# Structural Biochemistry/The Genetics of Bacteria
## Overview

Bacteria are very adaptable to their environments. They divide by binary fusion, preceded by replication of bacterial chromosome. Bacteria proliferate rapidly and cannot increase genetic diversity by meiosis and fertilization. They have low mutation rate, but can have a significant effect on genetic diversity because of rapid rate of proliferation. Also, genetic recombination also adds genetic diversity to a population.

## Genetic Recombination

Genetic recombination can produce new bacterial strains. Genetic recombination for bacteria is combining DNA from two individuals into a single individual. For example, arg +trp- and arg-trp+ strain. Genetic recombination can occur by transformation, transduction, and conjugation.

## Transformation

Transformation is the alternation of a bacteria’s genotype by the uptake of a naked, foreign piece of DNA. Foreign DNA can be incorporated into bacteria’s chromosome by crossing over at homologous (similar) sequences. If foreign DNA is plasmid DNA, it will remain independent. Example: Calcium chloride treatment stimulate E. coli to take up small pieces of foreign DNA.

## Transduction

Transduction is when phages carry DNA from one bacterium to another. Generalized transduction – DNA from infected cell is accidentally packaged into a phage, and transferred to another bacterium by infection. This occurs in lytic cycle. Specialized transduction – when prophage (lysogenic cycle) is excised from bacterial genome. It takes a small amount of bacterial DNA with it. This DNA is then package into a phage and also transferred to another bacterium by infection.

## Conjugation

Conjugation is the direct transfer of DNA between bacterial cells that are temporarily joined.
F factor is a piece of DNA conferred as “maleness”. F factor can exist in bacterial chromosome or as a plasmid. It encodes genes required for formation of sex pili. More specifically bacteria with F factor are F+. The “female” cells are F-.
“Male” bacteria form sex pili which attaches to “female” bacteria. If plasmid is just F factor, plasmid is transferred. If F factor is integrated into bacterial chromosome, bacterial DNA is also transferred. If F factor integrates into bacterial chromosome, bacteria is a Hfr (High frequency of recombination) cell.

## Mobile genetic elements

Transposon is a piece of DNA that can move from one point to another in a bacterial cell’s genome. It doesn’t exist independently. It can move DNA within bacterial chromosome or from one plasmid to another (i.e. to give multiple druge\ resistance). Cut and paste transposition – some transposons jump from one location to another. Replicative transposition – transposon is copied, and the copy inserts in the new location Insertion sequences are the simplest transposons. They contain one gene, transposase, which catalyzes transposition. Composite transposons contain addition genes. These additional genes are stuck between two insertion sequences that travel together. Mechanism: The DNA is cut in staggered fashion by transposase. Insertion sequence is inserted (also by transposase). The DNA polymerase and ligase fill in DNA and ligate ends. The DNA next to the insertion sequence thus contains direct repeats.

## Control of bacteria gene expression

There are two levels of metabolic control. Cells can vary the numbers of specific enzyme molecules made and regulate gene expression. Cells can adjust the activity of the enzyme already present. This occurs quickly, since it does not require transcription. Tryptophan Example: If the cell is growing in presence of tryptophan, it does not need to synthesize it. When tryptophan is present, it inhibits the first enzyme involved in synthesizing tryptophan. The presence of tryptophan also causes cell to stop making the enzymes needed for tryptophan synthesis (occurs at the level of transcription).

## Operons

In bacteria, the genes for a particular pathway are clustered together on the chromosome. A single promoter serves all the genes of the operon. The clustered genes constitute a transcription unit (one long mRNA is made). The long mRNA is translated into separate polypeptides because the mRNA contains separate start and stop codons for each polypeptide. An operon has a single on-off switch that controls the expression of all the genes. This switch is termed an operator. The operator is located within the promoter or between the promoter and the genes. It controls access of RNA polymerase to the genes. The cluster of genes, promoter and operator, is termed an operon. The operon can be switched off by a protein call a repressor. The repressor is the product of a regulatory gene, which is not part of the operon and has its own promoter. The regulatory genes are transcribed continuously at a low rate. Many repressors are allosteric molecules, with two shapes: active and inactive. Corepressor is a small molecule that interacts with a repressor to switch an operon off. Trp operon is an example of a repressible operon. It is normally transcribed. When tryptophan is present, it binds with the trp repressor, triggering an allosteric change. The trp repressor with bound tryptophan binds to the operator, shutting off transcription of the trp operon. The tryptophan is a corepressor.

## Repressible versus inducible operon

Trp operon is repressible because transcription is inhibited by a specific small molecule (i.e. tryptophan) interacts with a regulatory gene. Inducible operons are stimulated when a specific small molecule interacts with a regulatory protein. Lac operon is an example of an inducible operon. Lac operon encodes enzymes needed for metabolism of lactose (milk sugar). lacI is the regulatory gene. It encodes an allosteric repressor that binds to the operator in the absence of lactose. When lactose is present, an isomer, allolactose, binds to the repressor and causes a conformational change so that it can no longer bind to the operator. Lac operon is then transcribed. Allolactose is an inducer, as it induces transcription of operon. This is also an example of negative control, because the operon is turned off by the repressor.

## Positive gene regulation

Transcription of lac operon requires that lactose be present and that glucose be in short supply. If glucose levels are high, cell does not need to synthesize enzymes to catabolize glucose. Glucose levels are detected by interaction of an allosteric protein with a small organic molecule. Cyclic AMP accumulates when glucose is absent. cAMP receptor protein (CRP) binds cAMP, and is an activator of transcription. CRP binding site is next to the promoter of lac operon. CRP plus cAMP bind this site, and makes it easier for RNA polymerase to bind to the promoter and start transcription.

## Reference

* http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/Avery.html
* http://en.wikipedia.org/wiki/Operon
* http://www.britannica.com/EBchecked/topic/429974/operon
* Sadava, David et al. (2009). Life: The Science of Biology (9th ed.). Macmillan. p. 349.