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Nucleoid
The nucleoid (meaning nucleus-like) is an irregularly shaped region within the prokaryotic cell that contains all or most of the genetic material. The chromosome of a typical prokaryote is circular, and its length is very large compared to the cell dimensions, so it needs to be compacted in order to fit. In contrast to the nucleus of a eukaryotic cell, it is not surrounded by a nuclear membrane. Instead, the nucleoid forms by condensation and functional arrangement with the help of chromosomal architectural proteins and RNA molecules as well as DNA supercoiling. The length of a genome widely varies (generally at least a few million base pairs) and a cell may contain multiple copies of it.
There is not yet a high-resolution structure known of a bacterial nucleoid, however key features have been researched in Escherichia coli as a model organism. In E. coli, the chromosomal DNA is on average negatively supercoiled and folded into plectonemic loops, which are confined to different physical regions, and rarely diffuse into each other. These loops spatially organize into megabase-sized regions called macrodomains, within which DNA sites frequently interact, but between which interactions are rare. The condensed and spatially organized DNA forms a helical ellipsoid that is radially confined in the cell. The 3D structure of the DNA in the nucleoid appears to vary depending on conditions and is linked to gene expression so that the nucleoid architecture and gene transcription are tightly interdependent, influencing each other reciprocally.
In many bacteria, the chromosome is a single covalently closed (circular) double-stranded DNA molecule that encodes the genetic information in a haploid (monoploid) form. The size of the DNA varies from 500,000 to several million base pairs (bp) encoding from 500 to several thousand genes depending on the organism. The chromosomal DNA is present in cells in a highly compact, organized form called the nucleoid (meaning nucleus-like), which is not encased by a nuclear membrane as in eukaryotic cells. The isolated nucleoid contains 80% DNA, 10% protein, and 10% RNA by weight.
The gram-negative bacterium Escherichia coli is a model system for nucleoid research into how chromosomal DNA becomes the nucleoid, the factors involved therein, what is known about its structure, and how some of the DNA structural aspects influence gene expression.
There are two essential aspects of nucleoid formation; condensation of a large DNA into a small cellular space and functional organization of DNA in a three-dimensional form. The haploid circular chromosome in E. coli consists of ~ 4.6 million bp. If DNA is relaxed in the B form, it would have a circumference of ~1.5 millimeters (0.332 nm x 4.6 million). However, a large DNA molecule such as the E. coli chromosomal DNA does not remain a straight rigid molecule in a suspension. Brownian motion will generate curvature and bends in DNA. The maximum length up to which a double-helical DNA remains straight by resisting the bending enforced by Brownian motion is ~50 nm or 150 bp, which is called the persistence length. Thus, pure DNA becomes substantially condensed without any additional factors; at thermal equilibrium, it assumes a random coil form. The random coil of E. coli chromosomal DNA would occupy a volume (4/3 π r3) of ~ 523 μm3, calculated from the radius of gyration (Rg = (√N a)/√6) where a is the Kuhn length (2 x persistence length), and N is the number of Kuhn length segments in the DNA (total length of the DNA divided by a). Although DNA is already condensed in the random coil form, it still cannot assume the volume of the nucleoid which is less than a micron. Thus, the inherent property of DNA is not sufficient: additional factors must help condense DNA further on the order of ~103 (volume of the random coil divided by the nucleoid volume). The second essential aspect of nucleoid formation is the functional arrangement of DNA. Chromosomal DNA is not only condensed but also functionally organized in a way that is compatible with DNA transaction processes such as replication, recombination, segregation, and transcription. Almost five decades of research beginning in 1971, has shown that the final form of the nucleoid arises from a hierarchical organization of DNA. At the smallest scale (1 kb or less), nucleoid-associated DNA architectural proteins condense and organize DNA by bending, looping, bridging or wrapping DNA. At a larger scale (10 kb or larger), DNA forms plectonemic loops, a braided form of DNA induced by supercoiling. At the megabase scale, the plectonemic loops coalesce into six spatially organized domains (macrodomains), which are defined by more frequent physical interactions among DNA sites within the same macrodomain than between different macrodomains. Long- and short-range DNA-DNA connections formed within and between the macrodomains contribute to condensation and functional organization. Finally, the nucleoid is a helical ellipsoid with regions of highly condensed DNA at the longitudinal axis.
In eukaryotes, genomic DNA is condensed in the form of a repeating array of DNA-protein particles called nucleosomes.
A nucleosome consists of ~146 bp of DNA wrapped around an octameric complex of the histone proteins. Although bacteria do not have histones, they possess a group of DNA binding proteins referred to as nucleoid-associated proteins (NAPs) that are functionally analogous to histones in a broad sense. NAPs are highly abundant and constitute a significant proportion of the protein component of nucleoid.
A distinctive characteristic of NAPs is their ability to bind DNA in both a specific (either sequence- or structure-specific) and non-sequence specific manner. As a result, NAPs are dual function proteins. The specific binding of NAPs is mostly involved in gene-specific transcription, DNA replication, recombination, and repair. At the peak of their abundance, the number of molecules of many NAPs is several orders of magnitude higher than the number of specific binding sites in the genome. Therefore, it is reasoned that NAPs bind to the chromosomal DNA mostly in the non-sequence specific mode and it is this mode that is crucial for chromosome compaction. Non-sequence specific binding of a NAP may not be completely random; there could be low-sequence specificity and or structural specificity due to sequence-dependent DNA conformation or DNA conformation created by other NAPs.
