Limits...
The dynamic nature and territory of transcriptional machinery in the bacterial chromosome.

Jin DJ, Cagliero C, Martin CM, Izard J, Zhou YN - Front Microbiol (2015)

Bottom Line: In this review we use a systems biology perspective to summarize the advances in the cell biology of RNAP in E. coli, including the discoveries of the bacterial nucleolus, the spatial compartmentalization of the transcription machinery at the periphery of the nucleoid, and the segregation of the chromosome territories for the two major cellular functions of transcription and replication in fast-growing cells.Our understanding of the coupling of transcription and bacterial chromosome (or nucleoid) structure is also summarized.Using E. coli as a simple model system, co-imaging of RNAP with DNA and other factors during growth and stress responses will continue to be a useful tool for studying bacterial growth and adaptation in changing environment.

View Article: PubMed Central - PubMed

Affiliation: Transcription Control Section, Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health Frederick, MD, USA.

ABSTRACT
Our knowledge of the regulation of genes involved in bacterial growth and stress responses is extensive; however, we have only recently begun to understand how environmental cues influence the dynamic, three-dimensional distribution of RNA polymerase (RNAP) in Escherichia coli on the level of single cell, using wide-field fluorescence microscopy and state-of-the-art imaging techniques. Live-cell imaging using either an agarose-embedding procedure or a microfluidic system further underscores the dynamic nature of the distribution of RNAP in response to changes in the environment and highlights the challenges in the study. A general agreement between live-cell and fixed-cell images has validated the formaldehyde-fixing procedure, which is a technical breakthrough in the study of the cell biology of RNAP. In this review we use a systems biology perspective to summarize the advances in the cell biology of RNAP in E. coli, including the discoveries of the bacterial nucleolus, the spatial compartmentalization of the transcription machinery at the periphery of the nucleoid, and the segregation of the chromosome territories for the two major cellular functions of transcription and replication in fast-growing cells. Our understanding of the coupling of transcription and bacterial chromosome (or nucleoid) structure is also summarized. Using E. coli as a simple model system, co-imaging of RNAP with DNA and other factors during growth and stress responses will continue to be a useful tool for studying bacterial growth and adaptation in changing environment.

No MeSH data available.


Related in: MedlinePlus

Activerrnexpression is required to condense the nucleoid in the presence of chloramphenicol. Images of overlay of DNA (nucleoid) and cell, RNAP, and overlay of RNAP and DNA are shown. DNA in the DNA/cell overlay is shown in red (left column), RNAP is shown in green (middle column), and the RNAP (green) and DNA (red) overlay is shown (right column). The panels on the top row show rapidly growing cells (rpoC-gfp) in LB, at 30°C, and RNAP foci are indicated by arrows; panels in the center row show cells treated with chloramphenicol (100 μg/ml) for 100 min; panels in the bottom row show cells sequentially treated with chloramphenicol (100 μg/ml, 10 min) and rifampicin (100 μg/ml, 90 min). Modified and adapted from Cabrera et al. (2009).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4440401&req=5

Figure 10: Activerrnexpression is required to condense the nucleoid in the presence of chloramphenicol. Images of overlay of DNA (nucleoid) and cell, RNAP, and overlay of RNAP and DNA are shown. DNA in the DNA/cell overlay is shown in red (left column), RNAP is shown in green (middle column), and the RNAP (green) and DNA (red) overlay is shown (right column). The panels on the top row show rapidly growing cells (rpoC-gfp) in LB, at 30°C, and RNAP foci are indicated by arrows; panels in the center row show cells treated with chloramphenicol (100 μg/ml) for 100 min; panels in the bottom row show cells sequentially treated with chloramphenicol (100 μg/ml, 10 min) and rifampicin (100 μg/ml, 90 min). Modified and adapted from Cabrera et al. (2009).

Mentions: Co-imaging of RNAP and DNA in cells undergoing physiological perturbations has also revealed that global changes in the distribution of RNAP accompany alterations in nucleoid structure, indicating an important role of RNAP and transcription in the organization of the bacterial chromosome (Jin and Cabrera, 2006; Jin et al., 2013). The changes are stress-dependent and in most cases studied, as shown in Figures 2, 3, redistribution of RNAP from a few prominent foci at the clustering of rrn to the nucleoid homogeneously leads to nucleoid expansion. In an effort to determine whether active rRNA synthesis is required to condense the nucleoid, the effects of the antibiotics chloramphenicol and rifampin as well as two mutations that decrease rRNA synthesis, on the nucleoid structure have been reexamined (Cabrera et al., 2009). The nucleoids are condensed in fast-growing cells (LB) treated with the translation inhibitor chloramphenicol (Woldringh et al., 1995; van Helvoort et al., 1996); however, if cells are treated sequentially with chloramphenicol first and then rifampicin, the nucleoids become expanded and RNAP foci disappear (Figure 10). Moreover, the nucleoids remain expanded in the above-described RNAP mutant cells defective in the transcription of rrn in LB when treated with chloramphenicol. Similarly, even with chloramphenicol treatment, the nucleoids remain expanded in the Δ6rrn cells that have only one copy of rrn remaining in the chromosome. Together, these results support the role of active rRNA synthesis from the clustering of rrn in nucleoid compaction in fast-growing cells. Because transcription and supercoiling are coupled (Liu and Wang, 1987), it is possible that transcription-induced supercoiling at the clustering of rrn (Jin et al., 2012) contributes to the nucleoid compaction in fast-growing cells.


