Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 112, Issue 32, Pages E4390-E4399Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1507592112
Keywords
RNA polymerase; transcription; superresolution; single-molecule tracking; protein-DNA interactions
Categories
Funding
- European Commission [HEALTH-F4-2008-201418]
- UK Biotechnology and Biological Sciences Research Council [BB/H01795X/1]
- European Research Council [261227]
- Engineering and Physical Sciences Research
- Consejo Nacional de Ciencia y Technologia/I2T2
- St. John's College Oxford
- Wellcome Trust [WT083469MA]
- Biotechnology and Biological Sciences Research Council [BB/H01795X/1] Funding Source: researchfish
- Engineering and Physical Sciences Research Council [1104939] Funding Source: researchfish
- Medical Research Council [MR/K01577X/1] Funding Source: researchfish
- BBSRC [BB/H01795X/1] Funding Source: UKRI
- MRC [MR/K01577X/1] Funding Source: UKRI
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Despite the fundamental importance of transcription, a comprehensive analysis of RNA polymerase (RNAP) behavior and its role in the nucleoid organization in vivo is lacking. Here, we used superresolution microscopy to study the localization and dynamics of the transcription machinery and DNA in live bacterial cells, at both the single-molecule and the population level. We used photoactivated single-molecule tracking to discriminate between mobile RNAPs and RNAPs specifically bound to DNA, either on promoters or transcribed genes. Mobile RNAPs can explore the whole nucleoid while searching for promoters, and spend 85% of their search time in nonspecific interactions with DNA. On the other hand, the distribution of specifically bound RNAPs shows that low levels of transcription can occur throughout the nucleoid. Further, clustering analysis and 3D structured illumination microscopy (SIM) show that dense clusters of transcribing RNAPs form almost exclusively at the nucleoid periphery. Treatment with rifampicin shows that active transcription is necessary for maintaining this spatial organization. In faster growth conditions, the fraction of transcribing RNAPs increases, as well as their clustering. Under these conditions, we observed dramatic phase separation between the densest clusters of RNAPs and the densest regions of the nucleoid. These findings show that transcription can cause spatial reorganization of the nucleoid, with movement of gene loci out of the bulk of DNA as levels of transcription increase. This work provides a global view of the organization of RNA polymerase and transcription in living cells.
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