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Nucleoid AI simulator
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Nucleoid
The nucleoid (meaning nucleus-like) is an irregularly shaped region within the prokaryotic cell that contains all or most of the genetic material. The chromosome of a typical prokaryote is circular, and its length is very large compared to the cell dimensions, so it needs to be compacted in order to fit. In contrast to the nucleus of a eukaryotic cell, it is not surrounded by a nuclear membrane. Instead, the nucleoid forms by condensation and functional arrangement with the help of chromosomal architectural proteins and RNA molecules as well as DNA supercoiling. The length of a genome widely varies (generally at least a few million base pairs) and a cell may contain multiple copies of it.
There is not yet a high-resolution structure known of a bacterial nucleoid, however key features have been researched in Escherichia coli as a model organism. In E. coli, the chromosomal DNA is on average negatively supercoiled and folded into plectonemic loops, which are confined to different physical regions, and rarely diffuse into each other. These loops spatially organize into megabase-sized regions called macrodomains, within which DNA sites frequently interact, but between which interactions are rare. The condensed and spatially organized DNA forms a helical ellipsoid that is radially confined in the cell. The 3D structure of the DNA in the nucleoid appears to vary depending on conditions and is linked to gene expression so that the nucleoid architecture and gene transcription are tightly interdependent, influencing each other reciprocally.
In many bacteria, the chromosome is a single covalently closed (circular) double-stranded DNA molecule that encodes the genetic information in a haploid (monoploid) form. The size of the DNA varies from 500,000 to several million base pairs (bp) encoding from 500 to several thousand genes depending on the organism. The chromosomal DNA is present in cells in a highly compact, organized form called the nucleoid (meaning nucleus-like), which is not encased by a nuclear membrane as in eukaryotic cells. The isolated nucleoid contains 80% DNA, 10% protein, and 10% RNA by weight.
The gram-negative bacterium Escherichia coli is a model system for nucleoid research into how chromosomal DNA becomes the nucleoid, the factors involved therein, what is known about its structure, and how some of the DNA structural aspects influence gene expression.
There are two essential aspects of nucleoid formation; condensation of a large DNA into a small cellular space and functional organization of DNA in a three-dimensional form. The haploid circular chromosome in E. coli consists of ~ 4.6 million bp. If DNA is relaxed in the B form, it would have a circumference of ~1.5 millimeters (0.332 nm x 4.6 million). However, a large DNA molecule such as the E. coli chromosomal DNA does not remain a straight rigid molecule in a suspension. Brownian motion will generate curvature and bends in DNA. The maximum length up to which a double-helical DNA remains straight by resisting the bending enforced by Brownian motion is ~50 nm or 150 bp, which is called the persistence length. Thus, pure DNA becomes substantially condensed without any additional factors; at thermal equilibrium, it assumes a random coil form. The random coil of E. coli chromosomal DNA would occupy a volume (4/3 π r3) of ~ 523 μm3, calculated from the radius of gyration (Rg = (√N a)/√6) where a is the Kuhn length (2 x persistence length), and N is the number of Kuhn length segments in the DNA (total length of the DNA divided by a). Although DNA is already condensed in the random coil form, it still cannot assume the volume of the nucleoid which is less than a micron. Thus, the inherent property of DNA is not sufficient: additional factors must help condense DNA further on the order of ~103 (volume of the random coil divided by the nucleoid volume). The second essential aspect of nucleoid formation is the functional arrangement of DNA. Chromosomal DNA is not only condensed but also functionally organized in a way that is compatible with DNA transaction processes such as replication, recombination, segregation, and transcription. Almost five decades of research beginning in 1971, has shown that the final form of the nucleoid arises from a hierarchical organization of DNA. At the smallest scale (1 kb or less), nucleoid-associated DNA architectural proteins condense and organize DNA by bending, looping, bridging or wrapping DNA. At a larger scale (10 kb or larger), DNA forms plectonemic loops, a braided form of DNA induced by supercoiling. At the megabase scale, the plectonemic loops coalesce into six spatially organized domains (macrodomains), which are defined by more frequent physical interactions among DNA sites within the same macrodomain than between different macrodomains. Long- and short-range DNA-DNA connections formed within and between the macrodomains contribute to condensation and functional organization. Finally, the nucleoid is a helical ellipsoid with regions of highly condensed DNA at the longitudinal axis.
In eukaryotes, genomic DNA is condensed in the form of a repeating array of DNA-protein particles called nucleosomes.
A nucleosome consists of ~146 bp of DNA wrapped around an octameric complex of the histone proteins. Although bacteria do not have histones, they possess a group of DNA binding proteins referred to as nucleoid-associated proteins (NAPs) that are functionally analogous to histones in a broad sense. NAPs are highly abundant and constitute a significant proportion of the protein component of nucleoid.
A distinctive characteristic of NAPs is their ability to bind DNA in both a specific (either sequence- or structure-specific) and non-sequence specific manner. As a result, NAPs are dual function proteins. The specific binding of NAPs is mostly involved in gene-specific transcription, DNA replication, recombination, and repair. At the peak of their abundance, the number of molecules of many NAPs is several orders of magnitude higher than the number of specific binding sites in the genome. Therefore, it is reasoned that NAPs bind to the chromosomal DNA mostly in the non-sequence specific mode and it is this mode that is crucial for chromosome compaction. Non-sequence specific binding of a NAP may not be completely random; there could be low-sequence specificity and or structural specificity due to sequence-dependent DNA conformation or DNA conformation created by other NAPs.