The dynamic nature and territory of transcriptional machinery in the bacterial chromosome.

Jin DJ, Cagliero C, Martin CM, Izard J, Zhou YN - Front Microbiol (2015)

Activerrnexpression is required to condense the nucleoid in the presence of chloramphenicol. Images of overlay of DNA (nucleoid) and cell, RNAP, and overlay of RNAP and DNA are shown. DNA in the DNA/cell overlay is shown in red (left column), RNAP is shown in green (middle column), and the RNAP (green) and DNA (red) overlay is shown (right column). The panels on the top row show rapidly growing cells (rpoC-gfp) in LB, at 30°C, and RNAP foci are indicated by arrows; panels in the center row show cells treated with chloramphenicol (100 μg/ml) for 100 min; panels in the bottom row show cells sequentially treated with chloramphenicol (100 μg/ml, 10 min) and rifampicin (100 μg/ml, 90 min). Modified and adapted from Cabrera et al. (2009).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4440401&req=5

Figure 10: Activerrnexpression is required to condense the nucleoid in the presence of chloramphenicol. Images of overlay of DNA (nucleoid) and cell, RNAP, and overlay of RNAP and DNA are shown. DNA in the DNA/cell overlay is shown in red (left column), RNAP is shown in green (middle column), and the RNAP (green) and DNA (red) overlay is shown (right column). The panels on the top row show rapidly growing cells (rpoC-gfp) in LB, at 30°C, and RNAP foci are indicated by arrows; panels in the center row show cells treated with chloramphenicol (100 μg/ml) for 100 min; panels in the bottom row show cells sequentially treated with chloramphenicol (100 μg/ml, 10 min) and rifampicin (100 μg/ml, 90 min). Modified and adapted from Cabrera et al. (2009).
Mentions: Co-imaging of RNAP and DNA in cells undergoing physiological perturbations has also revealed that global changes in the distribution of RNAP accompany alterations in nucleoid structure, indicating an important role of RNAP and transcription in the organization of the bacterial chromosome (Jin and Cabrera, 2006; Jin et al., 2013). The changes are stress-dependent and in most cases studied, as shown in Figures 2, 3, redistribution of RNAP from a few prominent foci at the clustering of rrn to the nucleoid homogeneously leads to nucleoid expansion. In an effort to determine whether active rRNA synthesis is required to condense the nucleoid, the effects of the antibiotics chloramphenicol and rifampin as well as two mutations that decrease rRNA synthesis, on the nucleoid structure have been reexamined (Cabrera et al., 2009). The nucleoids are condensed in fast-growing cells (LB) treated with the translation inhibitor chloramphenicol (Woldringh et al., 1995; van Helvoort et al., 1996); however, if cells are treated sequentially with chloramphenicol first and then rifampicin, the nucleoids become expanded and RNAP foci disappear (Figure 10). Moreover, the nucleoids remain expanded in the above-described RNAP mutant cells defective in the transcription of rrn in LB when treated with chloramphenicol. Similarly, even with chloramphenicol treatment, the nucleoids remain expanded in the Δ6rrn cells that have only one copy of rrn remaining in the chromosome. Together, these results support the role of active rRNA synthesis from the clustering of rrn in nucleoid compaction in fast-growing cells. Because transcription and supercoiling are coupled (Liu and Wang, 1987), it is possible that transcription-induced supercoiling at the clustering of rrn (Jin et al., 2012) contributes to the nucleoid compaction in fast-growing cells.

Bottom Line: In this review we use a systems biology perspective to summarize the advances in the cell biology of RNAP in E. coli, including the discoveries of the bacterial nucleolus, the spatial compartmentalization of the transcription machinery at the periphery of the nucleoid, and the segregation of the chromosome territories for the two major cellular functions of transcription and replication in fast-growing cells.Our understanding of the coupling of transcription and bacterial chromosome (or nucleoid) structure is also summarized.Using E. coli as a simple model system, co-imaging of RNAP with DNA and other factors during growth and stress responses will continue to be a useful tool for studying bacterial growth and adaptation in changing environment.

View Article: PubMed Central - PubMed

Affiliation: Transcription Control Section, Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health Frederick, MD, USA.

ABSTRACT
Our knowledge of the regulation of genes involved in bacterial growth and stress responses is extensive; however, we have only recently begun to understand how environmental cues influence the dynamic, three-dimensional distribution of RNA polymerase (RNAP) in Escherichia coli on the level of single cell, using wide-field fluorescence microscopy and state-of-the-art imaging techniques. Live-cell imaging using either an agarose-embedding procedure or a microfluidic system further underscores the dynamic nature of the distribution of RNAP in response to changes in the environment and highlights the challenges in the study. A general agreement between live-cell and fixed-cell images has validated the formaldehyde-fixing procedure, which is a technical breakthrough in the study of the cell biology of RNAP. In this review we use a systems biology perspective to summarize the advances in the cell biology of RNAP in E. coli, including the discoveries of the bacterial nucleolus, the spatial compartmentalization of the transcription machinery at the periphery of the nucleoid, and the segregation of the chromosome territories for the two major cellular functions of transcription and replication in fast-growing cells. Our understanding of the coupling of transcription and bacterial chromosome (or nucleoid) structure is also summarized. Using E. coli as a simple model system, co-imaging of RNAP with DNA and other factors during growth and stress responses will continue to be a useful tool for studying bacterial growth and adaptation in changing environment.

No MeSH data available.


Related in: MedlinePlus