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.

Public Health Relevance

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.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Special Emphasis Panel (ZRG1)
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Melillo, Amanda A
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Massachusetts Institute of Technology
Schools of Arts and Sciences
United States
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Guo, Monica S; Haakonsen, Diane L; Zeng, Wenjie et al. (2018) A Bacterial Chromosome Structuring Protein Binds Overtwisted DNA to Stimulate Type II Topoisomerases and Enable DNA Replication. Cell 175:583-597.e23
Tran, Ngat T; Laub, Michael T; Le, Tung B K (2017) SMC Progressively Aligns Chromosomal Arms in Caulobacter crescentus but Is Antagonized by Convergent Transcription. Cell Rep 20:2057-2071
García-Bayona, Leonor; Guo, Monica S; Laub, Michael T (2017) Contact-dependent killing by Caulobacter crescentus via cell surface-associated, glycine zipper proteins. Elife 6:
Badrinarayanan, Anjana; Le, Tung B K; Spille, Jan-Hendrik et al. (2017) Global analysis of double-strand break processing reveals in vivo properties of the helicase-nuclease complex AddAB. PLoS Genet 13:e1006783
Wang, Xindan; Brandão, Hugo B; Le, Tung B K et al. (2017) Bacillus subtilis SMC complexes juxtapose chromosome arms as they travel from origin to terminus. Science 355:524-527
Le, Tung Bk; Laub, Michael T (2016) Transcription rate and transcript length drive formation of chromosomal interaction domain boundaries. EMBO J 35:1582-95
Lubin, Emma A; Henry, Jonathan T; Fiebig, Aretha et al. (2016) Identification of the PhoB Regulon and Role of PhoU in the Phosphate Starvation Response of Caulobacter crescentus. J Bacteriol 198:187-200
Liu, Jing; Francis, Laura I; Jonas, Kristina et al. (2016) ClpAP is an auxiliary protease for DnaA degradation in Caulobacter crescentus. Mol Microbiol 102:1075-1085
Aakre, Christopher D; Herrou, Julien; Phung, Tuyen N et al. (2015) Evolving new protein-protein interaction specificity through promiscuous intermediates. Cell 163:594-606
Badrinarayanan, Anjana; Le, Tung B K; Laub, Michael T (2015) Rapid pairing and resegregation of distant homologous loci enables double-strand break repair in bacteria. J Cell Biol 210:385-400

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