasmid maintenance 6) protein structure-function

Research

Chromosome Maintenance in Bacteria

The faithful replication of chromosomes and their segregation to incipient daughter cells before cell division are required for the stable transmission of the genome. A host of intricate control mechanisms allow chromosome duplication once and only once per cell cycle, and ensure that a full complement of chromosomes is passed into each daughter cell. Defects in any aspect of chromosome replication or segregation pose significant threats to genome stability, and underlie the development of many human diseases, foremost among them being cancer.

While most bacterial genomes consist of a single circular chromosome, it is becoming clear from genome sequencing projects that about 10% of bacterial genomes are divided into multiple chromosomes, as in eukaryotes. These bacteria provide a unique opportunity to probe the mechanisms involved in the maintenance of multiple chromosomes. We study how replication and segregation are controlled and coordinated in a model organism with a divided genome, Vibrio cholerae. It has two chromosomes (chrI and chrII) but otherwise it is closely related to the paradigmatic model organism Escherichia coli. V. cholerae is also a potent human pathogen. A better understanding of the mechanisms operating in bacterial models will enhance our general understanding of chromosome replication and segregation, and can guide the rational development of therapeutics for many human diseases.

Cell cycle control of V. cholerae replication. The chrI of V. cholerae, like the E. coli chromosome are controlled by the highly conserved initiator protein DnaA. The initiator is also homologous to one of the ORC proteins that initiate replication in eukaryotes. ChrII is controlled differently, but retains the salient features of bona fide chromosomal replication: initiation of replication once per cell cycle replication and at a particular time of the cell cycle. Understanding replication control of chrII thus is likely to provide a fresh perspective on the basic regulatory principles that govern chromosomal replication. We are determining the genetic basis of the regulation and, where identified, the mechanisms behind the functioning of the regulators.

The chrII initiator protein, RctB, as a therapeutic target. An added value of studying chrII replication is that the knowledge gained has the potential to contribute to anti-Vibrio therapy. V. cholerae causes significant human suffering world-wide, as recently evidenced in Haiti. The initiator protein specific to chrII, RctB, is essential for Vibrio survival and is unique to the Vibrio family, offering a specific target for chemotherapy. The protein has several distinct essential functions, offering the opportunities to develop drug inhibitors specific to the different functions. These considerations have prompted us to embark on a systematic structure-function analysis of the protein.

Inter-chromosome communication in V. cholerae. One of the advantages afforded in studying a bacterium with a divided genome is to be able to ask: Do the chromosomes communicate to improve stability of their maintenance? We are approaching this question by developing systems in which replication or segregation is specifically blocked one chromosome at a time. When chrI replication is selectively blocked, both chrII replication and cell division are inhibited. However, when chrII replication is blocked, replication and segregation of chrI and cell division remain unaffected. Apparently, there is no checkpoint to ensure completion of replication and segregation of both chromosomes before cell division. It also appears that there has been a one-way adaptation of chrII to the maintenance of the main chromosome (chrI), and not the reverse. An understanding of chromosome coordination is expected to bear on the evolutionary process of chromosome acquisition and cooption.

Communication between replication and segregation in V. cholerae. The processes that contribute to chromosome segregation in bacteria are still poorly understood. In addition to the range of mechanisms proposed, which includes chromosome replication, there are clearly additional mechanisms that anchor the centromere analog to the cell pole in some bacteria, including V. cholerae. We are specifically interested in studying the role of chromosome replication in the segregation process and how the centromeres are retained at the pole after they have segregated.

Most sequenced bacterial genomes have orthologs of genes that help in segregation/partition of plasmids (par genes). Studies in several bacteria indicate that par genes, in addition to their role in chromosome segregation, contribute to other cellular processes such as chromosome replication and cell division. We have found that one of the proteins encoded by the par locus of chrI both promotes chrI segregation and regulates chrI replication. The results are strikingly similar to those found in Bacillus subtilis. It is remarkable that the replication phenotype of par has been retained or has independently evolved in a convergent fashion in the two bacteria that are believed to have diverged more than a billion years ago. We are interested in determining whether par genes in general modulate chromosomal replication.

Scientific Focus Areas:
Chromosome Biology, Genetics and Genomics, Microbiology and Infectious Diseases, Molecular Biology and Biochemistry

Publications

Selected Key Publications
  1. Chattoraj DK, Gosule LC, Schellman A.
    J. Mol. Biol. 121: 327-37, 1978. [ Journal Article ]
  2. Chattoraj DK.
    Cell. 19: 143-9, 1980. [ Journal Article ]
  3. Chattoraj DK, Mason RJ, Wickner SH.
    Cell. 52: 551-7, 1988. [ Journal Article ]
  4. Park K, Han E, Paulsson J, Chattoraj DK.
    EMBO J. 20: 7323-32, 2001. [ Journal Article ]
  5. Baek JH, Chattoraj DK.
    PLoS Genet. 10: e1004184, 2014. [ Journal Article ]

Biography

Dr Chattoraj received his Ph.D. in Biophysics in 1970 from the University of Calcutta, India, where he studied chromatin structure. As a postdoctoral associate, he studied nucleic acid-protein interactions involved in phage DNA replication and recombination at the University of Wisconsin with Dr. Ross Inman and at the University of Oregon with Dr. Frank Stahl. His current research interest is on replication and segregation of chromosomes in the bacterial cell cycle. He is an editor of Plasmid and an editorial board member of the Journal of Bacteriology, and a Fellow of the American Academy of Microbiology.

Team

Name Position
Abhishek Goel Summer Student
Jyoti Jha Ph.D. Postdoctoral Fellow (Visiting)
Revathy Ramachandran Postdoctoral Fellow (Visiting)
Shanmuga Sozhamannan Ph.D. Special Volunteer