Mechanisms | Plasmids | Operons | Transposons

The nucleoid is the bacteria's circular DNA (bacterial chromosome) approximately 3000 genes - 4 million nucleotides long.  Plasmids are extra, circular, self-replicating (apart from the nucleoid) DNA of 4 to 24 genes.

Blue = origin of replication Red = termination of replication Green = polymerase Arrow = direction of replication along the nucleoid

Bacterial Mechanisms of genetic recombination

Bacteria have three mechanisms for the exchanging and incorporation of genetic material.  They are transformation
(the uptake of extracellular DNA), transduction (phages transfer bacterial genes from one host to another) and conjugation
(direct genomic transfer between temporarily joined bacterial cells).

Two Types of Transduction

There is general transduction where a small piece of the host's degraded DNA is packaged within a phage capsid.  The defective phage injects the host's DNA into a new host.  This DNA can replace its homologous region on the host's DNA.  There is also specialized transduction; this occurs when a temperate phage invades:  While exiting the lysogenic cycle the prophage may take adjoining bacterial DNA with it.

Conjugation Transfer

One way of recombination is the use of sex pili, cytoplasmic bridges adjoining two bacteria.  Since this type of transfer is unidirectional, the donor of the genetic content is called "male" and the recipient "female."  This is because the donor is always the originator of the sex pili. What separates those capable of forming sex pili from those incapable of this?  The F Plasmid. The donor must have this plasmid to form the cytoplasmic bridges; therefore F⁺ ("F positive") is indicative of maleness.

Plasmids

Some plasmids can incorporate themselves into the nucleoid.  These are called episomes (can refer to both plasmids and temperate viruses).  In other words, episomes can replicate like plasmids extrachromosomally or as part of the main bacterial chromosome.   A plasmid contains DNA not required for survival or reproduction but can help in antibiotic (or anti-antibiotic) synthesis and can have up to or about enough sequencing for 25 genes.

The F Plasmid ("F" means Fertility)

Replication of this plasmid is synchronized with that of the nucleoid.  If the F Plasmid integrates into the chromosome, the cell generates a HFR (high frequency of recombination).  Reason: HFR transfers F plasmid (episome) as well as some DNA; therefore as the F Plasmid replicates it is spread to other bacteria.

The R Plasmid ("R" for Resistance)

This plasmid carries genes that code for proteins that destory certain antibiotics.  It is transferrable during conjugation.

Operons and Metabolic Control

There are two levels of metabolic control:  long- and short-term.  Negative gene expression is an example of a long-term control.  Varying activities of already present enzymes is an example of a short-term control (e.g., feedback inhibition).  A structural gene codes for a protein promoter.  An operon is the set of operating units of a gene sequence; basically it turns genes on and off. This was determined by the scientists Jacob and Monod.

Negative Regulation (indirect) is a repressible (anabolic) control.  An operator controls RNA polymerases access to the structural gene.  The operator location lies within the promoter or between the promoter and targeted genes.  A repressor protein turns the operator off.  This repressor binds only to a certain operator of a certain operon.  It is a product of the regulatory gene, transcribed continously but slowly.  The repressor is initially turned "off" when first produced and be activated by binding to TRP (tryptophan - a co-repressor).  Inducible (catabolic) control is when a regulatory gene produces an activated repressor protein.  The inducer (de-repressor) activates a repressor; remember "inducer + repressor = transcription."  As an example, allolactose is a lactose isomer formed in small amounts from lactose after entering the cell.  The promoter is active only if there is no repressor present (e.g., lac operon -1 and 2 - below).

1) 2)

(Left) The lac Operon is an example of inducible negative gene regulation. inducible = initially inactive, made active negative = switched off by an active protein repressor A = DNA regulatory gene B = promoter region C = operator (on/off switch for the gene) D = repressor protein E = allolactose (inducer) F = inducer binding to repressor thus turning on the operon

Note:  an activator helps RNA polymerase attach to the promoter

Positive Regulation is a direct form of metabolic control. A catabolite is a molecule consumed in catabolism.  CAP stands for "catabolite activator protein."  The absence of glucose results in accumulation of cyclic Adenosine MonoPhosphate (cAMP). The camp-CAP association helps RNA polymerase find the operator to begin transcription.

(Left) This occurs when lactose builds up and there becomes a low glucose concentration.

Transposons are "Jumping Genes"

Transposons can be on a chromosome or plasmid.  They are called jumping genes because they move around; one time a transposon might be next to the phosphofructokinase gene and another it might be inserted smack in the middle of an insulin gene or something.  A conservative transposition is not replicated before moving.  In a replicative transposition, a copy is moved to another site (instead of the original moving).  Transposons are not site specific.  The simplest ones are insertion sequences; these contain only the DNA necessary for the act of transposition (one gene for transposase).  The transposase gene is bracketed by paired DNA sequences called inverted repeats:

... ATCCGAT ...  transposase gene ... ACCGGAT ... Strand 1
... TAGGCCA ...  transposase gene ... TGGCCTA ... Strand 2

Transposase recognizes these inverted repeats as the boundaries of the transposon.  DNA polymerase helps form identical DNA regions (directed repeats) at the insertion site of the transposon and may also insert sequences.  What does a transposon affect?  It influences the production of a protein, increasing or decreasing this by insertion into regulatory regions of DNA (ex. lac operon reg. region).  It likely also affects the phenotype of unicellular organisms.  Complex transposons and R Plasmids were first evidenced by Barbara McClintock in corn kernel color.

Next:  "Eukaryotic Genes."