CRISPR transcript processing: a mechanism for generating a large number of small interfering RNAs
<p>Abstract</p> <p>Background</p> <p>CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated sequences) is a recently discovered prokaryotic defense system against foreign DNA, including viruses and plasmids. CRISPR cassette is transcribe...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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BMC
2012-07-01
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| Series: | Biology Direct |
| Subjects: | |
| Online Access: | http://www.biology-direct.com/content/7/1/24 |
| _version_ | 1818960201373450240 |
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| author | Djordjevic Marko Djordjevic Magdalena Severinov Konstantin |
| author_facet | Djordjevic Marko Djordjevic Magdalena Severinov Konstantin |
| author_sort | Djordjevic Marko |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated sequences) is a recently discovered prokaryotic defense system against foreign DNA, including viruses and plasmids. CRISPR cassette is transcribed as a continuous transcript (pre-crRNA), which is processed by Cas proteins into small RNA molecules (crRNAs) that are responsible for defense against invading viruses. Experiments in <it>E. coli</it> report that overexpression of <it>cas</it> genes generates a large number of crRNAs, from only few pre-crRNAs.</p> <p>Results</p> <p>We here develop a minimal model of CRISPR processing, which we parameterize based on available experimental data. From the model, we show that the system can generate a large amount of crRNAs, based on only a small decrease in the amount of pre-crRNAs. The relationship between the decrease of pre-crRNAs and the increase of crRNAs corresponds to strong linear amplification. Interestingly, this strong amplification crucially depends on fast non-specific degradation of pre-crRNA by an unidentified nuclease. We show that overexpression of <it>cas</it> genes above a certain level does not result in further increase of crRNA, but that this saturation can be relieved if the rate of CRISPR transcription is increased. We furthermore show that a small increase of CRISPR transcription rate can substantially decrease the extent of <it>cas</it> gene activation necessary to achieve a desired amount of crRNA.</p> <p>Conclusions</p> <p>The simple mathematical model developed here is able to explain existing experimental observations on CRISPR transcript processing in <it>Escherichia coli</it>. The model shows that a competition between specific pre-crRNA processing and non-specific degradation determines the steady-state levels of crRNA and is responsible for strong linear amplification of crRNAs when <it>cas</it> genes are overexpressed. The model further shows how disappearance of only a few pre-crRNA molecules normally present in the cell can lead to a large (two orders of magnitude) increase of crRNAs upon <it>cas</it> overexpression. A crucial ingredient of this large increase is fast non-specific degradation by an unspecified nuclease, which suggests that a yet unidentified nuclease(s) is a major control element of CRISPR response. Transcriptional regulation may be another important control mechanism, as it can either increase the amount of generated pre-crRNA, or alter the level of <it>cas</it> gene activity.</p> <p>Reviewers</p> <p>This article was reviewed by Mikhail Gelfand, Eugene Koonin and L Aravind.</p> |
| first_indexed | 2024-12-20T11:53:46Z |
| format | Article |
| id | doaj.art-23e7fdeac7f743d89eec001b2c9941d9 |
| institution | Directory Open Access Journal |
| issn | 1745-6150 |
| language | English |
| last_indexed | 2024-12-20T11:53:46Z |
| publishDate | 2012-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Biology Direct |
| spelling | doaj.art-23e7fdeac7f743d89eec001b2c9941d92022-12-21T19:41:43ZengBMCBiology Direct1745-61502012-07-01712410.1186/1745-6150-7-24CRISPR transcript processing: a mechanism for generating a large number of small interfering RNAsDjordjevic MarkoDjordjevic MagdalenaSeverinov Konstantin<p>Abstract</p> <p>Background</p> <p>CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated sequences) is a recently discovered prokaryotic defense system against foreign DNA, including viruses and plasmids. CRISPR cassette is transcribed as a continuous transcript (pre-crRNA), which is processed by Cas proteins into small RNA molecules (crRNAs) that are responsible for defense against invading viruses. Experiments in <it>E. coli</it> report that overexpression of <it>cas</it> genes generates a large number of crRNAs, from only few pre-crRNAs.</p> <p>Results</p> <p>We here develop a minimal model of CRISPR processing, which we parameterize based on available experimental data. From the model, we show that the system can generate a large amount of crRNAs, based on only a small decrease in the amount of pre-crRNAs. The relationship between the decrease of pre-crRNAs and the increase of crRNAs corresponds to strong linear amplification. Interestingly, this strong amplification crucially depends on fast non-specific degradation of pre-crRNA by an unidentified nuclease. We show that overexpression of <it>cas</it> genes above a certain level does not result in further increase of crRNA, but that this saturation can be relieved if the rate of CRISPR transcription is increased. We furthermore show that a small increase of CRISPR transcription rate can substantially decrease the extent of <it>cas</it> gene activation necessary to achieve a desired amount of crRNA.</p> <p>Conclusions</p> <p>The simple mathematical model developed here is able to explain existing experimental observations on CRISPR transcript processing in <it>Escherichia coli</it>. The model shows that a competition between specific pre-crRNA processing and non-specific degradation determines the steady-state levels of crRNA and is responsible for strong linear amplification of crRNAs when <it>cas</it> genes are overexpressed. The model further shows how disappearance of only a few pre-crRNA molecules normally present in the cell can lead to a large (two orders of magnitude) increase of crRNAs upon <it>cas</it> overexpression. A crucial ingredient of this large increase is fast non-specific degradation by an unspecified nuclease, which suggests that a yet unidentified nuclease(s) is a major control element of CRISPR response. Transcriptional regulation may be another important control mechanism, as it can either increase the amount of generated pre-crRNA, or alter the level of <it>cas</it> gene activity.</p> <p>Reviewers</p> <p>This article was reviewed by Mikhail Gelfand, Eugene Koonin and L Aravind.</p>http://www.biology-direct.com/content/7/1/24CRISPR/CasTranscript processingSmall RNACRISPR expression regulationCRISPR/Cas response |
| spellingShingle | Djordjevic Marko Djordjevic Magdalena Severinov Konstantin CRISPR transcript processing: a mechanism for generating a large number of small interfering RNAs Biology Direct CRISPR/Cas Transcript processing Small RNA CRISPR expression regulation CRISPR/Cas response |
| title | CRISPR transcript processing: a mechanism for generating a large number of small interfering RNAs |
| title_full | CRISPR transcript processing: a mechanism for generating a large number of small interfering RNAs |
| title_fullStr | CRISPR transcript processing: a mechanism for generating a large number of small interfering RNAs |
| title_full_unstemmed | CRISPR transcript processing: a mechanism for generating a large number of small interfering RNAs |
| title_short | CRISPR transcript processing: a mechanism for generating a large number of small interfering RNAs |
| title_sort | crispr transcript processing a mechanism for generating a large number of small interfering rnas |
| topic | CRISPR/Cas Transcript processing Small RNA CRISPR expression regulation CRISPR/Cas response |
| url | http://www.biology-direct.com/content/7/1/24 |
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