Example for a temperate phage: bacteriophage lambda (lambda is a greek letter). (Fig. 5.37)
Bacteriophage lambda consists of:
Bacteriophage lambda specifically infects E. coli.
After infection, the linear lambda DNA is converted to a circular, supercoiled form and transcription of lambda genes starts. At this point, decision is made on which life cycle to follow (see Fig. 5.37).
What decides? Seems to be the concentration of an activator protein transcribed from lambda DNA this activator is designated cII:
high concentration of cII ---- lysogenic cycle favored
low concentration of cII ---- lytic cycle favored
But: concentration of activator not dependent on lambda but on host cell: concentration determined by amount of proteases present in the host cell which in turn depends on growth conditions:
favorable growth conditions ---- high amount of proteases ---- high degree of activator degradation ---- low levels of cII ----- lytic cycle
poor growth conditions ---- low amount of proteases ---- low degree of activator degradation ---- high levels of activator ----- lysogenic cycle
Therefore, phage progeny only produced when cell has many resources.
When infecting resource-depleted bacterium, lambda can "hide" in cell
Lysogenic Cycle:
Effect of prophage:
Bacterium is now immune to infection by another lambda phage, because lambda repressor continuously produced ----- new phage DNA can be injected into cell and is circularized but is not transcribed or replicated.
But prophage can be excised, because lambda cleverly uses host response system to potentially lethal situations:
TRANSDUCING PHAGE
Term transduction refers to the packaging of bacterial DNA (chromosomal DNA) into the phage capsid. This occurs with only a small % of phage.
In specialized transduction
During induction, a prophage is excised from the bacterial chromosome and carries along with it some of the chromosomal DNA. In other words, there is an imprecise excision of the prophage DNA. The chromosomal DNA probably does not represent entire genes, but when this phage infects a bacterial cell, homologous recombination is a likely possibility. [very similar to formation of F' bacterium]
In generalized transduction
Bacterial DNA fragments are randomly (and accidentally) packaged into the capsid along with the phage genome. This occurs during the lytic cycle and is especially common in situations in which the host cell DNA is fragmented during conversion phase.
Transposons (also called transposable elements) are sequences that can move throughout the genome by a process called transposition. ("jumping genes")
They represent a potent force for change within both prokaryotic and eukaryotic genomes.
They may actually be a major source of mutation. These mutations are sometimes completely reversible if the transposon is excised perfectly.
Eukaryotic transposons were first discovered by Barbara McClintock for maize in the 1940s but are now known for many eukaryotes and prokaryotes. She was awarded the Nobel prize in 1993.
There are two general classes of transposons:
those that move via DNA intermediates
those that move via RNA intermediates
Transposition via DNA intermediates:
The maize transposons first discovered by McClintock but also all known bacterial transposons move via DNA intermediates.
Simplest transposable element: insertion sequence:
consists of:
gene encoding the enzyme transposase (which catalyzes transposition)
this includes promoter and transcription and translation termination signals.
The insertion sequence is alwaysflanked by short inverted repeats.
AGTC...............................................GACT
TCAG................................................CTGA
Each insertion sequence is given an IS designation followed by a number.
Insertion sequences contain from ~800 to 2000 nucleotides.
Insertion sequences move by conservative transposition, which means that they are excised from one site and transposed to a second site without replication of the sequence.
Mechanism of transposition by insertion sequences: (Fig. 5. 45)
catalyzed by the enzyme they code for: transposase.
Transposase specifically cleaves at the ends of the inverted repeats of the insertion sequence (cleavage of a specific DNA sequence)......
but transposase also cleaves the target sequence. The target sequence is cleaved via staggered cuts.
Transposase then joints the overhanging ends of the target sequence to the transposable element.
The resulting short strech of single-stranded DNA on both sides of the transposon is finally repaired via DNA polymerase and DNA ligase ----- transposition always creates a short direct repeat of the target sequence that flanks the transposon! (This is true for any transposon.)
more complex transposons: (Fig. 5.44)
consist of
other DNA sequences
flanked by an insertion sequence on each side (each side contains a transposase gene flanked by short inverted repeats).
Complex transposons also move as a single unit. (Therefore actually any kind of DNA sequence may be part of a transposon and move throughout the genome, as long as it is flanked by insertion sequences.)
The frequency of transposition of composite transposons declines with increasing distance between IS sequences. The IS elements code for transposase activities that are responsible for both creating a target site and for recognizing the ends of the transposon.