Chromosomes harbor the genetic information thats support life. If fully stretched out, the chromosomal DNA of any organism would be ~1000 times longer than the cell or nucleus that contains it. Thus, chromosomes must be massively compacted. Additionally, chromosomal DNA must be packaged and organized in a manner that enables, and likely facilitates, a range of important cellular processes, including DNA replication, chromosome segregation, transcription, recombination, and repair. Despite the critical and central role of chromosomes in the life of a cell, the mechanisms responsible for their compaction and organization remain incompletely defined. Compaction is driven, in part, by DNA supercoiling, which is controlled by a series of topoisomerases. In addition, most organisms encode a suite of DNA-binding proteins that directly shape, compact, and organize genomic DNA. How these proteins structure and organize DNA, and how their activities impact DNA replication, transcription, and chromosome segregation remains poorly understood, particularly in bacteria, which do not encode histones.
We aim to address this gap in our knowledge, examining the model organism Caulobacter crescentus using a combination of genetic, biochemical, and cell biological assays, along with a set of genome-scale assays, including ChIP-Seq, RNA-Seq, and Hi-C. We will focus on elucidating the in vivo functions and roles of three key chromosome organization components. Specifically, we aim to (i) dissect the in vivo role of SMC (structural maintenance of chromosomes) in establishing the global configuration of the Caulobacter chromosome, (ii) elucidate the mechanisms by which a recently identified nucleoid-assoicated protein called CnpA affects DNA topology, DNA replication, and transcription, and (iii) identify and characterize the DNA-binding proteins that organize the terminus and promote chromosome segregation. We anticipate that the mechanisms and principles of chromosome organization learned studying Caulobacter will be broadly relevant to other bacteria and, given the universal problem of chromosome compaction, likely to eukaryotes as well. Additionally, because some of the proteins central to compacting bacterial chromosomes, such as topoisomerases, are major antibiotic targets, our work may inform or guide the development of new antibiotics that slow or halt the proliferation of important pathogens.
This project will aid efforts to develop new antibiotics by identifying and understanding the proteins that structure and organize bacterial chromosomes. Some of our most effective current antibiotics, such as quinolones and aminocoumarins, target topoisomerases suggesting that other proteins involved in chromosome organization may be effective new antibiotic targets. Additionally, many genes required for chromosome structure and organization are required for the virulence of bacterial pathogens.
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