Nucleoids

Azam, T., Ishihama, A. Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity. The Journal of Biological Chemistry, Vol.274, No.46, (November 1999), pp. 33105-33113, ISSN 0021-9258... 

Prior, S. and B. Riemann. 1998. Effects of tributyltin, linear alkylbenzenesulfonates, and nutrients (nitrogen and phosphorus) on nucleoid-containing bacteria. Environ. Toxicol. Chem. 17 1473-1480. 

Mitochondria (45-56) are organelles possessing a double membrane, the inner of which is invaginated as cristae. An intermembrane space exists between the inner and outer membranes. The inner membrane consists of an unusually high amount of protein and possesses spherically shaped particles approx 9 nm in diameter. These particles appear to be equivalent to F0, Fb and adenosine triphosphatase. In contrast to the inner membrane, the outer membrane is smooth and appears to be connected to the smooth er. This membrane is permeable to all molecules of 10,000 Dalton or less. A mitochondrial matrix is enclosed by the inner membrane and consists of a ground substance of particles, nucleoids, ribosomes, and electron-transparent regions containing DNA. 

Circadian rhythm of total protein synthesis— cytoplasm and chloroplasts of Gonyaulax polyhedra Sulfate incorporation in Udotea petiolata thalli Photosynthetic activity of phytoplankton Thymidine incorporation into Nostoc Chloroplast nucleoids of Zea mays Localization of chloroplast binding protein in cells of wheat leaves Distributon of [14C]-dichlorophenoxyacetic acid Donner et al. (13) Mariani and Favoli (14) Bourdier and Bohatier (15) Favoli and Grilli (16) Lindbeck et al. (17) Bronsema et al. (18)... 

Lindbeck AGC, Rose RJ, Lawrence ME, Possingham JV. The chloroplast nucleoids of the bundle sheath and meosophyll cells of Zea mays. Physiol Plant 1989 75 7-12. 

Figure 4.1 The comet assay. A single-cell suspension is embedded in agarose on a slide. Cells are then subject to lysis followed by electrophoresis. If present, damaged DNA migrates out of the nucleoid structure during electrophoresis to producing a characteristic comet shape. Double-strand breaks are revealed under neutral conditions, whereas alkali conditions additionally show single-strand breaks and alkali labile sites. Image analysis of stained DNA is used to quantitate the amount of damaged DNA in the comet tail.

A single E. coli cell has a volume of about 0.88 pm. One-sixth of this consists of membranes and one-sixth is DNA (known as the nucleoid ). The rest of the internal space of the cell is known as cytoplasm (not cytosol see p. 198). 

FIGURE 1-3 The universal features of living cells. All cells have a nucleus or nucleoid, a plasma membrane, and cytoplasm. The cytosol is defined as that portion of the cytoplasm that remains in the supernatant after centrifugation of a cell extract at 150,000 g for 1 hour. 

All cells have, for at least some part of their life, either a nucleus or a nucleoid, in which the genome—... 

Bacterial cells share certain common structural features, but also show group-specific specializations (Fig. 1-6). E. coli is a usually harmless inhabitant of the human intestinal tract. The E. coli cell is about 2 prri long and a little less than 1 prri in diameter. It has a protective outer membrane and an inner plasma membrane that encloses the cytoplasm and the nucleoid. Between the inner and outer membranes is a thin but strong layer of polymers called peptidoglycans, which gives the cell its shape and rigidity. The plasma membrane and the... 

Nucleoid Contains a single, simple, long circular DNA molecule. 

The cytoplasm of E. coli contains about 15,000 ribosomes, thousands of copies each of about 1,000 different enzymes, numerous metabolites and cofactors, and a variety of inorganic ions. The nucleoid contains a single, circular molecule of DNA, and the cytoplasm (like that of most bacteria) contains one or more smaller, circular segments of DNA called plasmids. In nature, some plasmids confer resistance to toxins and antibiotics in the environment. In the laboratory, these DNA segments are especially amenable to experimental manipulation and are extremely useful to molecular geneticists. 

