October 22


So far in the course, we have been considering the genetics of eukaryotic organisms. Bacteria (prokaryotes) are much smaller in size than eukaryotic cells, and they have much smaller genomes.


1. What are the basic properties of the genomes of bacteria?

Most bacteria have a genome that consists of a single DNA molecule (i.e., one chromosome) that is several million base pairs in size and is "circular" (doesn't have ends like chromosomes of eukaryotic organisms). In addition, bacteria may have one or more smaller circular DNA molecules, called plasmids, that contain (usually) non-essential genes.

In general, a single bacterium will be replicating its DNA whenever possible (i.e., if "food" chemicals are present in an aqueous environment in the right temperature range). Once the genome is completely replicated, the two circular DNAs separate and the cell divides. The process is a lot simpler than mitosis or meiosis, because bacteria don't have multiple chromosomes that have to be sorted out correctly to the two daughter cells. Thus, bacteria are able to grow and divide much faster than eukaryotic cells can.


2. Since bacteria are haploid, is there any way that something at all similar to crossing-over can ever occur in bacteria?

Figure 8.3: Some E.coli have a plasmid called F (~100 Kbp containing about 50 non-essential genes), which can spread, via DNA replication, to another E. coli cell. This transfer of DNA is possible because some of the genes on F code for proteins that interact together to form a hollow tubular "pilus" which forms a connecting bridge through which single stranded plasmid DNA passes.

Figure 8.11: A region along the F plasmid is homologous with several regions along the chromosome, and thus a recombination process (equivalent of a single cross-over) can cause F to become integrated into the chromosome. An E. coli that has F in the chromosome is called an Hfr strain.

Figure 8.12: An Hfr E. coli cell is able to transfer portions of its chromosome to an F-minus E. coli. Subsequent homologous recombination (now the equivalent of a two-strand double cross-over) can change the genotype of the F-minus cell. For example, imagine that the Hfr cell has allele A of gene alpha, while the F-minus cell has allele a. If allele A gets transferred over to the F-minus cell, followed by a double cross-over that spans gene alpha, the end result is that the F-minus cell's alpha genotype has changed from a to A.


3. What common features are found in bacterial genomes that have been sequenced?

The genome of E. coli (sequenced in 1997) is about 4 million base pairs with about 3000 genes. These numbers are quite average for bacteria; i.e., most have a genome size of several million base pairs containing a few thousand genes. (For example, in a study done here at Lehigh in the 1990's, we found that the pathogenic bacterium Clostridium difficile has a genome size of 4.4 million base pairs ( Norwood and Sands, Gene vol. 201, 159-168 (1997) ). Thus, bacterial genomes are only about 0.1% as big as the human genome, and have about 10% as many genes as we do.

A comparison of those two percentages shows immediately that in bacteria the "gene density" (how many genes there are per unit length along the genome) is much higher than in humans. That is, whereas a one million base pair length in us contains on average about 10 genes, one million base pairs of bacterial DNA contains about 500 to 1000 genes. This much greater gene density is due to a combination of factors: (1) bacterial genes have no introns, (2) the average number of codons in bacterial genes is less than in human genes, (3) neighboring genes are very close together throughout the genome; i.e., there are hardly any big regions of non-coding DNA between genes.