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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

Nascent rRNA-binding protein NusB forms foci and colocalizes with transcription foci in fast-growing cells. (A) Images of NusB, RNAP, DNA (nucleoid), overlay of NusB (red) and DNA (green), and overlay of RNAP (green) and NusB (red) from a representative fast-growing E. coli cell, as described in the legend to Figure 7. NusB foci are at the periphery of the nucleoid (separate red and green colors on the RNAP/NusB overlay) and the NusB signals perfectly colocalize with RNAP signals (overall yellow color on the RNAP/NusB overlay). (B) The distribution of apparent NusB-mCherry foci in fast-growing cells. The red line in the histogram indicates the median number of NusB foci in the population of cells. Note that the median number of NusB foci is close to that of RNAP foci in fast-growing cells. (C) Cumulative distribution of the distances between NusB foci and their closest RNAP foci in the population of cells. (—-) NusB-mCherry RNAP-Venus, and (- - -) NusB-mCherry RNAP-Venus random. The gray rectangle represents the colocalization area (≤140 nm), as the theoretical SIM microscope resolution for the mCherry is 140 nm. 87.1% of the NusB foci are within 140 nm of the closest transcription foci. Adapted from Cagliero et al. (2014).
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Figure 8: Nascent rRNA-binding protein NusB forms foci and colocalizes with transcription foci in fast-growing cells. (A) Images of NusB, RNAP, DNA (nucleoid), overlay of NusB (red) and DNA (green), and overlay of RNAP (green) and NusB (red) from a representative fast-growing E. coli cell, as described in the legend to Figure 7. NusB foci are at the periphery of the nucleoid (separate red and green colors on the RNAP/NusB overlay) and the NusB signals perfectly colocalize with RNAP signals (overall yellow color on the RNAP/NusB overlay). (B) The distribution of apparent NusB-mCherry foci in fast-growing cells. The red line in the histogram indicates the median number of NusB foci in the population of cells. Note that the median number of NusB foci is close to that of RNAP foci in fast-growing cells. (C) Cumulative distribution of the distances between NusB foci and their closest RNAP foci in the population of cells. (—-) NusB-mCherry RNAP-Venus, and (- - -) NusB-mCherry RNAP-Venus random. The gray rectangle represents the colocalization area (≤140 nm), as the theoretical SIM microscope resolution for the mCherry is 140 nm. 87.1% of the NusB foci are within 140 nm of the closest transcription foci. Adapted from Cagliero et al. (2014).

Mentions: NusA and NusB are involved in rrn antitermination and rRNA processing systems. SIM co-imaging of RNAP-Venus with DNA and NusA-mCherry or NusB-mCherry in fast-growing cells has demonstrated that, (i) like RNAP, NusA, or NusB forms foci at the periphery of the nucleoid, and the median number of NusA or NusB foci per cell is similar to that of the RNAP foci, and (ii) the NusA or NusB foci are co-localized with RNAP foci (Cagliero et al., 2014). For example, Figure 8 shows the SIM images of NusB and its spatial relationship with DNA (DNA/NusB overlay) and with RNAP (RNAP/NusB) in a typical fast-growing cell (LB at 37°C) (Figure 8A). There were six NusB foci per cell on average in a population of fast-growing cells (Figure 8B), a value that is close to that of RNAP foci. The cumulative distribution of NusB foci and RNAP foci from a population of fast-growing cells has confirmed that most of NusB foci (>87%) are colocalized with RNAP foci at the clustering of rrn or bacterial nucleolus (Figure 8C), demonstrating that rRNA synthesis and processing are intimately coupled in space. It remains to be determined what other components are associated with transcription foci 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)

Nascent rRNA-binding protein NusB forms foci and colocalizes with transcription foci in fast-growing cells. (A) Images of NusB, RNAP, DNA (nucleoid), overlay of NusB (red) and DNA (green), and overlay of RNAP (green) and NusB (red) from a representative fast-growing E. coli cell, as described in the legend to Figure 7. NusB foci are at the periphery of the nucleoid (separate red and green colors on the RNAP/NusB overlay) and the NusB signals perfectly colocalize with RNAP signals (overall yellow color on the RNAP/NusB overlay). (B) The distribution of apparent NusB-mCherry foci in fast-growing cells. The red line in the histogram indicates the median number of NusB foci in the population of cells. Note that the median number of NusB foci is close to that of RNAP foci in fast-growing cells. (C) Cumulative distribution of the distances between NusB foci and their closest RNAP foci in the population of cells. (—-) NusB-mCherry RNAP-Venus, and (- - -) NusB-mCherry RNAP-Venus random. The gray rectangle represents the colocalization area (≤140 nm), as the theoretical SIM microscope resolution for the mCherry is 140 nm. 87.1% of the NusB foci are within 140 nm of the closest transcription foci. Adapted from Cagliero et al. (2014).
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Figure 8: Nascent rRNA-binding protein NusB forms foci and colocalizes with transcription foci in fast-growing cells. (A) Images of NusB, RNAP, DNA (nucleoid), overlay of NusB (red) and DNA (green), and overlay of RNAP (green) and NusB (red) from a representative fast-growing E. coli cell, as described in the legend to Figure 7. NusB foci are at the periphery of the nucleoid (separate red and green colors on the RNAP/NusB overlay) and the NusB signals perfectly colocalize with RNAP signals (overall yellow color on the RNAP/NusB overlay). (B) The distribution of apparent NusB-mCherry foci in fast-growing cells. The red line in the histogram indicates the median number of NusB foci in the population of cells. Note that the median number of NusB foci is close to that of RNAP foci in fast-growing cells. (C) Cumulative distribution of the distances between NusB foci and their closest RNAP foci in the population of cells. (—-) NusB-mCherry RNAP-Venus, and (- - -) NusB-mCherry RNAP-Venus random. The gray rectangle represents the colocalization area (≤140 nm), as the theoretical SIM microscope resolution for the mCherry is 140 nm. 87.1% of the NusB foci are within 140 nm of the closest transcription foci. Adapted from Cagliero et al. (2014).
Mentions: NusA and NusB are involved in rrn antitermination and rRNA processing systems. SIM co-imaging of RNAP-Venus with DNA and NusA-mCherry or NusB-mCherry in fast-growing cells has demonstrated that, (i) like RNAP, NusA, or NusB forms foci at the periphery of the nucleoid, and the median number of NusA or NusB foci per cell is similar to that of the RNAP foci, and (ii) the NusA or NusB foci are co-localized with RNAP foci (Cagliero et al., 2014). For example, Figure 8 shows the SIM images of NusB and its spatial relationship with DNA (DNA/NusB overlay) and with RNAP (RNAP/NusB) in a typical fast-growing cell (LB at 37°C) (Figure 8A). There were six NusB foci per cell on average in a population of fast-growing cells (Figure 8B), a value that is close to that of RNAP foci. The cumulative distribution of NusB foci and RNAP foci from a population of fast-growing cells has confirmed that most of NusB foci (>87%) are colocalized with RNAP foci at the clustering of rrn or bacterial nucleolus (Figure 8C), demonstrating that rRNA synthesis and processing are intimately coupled in space. It remains to be determined what other components are associated with transcription foci 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