1) Do you always leave a portion of the phage genome behind in specialised transduction?The answer is YES.
It is pretty inevitable because for specialised transduction to take place, there is incorrect excision (such an event is actually quite rare!) and we called the subsequent resultant a "
defective phage" because it does not contain all its viral genetic material anymore.
The part of viral genome left behind (and hence part of the bacterial genome removed) can be from either ends of the prophage.
[The next question that comes to mind will be "is it possible to have an incorrect excision such that the viral capsid and sheath does not form because their genes are not excised out?" Theoretically possible but what is the point if there is no transducing phage form? Since there won't be any genetic transfer, it is therefore of no interest to us - similarly if there isn't any intact bacterial gene.
What scientists want to determine is really if there is genetic transfer to bring about variation in a particular species of bacteria. This is all about evolution.]
I realised that I have answered some of these questions before so I am refering you to:
http://chansensei.blogspot.com/2006/09/how-plasmidvirus-integrate-into.html
I would like to point out a couple of interesting notes in the last picture to you, showing integration and correct/incorrect excision of plasmid:
1) integration is a single crossing over event at the att site (att-attachment)
- result: you should appreciate where the genetic markers (a,b,c) are before and after integration
2) bonus question: does only recombination occur for
specialised transduction?
- answer: NO but recombination is the most common. the other possible is shown in the diagram and explain below: (not impt though)
[Question: Does the truncated viral DNA injected by the defective phage into the host bacteria behave like a typical phage DNA? The behaviour of that piece of DNA really depends on the viral genes that have been removed upon incorrect excision e.g. if the gene for proteins needed for integration is removed, the DNA will not be integrated into the bacterial chromosome OR (from bonus question) if the defective phage infects a bacteria that has been earlier infected by a normal phage (now serves as a helper phage) and the truncated viral DNA integrates into the bacteria chromosome (you get a double lysogen!) - any missing genes can be expressed by the intact DNA of the normal phage.]
http://books.google.com/books?id=3E_0H6dEvfQC&pg=PA386&lpg=PA386&dq=phage+helper+specialized+transduction&source=bl&ots=tpe0i6OXar&sig=tQFGjX3FUvMX0TfNWJHFCi4jHlQ&hl=en&sa=X&oi=book_result&resnum=6&ct=result
So we shall end our discussion here, leaving it to you, if you are interested, to find out about specific example. Lambda phage is the most common example.
But the DNA should circularize as per normal and we do expect the
phenotype of the bacteria to change due to the genetic transfer.
2) Why some plasmid integrated into the bacterial chromosome to form Hfr?
There is no particular reason except for the fact that these plasmid contain a IS (insertion sequence) element and there is a homologous copy on the bacterial chromosome. Different Hfr strains have the plasmid inserted at different locations and at either orientation.
IS sequences, like transposons, are mobile elements so there is no fixed location where it can be found on the bacterical chromosomes. They may even be found in transposons.
http://en.wikipedia.org/wiki/Insertion_sequence
The plasmid can actually exist independently or be integrated so it can be referred to as an episome.
The integrated plasmid is only about 2% of the bacterial chromosome.
Diagram showing that the sex pilus is a separate entity from the mating bridge
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