Question

Analysis of protein-nucleoprotein interactions and mechanism in CRISPR (cluster of regularly interspaced palindromic repeats) type I-E between cas3 (CRISPR associated) protein and the interference complex (cse1,cse2,cas7,cas5,cas6e)

Answer 1

If anyone are sitting on any interesting articles or knowledge about the following as the title indicate, please post it below.
Make sure to have your references correct.

Answer 2

What do you have to write / do about CRISPR?

I think I have some slides back from my University times that I can go look for in my 'archives'

What do you know so far? I know some basic things, but those are mostly DNA interactions in the CRISPR system.

(For those of you who don't know: CRISPR is basically the immune system of bacteria. Highly versatile and specific, mostly against phages and viruses.)

I have found one kinda promising paper, but didn't get to reading it thoroughly yet. I will post the link and hope that you can somehow access it ^^

http://www.ncbi.nlm.nih.gov/pubmed/20056882

There should be much more information out by now, but I don't expect any books until the whole process is published.

Answer 3

Rodolphe Barrangou is one of the top scientists in the area yes, also seen the article, unfortunately it's not specific to describe my area. I was think specifically cas3 and the cascade complex [cse1,cse2,cas7,cas5,cas6e].
About my own knowledge so far. Been reading multiple review that are less than 4 years old and general articles regarding the proposed mechanisms in CRISPR.

Answer 4

This is what I got so far and already been reading:

Sinkunas, T et al. (2013). In vitro reconstitution of Cascade-mediated CRISPR immunity in Streptococcus thermophilus. The EMBO Journal. 32 (3), p385–394..

Sinkunas, T et al. (2011). Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system. The EMBO Journal. 30 (7), p1335–1342.

Westra, E et al. (2012). CRISPR Immunity Relies on the Consecutive Binding and Degradation of Negatively Supercoiled Invader DNA by Cascade and Cas3. Molecular Cell. 46, p595–605.

Jore, M et al. (2011). Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nature Structural & Molecular Biology. 18 (5), p529-537.

Beloglazova, N et al. (2011). Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference. The EMBO Journal. 30 (22), p4616–4627.

Wiedenheft, B et al. (2011). Structures of the RNA-guided surveillance complex from a bacterial immune system. Nature. 477, p486-490.

Wiedenheft, B et al. (2011). RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions. PNAS. 108 (25), p10092–10097.

Answer 5

@Schleifspur Exactly what I am doing, is that I am making a model of the type 1-E interference system. So I look at others data and creating a model that can explain the data.
For example I am investigating Cascade dissociation, currently I am suspecting it may involve Cas3's helicase activity.

@thomaster Are you into CRISPR?

Answer 6

@Schleifspur "but I don't expect any books until the whole process is published." There actually is from Barrangou and van der Oost. Van der Oost's litterature from 2011-2012 have been the most interesting, (unfortunately) he has changed focus here in 2014 to work with type 3 instead. I guess some other co-worker of his is taking over, but don't know who.

@shrutipande9 what do you think? :)

Answer 7

UPDATE:
I've been able to model the interference pathway in type I-E, but lacking experimental evidence for the dissociation of Cas3 from Cascade, data points towards it happens (Westra et al. 2012), but I've not been able to find an reason why it may happen, current hypothesis is:

Change in DNA topology from nsDNA to relaxed DNA. (The affinity between Cascade and the protospacer's topology has to been shown to have effect in some organisms [Westra et al. 2012. Sinkunas et al. 2013])... this may be caused by the Cas3's helicase activity (Sinkunas et al. 2011).

Answer 8

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890593/
i found this latest article which u haven't mentioned earlier. hope this helps u..:)

Answer 9

@Frostbite Go to google scholar <scholar.google.com> and search for articles. I suggest you take a few of the major articles, search for them in scholar, and then check to se what papers have cited the search paper.

If you haven't used google scholar before the list of articles that cited any result is at the bottom of each results section.

Answer 10

All the articles in this topic are not free (peer-reviewed that is) creating a limit for google scholar being effective.

Answer 11

And I have been seatching in multiple citation websites. Web of Knowledge, Pubmed, ect ect.

Answer 12

@Frostbite What is your situation? Do you have institutional access to anything? Can your request an interlibrary loan? Google scholar indexes all of those sites so you are really wasting time searching through them individually.

