Species-specific supercoil dynamics of the bacterial nucleoid

Abstract

Bacteria organize DNA into self-adherent conglomerates called nucleoids that are replicated, transcribed, and partitioned within the cytoplasm during growth and cell division. Three classes of proteins help condense nucleoids: (1) DNA gyrase generates diffusible negative supercoils that help compact DNA into a dynamic interwound and multiply branched structure; (2) RNA polymerase and abundant small basic nucleoid-associated proteins (NAPs) create constrained supercoils by binding, bending, and forming cooperative protein-DNA complexes; (3) a multi-protein DNA condensin organizes chromosome structure to assist sister chromosome segregation after replication. Most bacteria have four topoisomerases that participate in DNA dynamics during replication and transcription. Gyrase and topoisomerase I (Topo I) are intimately involved in transcription; Topo III and Topo IV play critical roles in decatenating and unknotting DNA during and immediately after replication. RNA polymerase generates positive (+) supercoils downstream and negative (−) supercoils upstream of highly transcribed operons. Supercoil levels vary under fast versus slow growth conditions, but what surprises many investigators is that it also varies significantly between different bacterial species. The MukFEB condensin is dispensable in the high supercoil density (σ) organism Escherichia coli but is essential in Salmonella spp. which has 15 % fewer supercoils. These observations raise two questions: (1) How do different species regulate supercoil density? (2) Why do closely related species evolve different optimal supercoil levels? Control of supercoil density in E. coli and Salmonella is largely determined by differences encoded within the gyrase subunits. Supercoil differences may arise to minimalize toxicity of mobile DNA elements in the genome.

Single-nucleotide-resolution mapping of DNA gyrase cleavage sites across theEscherichia coligenome

“…The combination of a specific sequencing protocol with a cleavage pattern detecting algorithm results in single-nucleotide precision of Topo-Seq. Our method can be directly applied to different bacteria including pathogens such as Salmonella or Mycobacteria , whose global supercoiling dynamics must be significantly different from that of E. coli (102,103), and to Caulobacter crescentus and genome-reduced Mycoplasma , in which supercoiling was shown to contribute to chromosomal domain organization (104,105). The Cfx-sensitive gyrase is found in eukaryotes such as plants and Apicomplexa (106–108).…”

Network Rewiring: Physiological Consequences of Reciprocally Exchanging the Physical Locations and Growth-Phase-Dependent Expression Patterns of the Salmonella fis and dps Genes

“…Together, these data indicate that other factors (including bacterial species differences) affect fis expression at a given location on the bacterial chromosome. Among these species-specific factors may be the known differences in DNA supercoiling set points that exist between E. coli and S. Typhimurium ( 62 – 64 ). The impact of Fis on the homeostatic control of DNA supercoiling, either through its influence on topoisomerase gene expression ( 36 – 39 ) or via direct Fis-mediated buffering of local DNA topology ( 31 ), may account for the changes to the transcriptome that we detected.…”

Rules and Exceptions: The Role of Chromosomal ParB in DNA Segregation and Other Cellular Processes

“…A similar number of CIDs ranging in size from 50 to 300 kbp were identified in the Bacillus subtilis genome [16]. The boundaries of CIDs frequently co-localize with highly transcribed genes [9,[19][20][21][22]. The role of NAPs in chromosomal long-and short-range interactions [4,23,24] and among them, the structural maintenance of chromosome proteins (SMCs and MukBs) [25][26][27][28], has been widely documented.…”