In the Cell and Life and Biodiversity topics, we discussed the differences between prokaryotes and eukaryotes. One of the major differences discussed was the absence of a nucleus in prokaryotes, which actually gives them some advantages. We will talk in this topic about how DNA is arranged in prokaryotes and why it is designed the way it is.
Bacterial genome
The totality of hereditary material contained in every cell of an organism is called the genome. From a chemical point of view, the DNA that bacteria have is the same as eukaryotic DNA. It contains the same nitrogenous bases and forms the same types of spirals (for more information read the DNA topic). However, bacteria don't have histone proteins, nuclei, and some other molecules that eukaryotes have, so bacterial DNA is structured differently. The genome of bacteria can exist in two possible forms – a large chromosome in a nucleus – type area or an additional circular plasmid, which is an optional form of DNA (pic. 1).
The main genetic information is stored in a chromosome – a large, circular molecule located in the center of a nucleus-like zone, which is associated with a protein. RNA is copied from this DNA, and cellular proteins are synthesized from that RNA. This chromosome can be linear or circular. The functions of a "large" chromosome do not differ much from the functions of the chromosomes of eukaryotic animals, but prokaryotic chromosomes are usually more compact and contain fewer "idle" elements.
Although bacteria do not have a well-formed nucleus, DNA does not just float in a cell. In the center of the cell, there is usually a zone called a nucleoid – this is where compact DNA is stored, as well as some auxiliary proteins. Although these proteins differ in structure from eukaryotic histones, they are functionally very similar, therefore they are often called histone-like. RNA is also most often found in this nucleoid zone.
The bacterial genome is generally smaller than the eukaryotic one, but its size varies from strain to strain. One of the most famous model organisms in biology – Escherichia coli – has about 4000 genes (or 4.6 Mb), while a mitochondrion, an organelle that was once a normal prokaryotic cell, has only about 30 (16.6 kB).
Bacterial transcription
To increase efficiency, genes in the chromosome often overlap, and the DNA itself is arranged according to an operon principle. An operon is a group of functionally interconnected genes (pic. 2). Proteins encoded by the genes of one operon are, most often, enzymes that catalyze different stages of one metabolic pathway. Transcription of an operon gene leads to the synthesis of one common mRNA molecule. Such a system allows the bacterium to respond very quickly to changes in the environment, immediately synthesizing all the necessary proteins.
During transcription, DNA is copied into newly synthesized RNA (read the topic Central Dogma for more information). From the point of view of a bacterial genome, we are interested in two things here.
First, bacterial RNA polymerase has an additional subunit called the σ factor (eukaryotes do not have this factor, their transcription is regulated differently) that is necessary for the polymerase to recognize specific binding sequences in DNA called promoters.
Second, transcription and translation in bacterial cells can occur simultaneously in the cytoplasm of the cell because there is no nucleus, whereas in eukaryotes, transcription occurs in the nucleus, and translation occurs in the cytoplasm. This system also adds to the bacterial cell's maneuverability, since extra time is not spent on transporting RNA into the cytoplasm.
Plasmids
Plasmids are additional structures separate from the main genome. They look like a small, closed ring of DNA. They are mainly found in bacteria, but you also can find them in some archaea and, rarely, in eukaryotes (fungi and higher plants). Plasmids present another way to store DNA, and they are not found in all cells. They exist separately from chromosomes, and they are able to carry out independent replication. Cells can contain either one, two, or dozens of copies of plasmids. The size of plasmids is calculated in kilobase pairs (kilobases, kbp). 1 kb is equal to 1000 nucleotides in RNA and single-stranded DNA or 1000 pairs of nucleotides (bp) in double-stranded DNA.
The main function of plasmids is to contain special genes responsible for the adaptability of bacteria to external influences and irritants – for example, antibiotic resistance genes (pic. 3). A plasmid carrying a gene for resistance to an antibiotic or antibiotics is called an R-plasmid or R-factor. Synthesizing the proteins encoded in such a plasmid allows the cell to become resistant to antibiotic exposure. Plasmids often encode a protein that disrupts the transport of antibiotics into the cell. Plasmids transfer easily to neighboring bacteria during an exchange process called conjugation (pic. 4).
R-plasmids can even be transferred between bacteria of different genera and species: for example, from Pseudomonas aeruginosa to Escherichia coli. This means that resistance can spread widely, and at some point, there may be a situation where not a single existing antibiotic will destroy a particular bacterium.
Plasmids can be transferred from one bacteria to another during the conjugation process, and biologists often introduce specially prepared plasmids into bacteria so they will produce the protein coded in the plasmid. This process is called transformation.
Conclusion
The bacterial genome differs in structure from the eukaryotic genome. In addition to a main circular chromosome, most prokaryotes have a small circular plasmid that carries "useful" genes and which they can exchange with other bacteria. Bacteria have nucleoids, which are analogous to the nucleus in eukaryotes, but they don't have nuclear membranes or histone proteins. They do have auxiliary DNA-associated proteins though. Transcription in bacteria is slightly different from eukaryotic transcription. Bacterial polymerases rely on a protein called the σ-factor to help them recognize promoter regions, and transcription and translation both occur in the cytoplasm due to the lack of a nucleus.