All cells are bounded by a plasma membrane have a cytosol containing metabolites, coenzymes, inorganic ions, and enzymes and have a set of genes contained within a nucleoid (prokaryotes) or nucleus (eukaryotes). 

Bacterial cells contain cytosol, a nucleoid, and plasmids. Eukaryotic cells have a nucleus and are multicompartmented, segregating certain processes in specific organelles, which can be separated and studied in isolation. 

Genome DNA with nonhistone protein genome in nucleoid, not surrounded by membrane DNA complexed with histone and nonhistone proteins in chromosomes chromosomes in nucleus with membranous envelope... 

As in the case of protein structure (Chapter 4), it is sometimes useful to describe nucleic acid structure in terms of hierarchical levels of complexity (primary, secondary, tertiary). The primary structure of a nucleic acid is its covalent structure and nucleotide sequence. Any regular, stable structure taken up by some or all of the nucleotides in a nucleic acid can be referred to as secondary structure. All structures considered in the remainder of this chapter fall under the heading of secondary structure. The complex folding of large chromosomes within eukaryotic chromatin and bacterial nucleoids is generally considered tertiary structure this is discussed in Chapter 24. 

We now turn briefly to the structure of bacterial chromosomes. Bacterial DNA is compacted in a structure called the nucleoid, which can occupy a significant... 

FIGURE 24-36 E. coli cells showing nucleoids. The DNA is stained with a dye that fluoresces when exposed to UV light. The light area defines the nucleoid. Note that some cells have replicated their DNA but have not yet undergone cell division and hence have multiple nucleoids. 

Bacterial chromosomes are also extensively compacted into the nucleoid, but the chromosome appears to be much more dynamic and irregular in structure than eukaryotic chromatin, reflecting the shorter cell cycle and very active metabolism of a bacterial cell. 

DNA is a polydeoxyribonucleotide that contains many monodeoxy-ribonucleotides covalently linked by 3 ->5 -phosphodiester bonds. With the exception of a few viruses that contain single-stranded DNA, DNA exists as a double-stranded molecule, in which the two strands wind around each other, forming a double helix. In eukaryotic cells, DNA is found associated with various types of proteins (known collectively as nucleoprotein) present in the nucleus, whereas in prokaryotes, the protein-DNA complex is present in the nucleoid. 

Each nucleotide pair contributes 0.34 nm to the length of the DNA molecule thus, the total length of DNA of an E. coli chromosome is 1.4 mm. This is about 700 times the length of the cell which contains it. Clearly, the molecules of DNA are highly folded, a fact that accounts for their appearance in the electron microscope as dense aggregates called nucleoids, which occupy about one-fifth of the cell volume (Fig. 1-4). 

If bacterial cells are lysed under certain conditions, e.g., in 1 M NaCl or in the presence of a "physiological" 5 mM spermidine, the entire bacterial chromosome can be isolated.10 The DNA in these isolated chromosomes retains some torsional tension that, however, can be relaxed by nicking with nucleases or by y-irradiation. However, a single nick relaxes the DNA very little. The explanation appears to be that the DNA is held by proteins of the nucleoid matrix in a series of loops (Fig. 27-2). A single nick relaxes just... 

In bacteria transcription and translation are closely linked. Polyribosomes may assemble on single DNA strands as shown in Fig. 28-5. It has often been assumed that RNA synthesis occurs on loops of DNA that extend out into the cytosol. However, recent studies indicate that most transcription occurs in the dense nucleoid and that assembly of ribosomes takes place in the cytosol.2683 In a similar way eukaryotic transcription occurs in the nucleus and protein synthesis in the cytosol. Nevertheless, some active ribosomes are present in the nucleus.26813... 

Location Nucleoid, chromatin body or Nucleus, mitochondria,... 

---