If you absolutely need open sources I suggest you focus on PNAS, PLOS One, and use this < http://doaj.org/ > to search for open access material. Don't forget to look at the authors' webpage. Frequently you can get the paper there even if the journal is not open access.

Answer 13

I got access to all the databases yes, but I do fear that I've may have hit the limit. van der Oost was basically the pioneer in CRISPR/Cas interference.

Answer 14

@Frostbite Oh, and you can also make things much easier by using the boolean and advanced search abilities of search engines like google. For instance, I just search CRISPR and there is a bunch of stuff: citation only, HTML, open access, closed access, etc. But, if I search for this:

CRISPR AND filetype:pdf

I get near exclusively results with pdf available. By "hit the limit" do you mean you have maxed out the number of downloads possible in a certain time period? Like host JSTOR limits the number of downloads you can do in a day.

Answer 15

When I say hit the limit. I mean the research simply don't exists yet. That nobody today understand that process I'm currently trying to review.

Answer 16

@Frostbite Ah, yes, in new areas that can be quite and issue. I would say it is time to move on to similar research that can be used to further the CRISPR research you want to review. But I do find it somewhat hard to believe since this publication:

Structural basis for CRISPR RNA-guided DNA recognition by Cascade

Has been cited 142 times.

And this one:

CRISPR provides acquired resistance against viruses in prokaryotes

884 times.

Answer 17

Jore, M et al. (2011). Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nature Structural & Molecular Biology. 18 (5), p529-537.

It mostly focus on the binding of the protospacer to Cascade, but does not involve the dissociation.

Answer 18

Last article is by Barrangou explaining the discovery of CRISPR being a anti viral defense. (Which it may not even be, because it is super inefficient ^^ )

Answer 19

@Frostbite I don't know much about it, I am an evolutionary systematist. Still, just because the papers do not focus on exactly what you are looking for, you should still read enough to know if it has any potential or not. You never know when something that seems unrelated to your interests will prove useful. Look at microwaves, lasers, superglue; all things that were made by accident and suddenly became extremely useful.

You know more about it than I do, but you could at least read through the abstracts of even closed access papers. Abstracts are almost always open access.

Answer 20

Oh @mrdoldum the literature you have been mentioning I have been studying closely and to every detail. Especially the article by Jore as I among others build my thesis on that article. And it is also a great article for the protospacer Cascade interaction.

Answer 21

@Frostbite I only mentioned them specifically because I took them from your list and searched google scholar with their titles.

What about something like this?

Makarova, Kira S., et al. "Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems." Biol Direct 6.1 (2011): 38.

Answer 22

I also appreciate that. Basiclly I've only been roaming around Van der Oost Ph.D and master students.

Hmmm that article I haven't been reading, might be worth taking a look at.

Answer 23

@Frostbite I used this search in google scholar to get that result, which has a pdf:

(CRISPR AND (cas3 OR cse1 OR cse2 OR cas7 OR cas5 OR cas6e)) AND filetype:pdf

Do you know boolean searching and the like? I think it is probably self explanatory as to what each operator is doing but I thought i would just ask to make sure.

Answer 24

Yes I've been introduced to it very slightly, but I get the principle behind it. Doing might be another story.

Answer 25

I cannot remember if google will let you use things besides (), so best ot use them, but most of the time any pairs of non-alphanum things will work. EG. ``

Just like math, terms in () stay together. The most common operators are AND, OR, and NOT. They have to be in full caps, every letter. If you want to search specific terms put it in quotes. This can have a huge impact on your results though. For instance, searching CRISPR Type 1-E gives you results, but CRISPR AND "Type 1-e" give you nothing.

And, finally as you can see from what I searched, you can make nested logic statements. In a sentence my search says, search for all content that has CRISPR and at least one of the following casX terms, and of that content only return results that have a file type of pdf.

That should do you for now, but there are way more powerful tools to use. Those tools have a very limited capacity in google scholar though and are really only useful in a general web search.

You might want to search for ppt and pptx (powerpoint files) as well. That can bring up lectures and talks which can be even more useful than papers sometimes.

Answer 26

@Frostbite see above, forgot to tag you in it.