Nucleoid in Prokaryotic cell
B. PROKARYOTIC CELL ANATOMY
In this section on Prokaryotic Cell Anatomy we are looking at the various anatomical parts that make up a bacterium. As mentioned in the introduction to this section, a typical bacterium usually consists of:
We will now look at the bacterial chromosome located in the nuclear region called the nucleoid.
A. Structure and Composition of the Bacterial Chromosome
The term genome (def) refers to the sum of an organism's genetic material. The bacterial genome is composed of a single molecule of chromosomal deoxyribonucleic acid or DNA and is located in a region of the bacterial cytoplasm visible when viewed with an electron microscope called the nucleoid. Unlike the eukaryotic nucleus, the bacterial nucleoid has no nuclear membrane or nucleoli (see Fig. 1).
In general it is thought that during DNA replication (discussed in Unit 6), each strand of the replicating bacterial DNA attaches to proteins at what will become the cell division plane. For example, Par proteins function to separate bacterial chromosomes to opposite poles of the cell during cell division. They bind to the origin of replication of the DNA and physically pull or push the chromosomes apart, similar to the mitotic apparatus of eukaryotic cells.
In the center of the bacterium, a group of proteins called Fts (filamentous temperature sensitive) proteins interact to form a ring at the cell division plane. These proteins form the cell division apparatus known as the divisome and are directly involved in bacterial cell division by binary fission. The divisome is responsible for directing the synthesis of new cytoplasmic membrane and new peptidoglycan to form the division septum.
Since bacteria are haploid (def), that is they have only one chromosome and only reproduce asexually, there is also no meiosis (def) in bacteria.
The bacterial chromosome is one long, single molecule of double stranded, helical, supercoiled DNA (def). In most bacteria, the two ends of the double-stranded DNA covalently bond together to form both a physical and genetic circle (def). The chromosome is generally around 1000 µm long and frequently contains as many as 3500 genes (see Fig. 3). E. coli, a bacterium that is 2-3 µm in length, has a chromosome approximately 1400 µm long.
To enable a macromolecule this large to fit within the bacterium, histone-like proteins bind to the DNA, segregating the DNA molecule into around 50 chromosomal domains and making it more compact. A DNA topoisomerase enzyme called DNA gyrase then supercoils each domain around itself, forming a compacted mass of DNA approximately 0.2 µm in diameter. In actively growing bacteria, projections of the nucleoid extend into the cytoplasm. Presumably, these projections contain DNA that is being transcribed into mRNA.Supercoils are both inserted and removed by topoisomerases.
DNA topoisomerases (def) are, therefore, essential in the unwinding, replication, and rewinding of the circular, supercoiled bacterial DNA. In order for the long molecule of DNA to fit within the bacterium, the DNA must be supercoiled. However, this supercoiled DNA must be uncoiled and relaxed in order for DNA polymerase to bind for DNA replication and RNA polymerase to bind for transcription of the DNA. For example, a topoisomerase called DNA gyrase catalyzes the negative supercoiling of the circular DNA found in bacteria. Topoisomerase IV, on the other hand, is involved in the relaxation of the supercoiled circular DNA, enabling the separation of the interlinked daughter chromosomes at the end of bacterial DNA replication.
B. DNA Replication in Bacteria
In general, DNA is replicated by uncoiling of the helix, strand separation by breaking of the hydrogen bonds between the complementary strands, and synthesis of two new strands by complementary base pairing (def). Replication begins at a specific site in the DNA called the origin of replication (oriC).
DNA replication is bidirectional from the origin of replication. To begin DNA replication, unwinding enzymes called DNA helicases (def) cause short segments of the two parent DNA strands to unwind and separate from one another at the origin of replication to form two "Y"-shaped replication forks (def). These replication forks are the actual site of DNA copying (see Fig. 4). All the proteins involved in DNA replication aggregate at the replication forks to form a replication complex called a replisome .
Single-strand binding proteins bind to the single-stranded regions so the two strands do not rejoin. Unwinding of the double-stranded helix generates positive supercoils ahead of the replication fork. Enzymes called topoisomerases counteract this by producing breaks in the DNA and then rejoin them to form negative supercoils in order to relieve this stress in the helical molecule during replication.
As the strands continue to unwind and separate in both directions around the entire DNA molecule, new complementary strands are produced by the hydrogen bonding of free DNA nucleotides with those on each parent strand. As the new nucleotides line up opposite each parent strand by hydrogen bonding, enzymes called DNA polymerases join the nucleotides by way of phosphodiester bonds. Actually, the nucleotides lining up by complementary base pairing are deoxynucleotide triphosphates, composed of a nitrogenous base, deoxyribose, and three phosphates. As the phosphodiester bond forms between the 5' phosphate group of the new nucleotide and the 3' OH of the last nucleotide in the DNA strand, two of the phosphates are removed providing energy for bonding (see Fig. 6). In the end, each parent strand serves as a template to synthesize a complementary copy of itself, resulting in the formation of two identical DNA molecules (see Fig. 7). In bacteria, Par proteins function to separate bacterial chromosomes to opposite poles of the cell during cell division. They bind to the origin of replication of the DNA and physically pull or push the chromosomes apart, similar to the mitotic apparatus of eukaryotic cells. Fts proteins, such as FtsK in the divisome, also help in separating the replicated bacterial chromosome.
In reality, DNA replication is more complicated than this because of the nature of the DNA polymerases. DNA polymerase enzymes are only able to join the phosphate group at the 5' carbon of a new nucleotide to the hydroxyl (OH) group of the 3' carbon of a nucleotide already in the chain. As a result, DNA can only be synthesized in a 5' to 3' direction while copying a parent strand running in a 3' to 5' direction.
Each DNA strand has two ends. The 5' end of the DNA is the one with the terminal phosphate group on the 5' carbon of the deoxyribose; the 3' end is the one with a terminal hydroxyl (OH) group on the deoxyribose of the 3' carbon of the deoxyribose (see Fig. 8). The two strands are antiparallel, that is they run in opposite directions. Therefore, one parent strand - the one running 3' to 5' and called the leading strand (def) - can be copied directly down its entire length (see Fig. 9). However, the other parent strand - the one running 5' to 3' and called the lagging strand (def) - must be copied discontinuously in short fragments (Okazaki fragments) of around 100-1000 nucleotides each as the DNA unwinds. This occurs, as mentioned above, at the replisome. The lagging DNA strand loops out from the leading strand and this enables the replisome to move along both strands pulling the DNA through as replication occurs. It is the actual DNA, not the DNA polymerase that moves during bacterial DNA replication (see Fig. 5).