TY - JOUR
T1 - Spatial organization of bacterial transcription and translation
AU - Castellana, Michele
AU - Li, Sophia Hsin Jung
AU - Wingreen, Ned S.
N1 - Funding Information:
We thank E. Bonomi, B. Bratton, C. Broedersz, Z. Gitai, I. Golding, J.-F. Joanny, P. Sens, J.-C. Walter, J. C. Weisshaar, and M. Z. Wilson for valuable conversations and suggestions. Research was supported by National Science Foundation Grants PHY-1305525, PHY-1066293, GRFP DGE-1148900; by US National Institutes of Health Grants NIDA DP1DA026192 and NIAID R21AI102187; and by the hospitality of the Aspen Center for Physics. The numerical computations presented in this article were performed on computational resources supported by the Lewis-Sigler Institute for Integrative Genomics at Princeton University.
PY - 2016/8/16
Y1 - 2016/8/16
N2 - In bacteria such as Escherichia coli, DNA is compacted into a nucleoid near the cell center, whereas ribosomes-molecular complexes that translate mRNAs into proteins-are mainly localized to the poles. We study the impact of this spatial organization using a minimal reaction- diffusionmodel for the cellular transcriptional-translationalmachinery. Although genome-wide mRNA-nucleoid segregation still lacks experimental validation, our model predicts that ∼90%of mRNAs are segregated to the poles. In addition, our analysis reveals a "circulation" of ribosomes driven by the flux of mRNAs, from synthesis in the nucleoid to degradation at the poles. We show that our results are robust with respect to multiple, biologically relevant factors, such as mRNA degradation by RNase enzymes, different phases of the cell division cycle and growth rates, and the existence of nonspecific, transient interactions between ribosomes and mRNAs. Finally, we confirm that the observed nucleoid size stems from a balance between the forces that the chromosome and mRNAs exert on each other. This suggests a potential global feedback circuit in which gene expression feeds back on itself via nucleoid compaction.
AB - In bacteria such as Escherichia coli, DNA is compacted into a nucleoid near the cell center, whereas ribosomes-molecular complexes that translate mRNAs into proteins-are mainly localized to the poles. We study the impact of this spatial organization using a minimal reaction- diffusionmodel for the cellular transcriptional-translationalmachinery. Although genome-wide mRNA-nucleoid segregation still lacks experimental validation, our model predicts that ∼90%of mRNAs are segregated to the poles. In addition, our analysis reveals a "circulation" of ribosomes driven by the flux of mRNAs, from synthesis in the nucleoid to degradation at the poles. We show that our results are robust with respect to multiple, biologically relevant factors, such as mRNA degradation by RNase enzymes, different phases of the cell division cycle and growth rates, and the existence of nonspecific, transient interactions between ribosomes and mRNAs. Finally, we confirm that the observed nucleoid size stems from a balance between the forces that the chromosome and mRNAs exert on each other. This suggests a potential global feedback circuit in which gene expression feeds back on itself via nucleoid compaction.
KW - Bacteria
KW - Experiments
KW - Localization
KW - Modeling
KW - Translation
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U2 - 10.1073/pnas.1604995113
DO - 10.1073/pnas.1604995113
M3 - Article
C2 - 27486246
AN - SCOPUS:84982149292
SN - 0027-8424
VL - 113
SP - 9286
EP - 9291
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 - 33
ER -