SEA-PHAGES | attP Location

Link to this post \| posted 29 Mar, 2022 20:01
cellokiwi	Hello, I'm trying to find the attP of my temperate phage. I know it will be directly downstream of the integrase gene. However, how do we find the exact bp number? Is there a tool that will search for it? Is there a particular consensus I should be looking for? Thanks!

Link to this post \| posted 29 Mar, 2022 20:24
debbie	Hi Allison, There are a lot of routes that our phages take to integrate, and close to the integrase is a good way to address it. We - I mean Graham, has spent a lot of time looking for integration sites in the Mycobacteria and proving them biochemically. He is writing a review article that gives a great summary, so when it is available it will help a lot. In the meantime, the first thing you want to know is what kind of integrase you have. The large serine integrases can have an attachment site that is but 3 bases in length. so without some bench work, that is going to be difficult. The tyrosine integrases have arm extensions that make it more readily identifiable. You can look up Bxb1 integration (first author is Pallavi Ghosh). Some of our best data published is in M. abscessus (Dedrick, 2021) because we found the prophages and could see the sequences of the attL and attR in the hosts. Those reads should help to get you started. Some of our phages like to integrate into tRNAs. Being able to match the attP to an attB is also needed, so know in the host sequence will be needed. After you read the Dedrick papers, I think you will see why the answer to your questions are not simple. Having said all that, another paper in the works is a prophage finder, that will help identify attL and attR. So much to do!

Link to this post | posted 29 Mar, 2022 20:24

debbie

Hi Allison,
There are a lot of routes that our phages take to integrate, and close to the integrase is a good way to address it. We - I mean Graham, has spent a lot of time looking for integration sites in the Mycobacteria and proving them biochemically. He is writing a review article that gives a great summary, so when it is available it will help a lot. In the meantime, the first thing you want to know is what kind of integrase you have. The large serine integrases can have an attachment site that is but 3 bases in length. so without some bench work, that is going to be difficult. The tyrosine integrases have arm extensions that make it more readily identifiable. You can look up Bxb1 integration (first author is Pallavi Ghosh). Some of our best data published is in M. abscessus (Dedrick, 2021) because we found the prophages and could see the sequences of the attL and attR in the hosts. Those reads should help to get you started. Some of our phages like to integrate into tRNAs. Being able to match the attP to an attB is also needed, so know in the host sequence will be needed. After you read the Dedrick papers, I think you will see why the answer to your questions are not simple.
Having said all that, another paper in the works is a prophage finder, that will help identify attL and attR. So much to do!

Link to this post \| posted 31 Mar, 2022 14:55
cellokiwi	Debbie, Thank you SO much for the info. I feel much better for not being able to locate it since it is apparently a lot more complicated. Especially since it is a serine integrase.

Link to this post \| posted 31 Mar, 2022 15:00
debbie	Exactly!

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attP Location