TY - JOUR
T1 - Caulobacter chromosome in vivo configuration matches model predictions for a supercoiled polymer in a cell-like confinement
AU - Hong, Sun-Hae
AU - Toro, Esteban
AU - Mortensen, Kim
AU - de la Rosa, Mario A. Díaz
AU - Doniach, Sebastian
AU - Shapiro, Lucy
AU - Spakowitz, Andrew J.
AU - McAdams, Harley H.
PY - 2013
Y1 - 2013
N2 - We measured the distance between fluorescent-labeled DNA loci of various interloci contour lengths in Caulobacter crescentus swarmer cells to determine the in vivo configuration of the chromosome. For DNA segments less than about 300 kb, the mean interloci distances, 〈r〉, scale as n0.22, where n is the contour length, and cell-to-cell distribution of the interloci distance r is a universal function of r/n0.22 with broad cell-to-cell variability. For DNA segments greater than about 300 kb, the mean interloci distances scale as n, in agreement with previous observations. The 0.22 value of the scaling exponent for short DNA segments is consistent with theoretical predictions for a branched DNA polymer structure. Predictions from Brownian dynamics simulations of the packing of supercoiled DNA polymers in an elongated cell-like confinement are also consistent with a branched DNA structure, and simulated interloci distance distributions predict that confinement leads to “freezing” of the supercoiled configuration. Lateral positions of labeled loci at comparable positions along the length of the cell are strongly correlated when the longitudinal locus positions differ by
AB - We measured the distance between fluorescent-labeled DNA loci of various interloci contour lengths in Caulobacter crescentus swarmer cells to determine the in vivo configuration of the chromosome. For DNA segments less than about 300 kb, the mean interloci distances, 〈r〉, scale as n0.22, where n is the contour length, and cell-to-cell distribution of the interloci distance r is a universal function of r/n0.22 with broad cell-to-cell variability. For DNA segments greater than about 300 kb, the mean interloci distances scale as n, in agreement with previous observations. The 0.22 value of the scaling exponent for short DNA segments is consistent with theoretical predictions for a branched DNA polymer structure. Predictions from Brownian dynamics simulations of the packing of supercoiled DNA polymers in an elongated cell-like confinement are also consistent with a branched DNA structure, and simulated interloci distance distributions predict that confinement leads to “freezing” of the supercoiled configuration. Lateral positions of labeled loci at comparable positions along the length of the cell are strongly correlated when the longitudinal locus positions differ by
KW - chromosome organization
KW - DNA segregation
KW - polymer conformation
KW - computational modeling
KW - bacterial genome
U2 - 10.1073/pnas.1220824110
DO - 10.1073/pnas.1220824110
M3 - Journal article
C2 - 23319648
SN - 0027-8424
VL - 110
SP - 1674
EP - 1679
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
IS - 5
ER -