Prokaryotic Cell Structure: Structures Within the Cytoplasm

II. THE PROKARYOTIC CELL: BACTERIA

B. PROKARYOTIC CELL STRUCTURE

3. Structures Located Within the Cytoplasm

b. The Nucleoid

The overall purpose of this Learning Object is:
1) to learn the chemical makeup and the functions associated with the nucleoid of bacteria;
2) to introduce the relationship between components of the bacterial nucleoid and body defenses; and
3) to introduce how certain antimicrobial agents intefere with bacterial DNA replication.

LEARNING OBJECTIVES FOR THIS SECTION

In this section on Prokaryotic Cell Structure we are looking at the various organelles or structures that make up a bacterium. As mentioned in the introduction to this section, a typical bacterium usually consists of:

a cytoplasmic membrane surrounded by a peptidoglycan cell wall and maybe an outer membrane;
a fluid cytoplasm containing a nuclear region (nucleoid) and numerous ribosomes; and
often various external structures such as a glycocalyx, flagella, and pili.

Structures located within the cytoplasm of bacteria include the nucleoid, ribosomes, and in some bacteria, plasmids, endospores, inclusion bodies, and organelles used for photosynthesis. We will now look at the bacterial nucleoid.

The Nucleoid (def)

A. Structure and Composition

The term genome (def) refers to the sum of an organism's genetic material. The bacterial genome is composed of chromosomal deoxyribonucleic acid or DNA and represents the bacterium's nucleoid. Unlike the eukaryotic nucleus, the bacterial nucleoid has no nuclear membrane or nucleoli (see Fig. 1).

As mentioned earlier in this unit, the bacterial nucleoid does not divide by mitosis (def). 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. As the bacterium grows to full size, the newly replicated chromosomes become separated (see Fig. 3).

Since bacteria are haploid (def), that is they have only one chromosome and only reproduce asexually, there is also no meiosis (def) in bacteria.

For More Information: Deoxyribonucleic Acid DNA from Unit 6

The nucleoid 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. 2). 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 group of enzymes called DNA topoisomerases then supercoil 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 transcibed into mRNA.

The bacterial enzymes called DNA topoisomerases (def) are 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. Topoisomerases are essential for these processes. 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. Functions

The nucleoid is the genetic material of the bacterium. Genes (def) located along the DNA are transcribed into RNA that, in the case of mRNA, is then translated into protein at the ribosomes. In other words, DNA determines what proteins and enzymes an organism can synthesize and, therefore, what chemical reactions it is able to carry out.

For More Information: Prokaryotic DNA Replication from Unit 6

C. Significance to Initiating Body Defense

In order to protect against infection, one of the things the body must initially do is detect the presence of microorganisms. The body does this by recognizing molecules unique to microorganisms that are not associated with human cells. These unique molecules are called pathogen-associated molecular patterns or PAMPS. (Because all microbes, not just pathogenic microbes, possess PAMPs, pathogen-associated molecular patterns are sometimes referred to as microbe-associated molecular patterns or MAMPs.)

Bacterial and viral genomes contain a high frequency of unmethylated cytosine-guanine dinucleotide sequences (a cytosine lacking a methyl or CH₃ group and located adjacent to a guanine). Mammalian DNA has a low frequency of cytosine-guanine dinucleotides and most are methylated. These unmethylated cytosine-guanine dinucleotide sequences in bacterial DNA are PAMPS that bind to pattern-recognition receptors on a variety of defense cells of the body and triggers innate immune defenses such as inflammation, fever, and phagocytosis.

For More Information: Pathogen-Associated Molecular Patterns (PAMPs) from Unit 4

For More Information: Pattern-Recognition Receptors from Unit 4

D. Using Antimicrobial Agents that Inhibiting Normal Nucleic Acid Replication to Control Bacteria

Some antibacterial chemotherapeutic affect bacteria by inhibiting normal nucleic acid replication.

The fluoroquinolones (norfloxacin, lomefloxacin, fleroxacin, ciprofloxacin, enoxacin, trovafloxacin, etc.) work by inhibiting one or more of the topoisomerases (def), the enzymes needed for bacterial nucleic acid synthesis.

Co-trimoxazole, a combination of sulfamethoxazole and trimethoprim, block enzymes in the bacteria pathway required for the synthesis of tetrahydrofolic acid, a cofactor needed for bacteria to make the nucleotide bases thymine, guanine, uracil, and adenine. Without the tetrahydrofolic acid, the bacteria cannot synthesize DNA or RNA.

Flash animation illustrating a normal bacterial enzyme reaction.

Flash animation illustrating antimicrobial agents may inactivate a bacterial enzyme.

Antimicrobial chemotherapy will be discussed in greater detail later in Unit 2 under Control of Bacteria by Using Antibiotics and Disinfectants.

Preview of "Chemotherapeutic Control of Bacteria" from Unit 2.

For further information on the bacterial nucleoid and its functions see the online Microbiology Web Textbook at the University of Wisconsin-Madison.

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